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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/centrifuge">Debian Med / centrifuge</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/centrifuge/commit/f6f7b098137879381ca6b18e3e5ba7c4c327171f">f6f7b098</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-03-02T19:56:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.3</pre>
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<h4>13 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f11fb3bba37e7060bedcd5895812b7c511c52651">
MANUAL
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<li class="file-stats">
<a href="#465370da702349b6dcb3f9f2026872cad6877efa">
MANUAL.markdown
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#5caf7b101f4ba008ee8d93f74a20baefcf2b451a">
aln_sink.h
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<li class="file-stats">
<a href="#59b83604953a3f26d3eb5642de1c646924dd022b">
centrifuge
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<li class="file-stats">
<a href="#d8f5fe0588502d1a8ca61541057cc297e42bc963">
centrifuge-download
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<li class="file-stats">
<a href="#fd1054bfea308886c08eb1c3c254619085646a47">
centrifuge-kreport
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<li class="file-stats">
<a href="#5e28451c048cf424257052950561e0cae5208bf9">
<span class="new-file">
+
centrifuge-promote
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<li class="file-stats">
<a href="#3e44d076ff9b15d146f6db332bac2d871b3f4c64">
centrifuge.cpp
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<li class="file-stats">
<a href="#4d3778d4c482b69d10dbd5975319cc35b317d046">
classifier.h
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<li class="file-stats">
<a href="#368d22706ee41f76c191fb0b95fa48b9e2838247">
doc/manual.inc.html
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doc/sidebar.inc.shtml
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<li class="file-stats">
<a href="#aed90a934a04d9a3fa5df8eecf57722bbc05a662">
indices/Makefile
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<h4>Changes:</h4>
<li id="f11fb3bba37e7060bedcd5895812b7c511c52651">
<a href="https://salsa.debian.org/med-team/centrifuge/commit/f6f7b098137879381ca6b18e3e5ba7c4c327171f#f11fb3bba37e7060bedcd5895812b7c511c52651"><strong>MANUAL</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -198,7 +198,83 @@ can be generated from a GI taxid dump:</td>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="plaintext">### Custom database</span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="plaintext">TODO: Add toy example for nodes.dmp, names.dmp and seqid2taxid.map</span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">To build a custom database, you need the provide the follwing four files to `centrifuge-build`:</span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext"> - `--conversion-table`: tab-separated file mapping sequence IDs to taxonomy IDs. Sequence IDs are the header up to the first space or second pipe (`|`). </span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"> - `--taxonomy-tree`: `\t|\t`-separated file mapping taxonomy IDs to their parents and rank, up to the root of the tree. When using NCBI taxonomy IDs, this will be the `nodes.dmp` from `ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz`.</span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext"> - `--name-table`: '\t|\t'-separated file mapping taxonomy IDs to a name. A further column (typically column 4) must specify `scientific name`. When using NCBI taxonomy IDs, `names.dmp` is the appropriate file.</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext"> - reference sequences: The ID of the sequences are the header up to the first space or second pipe (`|`)</span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">When using custom taxonomy IDs, use only positive integers greater-equal to `1` and use `1` for the root of the tree.</span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">#### More info on `--taxonomy-tree` and `--name-table`</span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">The format of these files are based on `nodes.dmp` and `names.dmp` from the NCBI taxonomy database dump. </span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">- Field terminator is `\t|\t`</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">- Row terminator is `\t|\n`</span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext">The `taxonomy-tree` / nodes.dmp file consists of taxonomy nodes. The description for each node includes the following</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">fields:</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext"> tax_id -- node id in GenBank taxonomy database</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext"> parent tax_id -- parent node id in GenBank taxonomy database</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext"> rank -- rank of this node (superkingdom, kingdom, ..., no rank)</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">Further fields are ignored.</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">The `name-table` / names.dmp is the taxonomy names file:</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext"> tax_id -- the id of node associated with this name</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext"> name_txt -- name itself</span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext"> unique name -- the unique variant of this name if name not unique</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext"> name class -- (scientific name, synonym, common name, ...)</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext">`name class` **has** to be `scientific name` to be included in the build. All other lines are ignored</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext">#### Example</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext">*Conversion table `ex.conv`*: </span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext"> Seq1 11</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext"> Seq2 12</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext"> Seq3 13</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext"> Seq4 11</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext">*Taxonomy tree `ex.tree`*: </span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext"> 1 | 1 | root</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext"> 10 | 1 | kingdom</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext"> 11 | 10 | species</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext"> 12 | 10 | species</span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext"> 13 | 1 | species</span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext"></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext">*Name table `ex.name`*:</span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext"></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext"> 1 | root | | scientific name |</span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext"> 10 | Bacteria | | scientific name |</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext"> 11 | Bacterium A | | scientific name |</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext"> 12 | Bacterium B | | scientific name |</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext"> 12 | Some other species | | scientific name |</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext"></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext">*Reference sequences `ex.fa`*:</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext"></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext"> >Seq1</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext"> AAAACGTACGA.....</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext"> >Seq2</span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext"> AAAACGTACGA.....</span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext"> >Seq3</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext"> AAAACGTACGA.....</span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext"> >Seq4</span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext"> AAAACGTACGA.....</span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext">To build the database, call</span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext"> centrifuge-build --conversion-table ex.conv \</span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext"> --taxonomy-tree ex.tree --name-table ex.name \ </span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext"> ex.fa ex</span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext">which results in three index files named `ex.1.cf`, `ex.2.cf` and `ex.3.cf`.</span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="plaintext">### Centrifuge classification output</span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/centrifuge/commit/f6f7b098137879381ca6b18e3e5ba7c4c327171f#465370da702349b6dcb3f9f2026872cad6877efa"><strong>MANUAL.markdown</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -211,7 +211,84 @@ can be generated from a GI taxid dump:</td>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Custom database</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="markdown">TODO: Add toy example for nodes.dmp, names.dmp and seqid2taxid.map</span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="markdown">To build a custom database, you need the provide the follwing four files to <span class="sb" style="color: #d14;">`centrifuge-build`</span>:</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`--conversion-table`</span>: tab-separated file mapping sequence IDs to taxonomy IDs. Sequence IDs are the header up to the first space or second pipe (<span class="sb" style="color: #d14;">`|`</span>). </span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`--taxonomy-tree`</span>: <span class="sb" style="color: #d14;">`\t|\t`</span>-separated file mapping taxonomy IDs to their parents and rank, up to the root of the tree. When using NCBI taxonomy IDs, this will be the <span class="sb" style="color: #d14;">`nodes.dmp`</span> from <span class="sb" style="color: #d14;">`ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz`</span>.</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`--name-table`</span>: '<span class="se" style="color: #d14;">\t</span>|<span class="se" style="color: #d14;">\t</span>'-separated file mapping taxonomy IDs to a name. A further column (typically column 4) must specify <span class="sb" style="color: #d14;">`scientific name`</span>. When using NCBI taxonomy IDs, <span class="sb" style="color: #d14;">`names.dmp`</span> is the appropriate file.</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="markdown"><span class="p"> -</span> reference sequences: The ID of the sequences are the header up to the first space or second pipe (<span class="sb" style="color: #d14;">`|`</span>)</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="markdown">When using custom taxonomy IDs, use only positive integers greater-equal to <span class="sb" style="color: #d14;">`1`</span> and use <span class="sb" style="color: #d14;">`1`</span> for the root of the tree.</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### More info on `--taxonomy-tree` and `--name-table`</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="markdown">The format of these files are based on <span class="sb" style="color: #d14;">`nodes.dmp`</span> and <span class="sb" style="color: #d14;">`names.dmp`</span> from the NCBI taxonomy database dump. </span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="markdown"><span class="p">-</span> Field terminator is <span class="sb" style="color: #d14;">`\t|\t`</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="markdown"><span class="p">-</span> Row terminator is <span class="sb" style="color: #d14;">`\t|\n`</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="markdown">The <span class="sb" style="color: #d14;">`taxonomy-tree`</span> / nodes.dmp file consists of taxonomy nodes. The description for each node includes the following</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="markdown">fields:</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="markdown"><span class="sb" style="color: #d14;"> tax_id -- node id in GenBank taxonomy database</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="markdown"><span class="sb" style="color: #d14;"> parent tax_id -- parent node id in GenBank taxonomy database</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="markdown"><span class="sb" style="color: #d14;"> rank -- rank of this node (superkingdom, kingdom, ..., no rank)</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="markdown">Further fields are ignored.</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="markdown">The <span class="sb" style="color: #d14;">`name-table`</span> / names.dmp is the taxonomy names file:</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="markdown"><span class="sb" style="color: #d14;"> tax_id -- the id of node associated with this name</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="markdown"><span class="sb" style="color: #d14;"> name_txt -- name itself</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="markdown"><span class="sb" style="color: #d14;"> unique name -- the unique variant of this name if name not unique</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="markdown"><span class="sb" style="color: #d14;"> name class -- (scientific name, synonym, common name, ...)</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="markdown"><span class="sb" style="color: #d14;">`name class`</span> <span class="gs" style="font-weight: 600;">**has**</span> to be <span class="sb" style="color: #d14;">`scientific name`</span> to be included in the build. All other lines are ignored</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="markdown"></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Example</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="markdown"></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*Conversion table `ex.conv`*</span>: </span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="markdown"> Seq1 11</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="markdown"> Seq2 12</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="markdown"> Seq3 13</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="markdown"> Seq4 11</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="markdown"></span>
</pre>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="markdown"></span>
</pre>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*Taxonomy tree `ex.tree`*</span>: </span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="markdown"></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 1 | 1 | root</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 10 | 1 | kingdom</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 11 | 10 | species</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 12 | 10 | species</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 13 | 1 | species</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="markdown"></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*Name table `ex.name`*</span>:</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="markdown"></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 1 | root | | scientific name |</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 10 | Bacteria | | scientific name |</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 11 | Bacterium A | | scientific name |</span></span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 12 | Bacterium B | | scientific name |</span></span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="markdown"><span class="sb" style="color: #d14;"> 12 | Some other species | | scientific name |</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*Reference sequences `ex.fa`*</span>:</span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="markdown"><span class="sb" style="color: #d14;"> >Seq1</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="markdown"><span class="sb" style="color: #d14;"> AAAACGTACGA.....</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="markdown"><span class="sb" style="color: #d14;"> >Seq2</span></span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="markdown"><span class="sb" style="color: #d14;"> AAAACGTACGA.....</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="markdown"><span class="sb" style="color: #d14;"> >Seq3</span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="markdown"><span class="sb" style="color: #d14;"> AAAACGTACGA.....</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="markdown"><span class="sb" style="color: #d14;"> >Seq4</span></span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="markdown"><span class="sb" style="color: #d14;"> AAAACGTACGA.....</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="markdown">To build the database, call</span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="markdown"><span class="sb" style="color: #d14;"> centrifuge-build --conversion-table ex.conv \</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --taxonomy-tree ex.tree --name-table ex.name \ </span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="markdown"><span class="sb" style="color: #d14;"> ex.fa ex</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="markdown">which results in three index files named <span class="sb" style="color: #d14;">`ex.1.cf`</span>, <span class="sb" style="color: #d14;">`ex.2.cf`</span> and <span class="sb" style="color: #d14;">`ex.3.cf`</span>.</span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Centrifuge classification output</span></span>
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<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/centrifuge/commit/f6f7b098137879381ca6b18e3e5ba7c4c327171f#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -191,6 +191,7 @@ CENTRIFUGE_SCRIPT_LIST = centrifuge \</td>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="make"> centrifuge-build <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="make"> centrifuge-inspect <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="make"> centrifuge-download <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="make"> centrifuge-kreport <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>wildcard centrifuge-<span class="k" style="font-weight: 600;">*</span>.pl<span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="make"></span>
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<a href="https://salsa.debian.org/med-team/centrifuge/commit/f6f7b098137879381ca6b18e3e5ba7c4c327171f#5caf7b101f4ba008ee8d93f74a20baefcf2b451a"><strong>aln_sink.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2305,9 +2305,9 @@ void AlnSinkSam<index_t>::appendMate(</td>
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<pre style="margin: 0;"> <span id="LC2305" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">READ_ID</span><span class="p">:</span> <span class="n" style="color: #333;">appendReadID</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">rd</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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2306
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<pre style="margin: 0;"> <span id="LC2306" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">SEQ_ID</span><span class="p">:</span> <span class="n" style="color: #333;">appendSeqID</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">rs</span><span class="p">,</span> <span class="n" style="color: #333;">ebwt</span><span class="p">.</span><span class="n" style="color: #333;">tree</span><span class="p">());</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2307" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">SEQ</span><span class="p">:</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">rd</span><span class="p">.</span><span class="n" style="color: #333;">patFw</span><span class="p">.</span><span class="n" style="color: #333;">toZBuf</span><span class="p">())</span> <span class="o" style="font-weight: 600;">+</span> </span>
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<pre style="margin: 0;">-<span id="LC2308" class="line" lang="c"> <span class="p">(</span><span class="n" style="color: #333;">rdo</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"<span class="idiff left right">N</span>"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">rdo</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">patFw</span><span class="p">.</span><span class="n" style="color: #333;">toZBuf</span><span class="p">()))).</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2308" class="line" lang="c"> <span class="p">(</span><span class="n" style="color: #333;">rdo</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"<span class="idiff left right">_</span>"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">rdo</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">patFw</span><span class="p">.</span><span class="n" style="color: #333;">toZBuf</span><span class="p">()))).</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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2309
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<pre style="margin: 0;"> <span id="LC2309" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">QUAL</span><span class="p">:</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">rd</span><span class="p">.</span><span class="n" style="color: #333;">qual</span><span class="p">.</span><span class="n" style="color: #333;">toZBuf</span><span class="p">())</span> <span class="o" style="font-weight: 600;">+</span> </span>
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<pre style="margin: 0;">-<span id="LC2310" class="line" lang="c"> <span class="p">(</span><span class="n" style="color: #333;">rdo</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"<span class="idiff left right">I</span>"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">rdo</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">.</span><span class="n" style="color: #333;">toZBuf</span><span class="p">()))).</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2310" class="line" lang="c"> <span class="p">(</span><span class="n" style="color: #333;">rdo</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"<span class="idiff left right">_</span>"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">rdo</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">.</span><span class="n" style="color: #333;">toZBuf</span><span class="p">()))).</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2311" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC2312" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">SEQ1</span><span class="p">:</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">rd</span><span class="p">.</span><span class="n" style="color: #333;">patFw</span><span class="p">.</span><span class="n" style="color: #333;">toZBuf</span><span class="p">());</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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2313
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2313
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<pre style="margin: 0;"> <span id="LC2313" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">QUAL1</span><span class="p">:</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">rd</span><span class="p">.</span><span class="n" style="color: #333;">qual</span><span class="p">.</span><span class="n" style="color: #333;">toZBuf</span><span class="p">());</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/centrifuge/commit/f6f7b098137879381ca6b18e3e5ba7c4c327171f#59b83604953a3f26d3eb5642de1c646924dd022b"><strong>centrifuge</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -116,6 +116,13 @@ my %read_compress = ();</td>
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116
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$cap_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">undef</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># Filename for passthrough</span></span>
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<td class="diff-line-num old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
117
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$no_unal</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
118
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$large_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="perl"></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Variables handling the output format</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$outputFmtSam</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$tabFmtOptIdx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$needReadSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$removeSeqCols</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="perl"></span>
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119
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Remove whitespace</span></span>
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120
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="perl"><span class="k" style="font-weight: 600;">for</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$i</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">..</span><span class="nv" style="color: teal;">$#bt2_args</span><span class="p">)</span> <span class="p">{</span></span>
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121
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="perl"> <span class="nv" style="color: teal;">$bt2_args</span><span class="p">[</span><span class="nv" style="color: teal;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/^\s+//</span><span class="p">;</span> <span class="nv" style="color: teal;">$bt2_args</span><span class="p">[</span><span class="nv" style="color: teal;">$i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\s+$//</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -179,6 +186,7 @@ for(my $i = 0; $i < scalar(@bt2_args); $i++) {</td>
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179
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="perl"> <span class="p">}</span></span>
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180
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$rarg</span> <span class="p">(</span><span class="s" style="color: #d14;">"un-conc"</span><span class="p">,</span> <span class="s" style="color: #d14;">"al-conc"</span><span class="p">,</span> <span class="s" style="color: #d14;">"un"</span><span class="p">,</span> <span class="s" style="color: #d14;">"al"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
181
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$arg</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^--${rarg}$/</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$arg</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^--${rarg}-gz$/</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$arg</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^--${rarg}-bz2$/</span><span class="p">)</span> <span class="p">{</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="perl"> <span class="nv" style="color: teal;">$needReadSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="p">;</span></span>
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182
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<td class="diff-line-num new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="perl"> <span class="nv" style="color: teal;">$bt2_args</span><span class="p">[</span><span class="nv" style="color: teal;">$i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">undef</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
183
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: teal;">@args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$args</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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184
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<td class="diff-line-num new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="perl"> <span class="nv" style="color: teal;">$read_fns</span><span class="p">{</span><span class="nv" style="color: teal;">$rarg</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$args</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -193,7 +201,57 @@ for(my $i = 0; $i < scalar(@bt2_args); $i++) {</td>
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193
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="perl"> <span class="k" style="font-weight: 600;">last</span><span class="p">;</span></span>
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194
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="perl"> <span class="p">}</span></span>
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195
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="perl"> <span class="p">}</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$arg</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"--out-fmt"</span> <span class="p">)</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="perl"> <span class="p">{</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="perl"> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: teal;">@bt2_args</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">Fail</span><span class="p">(</span><span class="s" style="color: #d14;">"Argument expected in next token!\n"</span><span class="p">);</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="perl"> <span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$bt2_args</span><span class="p">[</span><span class="nv" style="color: teal;">$i</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"sam"</span> <span class="p">)</span> </span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="perl"> <span class="p">{</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="perl"> <span class="nv" style="color: teal;">$outputFmtSam</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="p">;</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="perl"> <span class="p">}</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#$bt2_args[$i] = undef;</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="perl"></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="perl"> <span class="p">}</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="perl"></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$arg</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"--tab-fmt-cols"</span> <span class="p">)</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="perl"> <span class="p">{</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="perl"> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: teal;">@bt2_args</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">Fail</span><span class="p">(</span><span class="s" style="color: #d14;">"Argument expected in next token!\n"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="perl"> <span class="nv" style="color: teal;">$tabFmtOptIdx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="p">;</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Determine whether we need to add two extra columns for seq and qual to out-fmt</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$needReadSeq</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span> <span class="nv" style="color: teal;">$tabFmtOptIdx</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$outputFmtSam</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="p">)</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="perl"><span class="p">{</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$i</span> <span class="p">;</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$needAdd</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="p">;</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$tabFmtOptIdx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="perl"> <span class="p">{</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="sr" style="color: #009926;">/,/</span><span class="p">,</span> <span class="nv" style="color: teal;">$bt2_args</span><span class="p">[</span> <span class="nv" style="color: teal;">$tabFmtOptIdx</span> <span class="p">]</span> <span class="p">;</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$f</span> <span class="p">(</span><span class="nv" style="color: teal;">@cols</span><span class="p">)</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="perl"> <span class="p">{</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$f</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"readSeq"</span> <span class="p">)</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="perl"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="perl"> <span class="nv" style="color: teal;">$needAdd</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> </span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="perl"> <span class="k" style="font-weight: 600;">last</span> <span class="p">;</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="perl"> <span class="p">}</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="perl"> <span class="p">}</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="perl"> <span class="p">{</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="nv" style="color: teal;">@bt2_args</span><span class="p">,</span> <span class="s" style="color: #d14;">"--tab-fmt-cols"</span> <span class="p">;</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="nv" style="color: teal;">@bt2_args</span><span class="p">,</span> <span class="s" style="color: #d14;">"readID,seqID,taxID,score,2ndBestScore,hitLength,queryLength,numMatches"</span> <span class="p">;</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="perl"> <span class="nv" style="color: teal;">$tabFmtOptIdx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span> <span class="nv" style="color: teal;">@bt2_args</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="p">;</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="perl"> <span class="p">}</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="perl"> </span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$needAdd</span> <span class="p">)</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="perl"> <span class="p">{</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="perl"> <span class="nv" style="color: teal;">$removeSeqCols</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="p">;</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="perl"> <span class="nv" style="color: teal;">$bt2_args</span><span class="p">[</span> <span class="nv" style="color: teal;">$tabFmtOptIdx</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">",readSeq,readQual"</span> <span class="p">;</span> </span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="perl"> <span class="p">}</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="perl"><span class="p">}</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="perl"></span>
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197
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># If the user asked us to redirect some reads to files, or to suppress</span></span>
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198
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># unaligned reads, then we need to capture the output from Centrifuge and pass it</span></span>
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199
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># through this wrapper.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -423,6 +481,17 @@ my $cmd = "$align_prog$debug_str --wrapper basic-0 ".join(" ", @bt2_args);</td>
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423
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481
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Possibly add read input on an anonymous pipe</span></span>
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424
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482
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="perl"><span class="nv" style="color: teal;">$cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$readpipe $cmd"</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$readpipe</span><span class="p">);</span></span>
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425
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483
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="perl"></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># The function removes the two extra columns that we added to get the read seq and qual</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">RemoveSeqCols</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="perl"><span class="p">{</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$line</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">;</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="sr" style="color: #009926;">/\t/</span><span class="p">,</span> <span class="nv" style="color: teal;">$line</span> <span class="p">;</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">pop</span> <span class="nv" style="color: teal;">@cols</span> <span class="p">;</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">pop</span> <span class="nv" style="color: teal;">@cols</span> <span class="p">;</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$tab</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"\t"</span> <span class="p">;</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">(</span> <span class="nv" style="color: teal;">$tab</span><span class="p">,</span> <span class="nv" style="color: teal;">@cols</span> <span class="p">)</span> <span class="p">;</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="perl"><span class="p">}</span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="perl"></span>
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426
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495
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="perl"><span class="nv" style="color: teal;">Info</span><span class="p">(</span><span class="s" style="color: #d14;">"$cmd\n"</span><span class="p">);</span></span>
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427
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496
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$ret</span><span class="p">;</span></span>
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428
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497
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$cap_out</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -485,30 +554,87 @@ if(defined($cap_out)) {</td>
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485
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554
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="perl"> <span class="p">}</span></span>
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486
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555
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="perl"> <span class="p">}</span></span>
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487
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556
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="perl"> <span class="p">}</span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="perl"></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$seqIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">;</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$qualIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">;</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$readIdIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">;</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$outputFmtSam</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="perl"> <span class="p">{</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$outputHeader</span> <span class="o" style="font-weight: 600;">=</span> <span class="sr" style="color: #009926;"><BT></span> <span class="p">;</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="sr" style="color: #009926;">/\t/</span><span class="p">,</span> <span class="nv" style="color: teal;">$outputHeader</span> <span class="p">;</span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span> <span class="nv" style="color: teal;">@cols</span> <span class="p">)</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="nv" style="color: teal;">$i</span> <span class="p">)</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="nv" style="color: teal;">$i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/readSeq/</span> <span class="p">)</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="perl"> <span class="p">{</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="perl"> <span class="nv" style="color: teal;">$seqIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$i</span> <span class="p">;</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="perl"> <span class="p">}</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="nv" style="color: teal;">$i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/readQual/</span> <span class="p">)</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="perl"> <span class="p">{</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="perl"> <span class="nv" style="color: teal;">$qualIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$i</span> <span class="p">;</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="perl"> <span class="p">}</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="nv" style="color: teal;">$i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/readID/</span> <span class="p">)</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="perl"> <span class="p">{</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="perl"> <span class="nv" style="color: teal;">$readIdIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$i</span> <span class="p">;</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="perl"> <span class="p">}</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="perl"> <span class="p">}</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$seqIndex</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: teal;">%read_fhs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="perl"> <span class="nv" style="color: teal;">Error</span><span class="p">(</span> <span class="s" style="color: #d14;">"Must use readSeq in --tabFmtCols in order to output unaligned reads."</span> <span class="p">)</span> <span class="p">;</span></span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="perl"> <span class="p">}</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="perl"> </span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="perl"> <span class="nv" style="color: teal;">$outputHeader</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">RemoveSeqCols</span><span class="p">(</span> <span class="nv" style="color: teal;">$outputHeader</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$removeSeqCols</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="p">;</span></span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="p">{</span><span class="nv" style="color: teal;">$ofh</span><span class="p">}</span> <span class="nv" style="color: teal;">$outputHeader</span> <span class="p">;</span></span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="perl"> <span class="p">}</span></span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="perl"> <span class="p">{</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="perl"> <span class="nv" style="color: teal;">$seqIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">9</span> <span class="p">;</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="perl"> <span class="nv" style="color: teal;">$qualIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span> <span class="p">;</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="perl"> <span class="nv" style="color: teal;">$readIdIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="perl"> <span class="p">}</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="perl"></span>
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488
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595
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="sr" style="color: #009926;"><BT></span><span class="p">)</span> <span class="p">{</span></span>
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489
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596
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span></span>
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490
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597
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$filt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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491
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598
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span><span class="p">(</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: teal;">$_</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"@"</span><span class="p">)</span> <span class="p">{</span></span>
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492
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599
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># If we are supposed to output certain reads to files...</span></span>
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493
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$tab1_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">index</span><span class="p">(</span><span class="nv" style="color: teal;">$_</span><span class="p">,</span> <span class="s" style="color: #d14;">"\t"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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494
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$tab2_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">index</span><span class="p">(</span><span class="nv" style="color: teal;">$_</span><span class="p">,</span> <span class="s" style="color: #d14;">"\t"</span><span class="p">,</span> <span class="nv" style="color: teal;">$tab1_i</span><span class="p">);</span></span>
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495
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$fl</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: teal;">$_</span><span class="p">,</span> <span class="nv" style="color: teal;">$tab1_i</span><span class="p">,</span> <span class="nv" style="color: teal;">$tab2_i</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$tab1_i</span><span class="p">);</span></span>
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496
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$unal</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nv" style="color: teal;">$fl</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#my $tab1_i = index($_, "\t") + 1;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#my $tab2_i = index($_, "\t", $tab1_i);</span></span>
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#my $fl = substr($_, $tab1_i, $tab2_i - $tab1_i);</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$unal</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="sr" style="color: #009926;">/unclassified/</span> <span class="p">)</span></span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="perl"> <span class="p">{</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="perl"> <span class="nv" style="color: teal;">$unal</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="p">;</span></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="perl"> <span class="p">}</span></span>
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497
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608
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<pre style="margin: 0;"> <span id="LC608" class="line" lang="perl"> <span class="nv" style="color: teal;">$filt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: teal;">$no_unal</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$unal</span><span class="p">;</span></span>
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498
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609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$passthru</span><span class="p">)</span> <span class="p">{</span></span>
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499
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: teal;">%read_fhs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: teal;">%read_fhs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$seqIndex</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff right"> </span><span class="p">)</span> <span class="p">{</span></span>
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500
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Next line is read with some whitespace escaped</span></span>
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$l</span> <span class="o" style="font-weight: 600;">=</span> <span class="sr" style="color: #009926;"><BT></span><span class="p">;</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>my $l = <BT>;</span></span>
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502
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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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503
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$mate1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="nv" style="color: teal;">$fl</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">64</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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504
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$mate2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="nv" style="color: teal;">$fl</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">128</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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505
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$unp</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: teal;">$mate1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: teal;">$mate2</span><span class="p">;</span></span>
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506
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$pair</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: teal;">$unp</span><span class="p">;</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="sr" style="color: #009926;">/\t/</span> <span class="p">;</span></span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$isPaired</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$pair</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="nv" style="color: teal;">$seqIndex</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/_/</span> <span class="p">)</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="perl"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="perl"> <span class="nv" style="color: teal;">$pair</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="p">;</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="perl"> <span class="p">}</span></span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$unp</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: teal;">$pair</span> <span class="p">;</span></span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="perl"></span>
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507
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623
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Next line is read with some whitespace escaped</span></span>
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508
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$l</span> <span class="o" style="font-weight: 600;">=</span> <span class="sr" style="color: #009926;"><BT></span><span class="p">;</span></span>
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509
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span><span class="p">(</span><span class="nv" style="color: teal;">$l</span><span class="p">);</span></span>
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510
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="perl"> <span class="nv" style="color: teal;">$l</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/%(..)/chr(hex($1))/eg</span><span class="p">;</span></span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#my $l = <BT>;</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#chomp($l);</span></span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#$l =~ s/%(..)/chr(hex($1))/eg;</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="perl"></span>
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511
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628
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="nv" style="color: teal;">un</span><span class="p">})</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="nv" style="color: teal;">al</span><span class="p">}))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$unp</span><span class="p">)</span> <span class="p">{</span></span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$l</span> <span class="p">;</span></span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$qualIndex</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">)</span></span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="perl"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="perl"> <span class="nv" style="color: teal;">$l</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"@"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$cols</span><span class="p">[</span> <span class="nv" style="color: teal;">$readIdIndex</span> <span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="nv" style="color: teal;">$seqIndex</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n+\n"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="nv" style="color: teal;">$qualIndex</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="perl"> <span class="p">}</span></span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> </span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="perl"> <span class="p">{</span></span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="perl"> <span class="nv" style="color: teal;">$l</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$cols</span><span class="p">[</span> <span class="nv" style="color: teal;">$readIdIndex</span> <span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="nv" style="color: teal;">$seqIndex</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span> <span class="p">;</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="perl"> <span class="p">}</span></span>
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512
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638
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$unal</span><span class="p">)</span> <span class="p">{</span></span>
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513
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639
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Failed to align</span></span>
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514
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640
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="p">{</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="nv" style="color: teal;">un</span><span class="p">}}</span> <span class="nv" style="color: teal;">$l</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="nv" style="color: teal;">un</span><span class="p">});</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -517,21 +643,42 @@ if(defined($cap_out)) {</td>
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517
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643
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="p">{</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="nv" style="color: teal;">al</span><span class="p">}}</span> <span class="nv" style="color: teal;">$l</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="nv" style="color: teal;">al</span><span class="p">});</span></span>
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518
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644
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="perl"> <span class="p">}</span></span>
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519
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645
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<pre style="margin: 0;"> <span id="LC645" class="line" lang="perl"> <span class="p">}</span></span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$warnedAboutLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span></span>
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520
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647
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="s" style="color: #d14;">"un-conc"</span><span class="p">})</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="s" style="color: #d14;">"al-conc"</span><span class="p">}))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$pair</span><span class="p">)</span> <span class="p">{</span></span>
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521
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$conc</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="nv" style="color: teal;">$fl</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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522
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$conc</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$mate1</span><span class="p">)</span> <span class="p">{</span></span>
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523
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="p">{</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="s" style="color: #d14;">"al-conc"</span><span class="p">}{</span><span class="mi" style="color: #099;">1</span><span class="p">}}</span> <span class="nv" style="color: teal;">$l</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="s" style="color: #d14;">"al-conc"</span><span class="p">});</span></span>
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524
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: teal;">$conc</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$mate2</span><span class="p">)</span> <span class="p">{</span></span>
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525
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="p">{</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="s" style="color: #d14;">"al-conc"</span><span class="p">}{</span><span class="mi" style="color: #099;">2</span><span class="p">}}</span> <span class="nv" style="color: teal;">$l</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="s" style="color: #d14;">"al-conc"</span><span class="p">});</span></span>
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526
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: teal;">$conc</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$mate1</span><span class="p">)</span> <span class="p">{</span></span>
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527
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="p">{</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="s" style="color: #d14;">"un-conc"</span><span class="p">}{</span><span class="mi" style="color: #099;">1</span><span class="p">}}</span> <span class="nv" style="color: teal;">$l</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="s" style="color: #d14;">"un-conc"</span><span class="p">});</span></span>
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: teal;">$conc</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$mate2</span><span class="p">)</span> <span class="p">{</span></span>
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529
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="p">{</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="s" style="color: #d14;">"un-conc"</span><span class="p">}{</span><span class="mi" style="color: #099;">2</span><span class="p">}}</span> <span class="nv" style="color: teal;">$l</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="s" style="color: #d14;">"un-conc"</span><span class="p">});</span></span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="sr" style="color: #009926;">/_/</span><span class="p">,</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="nv" style="color: teal;">$seqIndex</span><span class="p">]</span> <span class="p">;</span></span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="nv" style="color: teal;">$qualIndex</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span> <span class="nv" style="color: teal;">$seq</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">)</span> <span class="p">),</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="nv" style="color: teal;">$qualIndex</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span> <span class="nv" style="color: teal;">$seq</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="p">)</span> <span class="p">;</span></span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="perl"> </span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$l1</span> <span class="p">;</span></span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$l2</span> <span class="p">;</span></span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$qualIndex</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">)</span></span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="perl"> <span class="p">{</span></span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="perl"> <span class="nv" style="color: teal;">$l1</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"@"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$cols</span><span class="p">[</span> <span class="nv" style="color: teal;">$readIdIndex</span> <span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$seq</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n+\n"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$qual</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span> <span class="p">;</span></span>
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="perl"> <span class="p">}</span></span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> </span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="perl"> <span class="p">{</span></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="perl"> <span class="nv" style="color: teal;">$l1</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$cols</span><span class="p">[</span> <span class="nv" style="color: teal;">$readIdIndex</span> <span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$seq</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span> <span class="p">;</span></span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="perl"> <span class="p">}</span></span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$qualIndex</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">)</span></span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="perl"> <span class="p">{</span></span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="perl"> <span class="nv" style="color: teal;">$l2</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"@"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$cols</span><span class="p">[</span> <span class="nv" style="color: teal;">$readIdIndex</span> <span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$seq</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n+\n"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$qual</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="perl"> <span class="p">}</span></span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> </span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="perl"> <span class="p">{</span></span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="perl"> <span class="nv" style="color: teal;">$l2</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$cols</span><span class="p">[</span> <span class="nv" style="color: teal;">$readIdIndex</span> <span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$seq</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span> <span class="p">;</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="perl"> <span class="p">}</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="perl"></span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: teal;">$unal</span><span class="p">)</span> <span class="p">{</span></span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="p">{</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="s" style="color: #d14;">"al-conc"</span><span class="p">}{</span><span class="mi" style="color: #099;">1</span><span class="p">}}</span> <span class="nv" style="color: teal;">$l1</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="s" style="color: #d14;">"al-conc"</span><span class="p">});</span></span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="p">{</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="s" style="color: #d14;">"al-conc"</span><span class="p">}{</span><span class="mi" style="color: #099;">2</span><span class="p">}}</span> <span class="nv" style="color: teal;">$l2</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="s" style="color: #d14;">"al-conc"</span><span class="p">});</span></span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="p">{</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="s" style="color: #d14;">"un-conc"</span><span class="p">}{</span><span class="mi" style="color: #099;">1</span><span class="p">}}</span> <span class="nv" style="color: teal;">$l1</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="s" style="color: #d14;">"un-conc"</span><span class="p">});</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="p">{</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="s" style="color: #d14;">"un-conc"</span><span class="p">}{</span><span class="mi" style="color: #099;">2</span><span class="p">}}</span> <span class="nv" style="color: teal;">$l2</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$read_fhs</span><span class="p">{</span><span class="s" style="color: #d14;">"un-conc"</span><span class="p">});</span></span>
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676
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="perl"> <span class="p">}</span></span>
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677
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="perl"> <span class="p">}</span></span>
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678
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="perl"> <span class="p">}</span></span>
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533
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679
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<pre style="margin: 0;"> <span id="LC679" class="line" lang="perl"> <span class="p">}</span></span>
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534
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680
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<pre style="margin: 0;"> <span id="LC680" class="line" lang="perl"> <span class="p">}</span></span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="perl"> <span class="nv" style="color: teal;">$_</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">RemoveSeqCols</span><span class="p">(</span> <span class="nv" style="color: teal;">$_</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$removeSeqCols</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="p">;</span></span>
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535
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682
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="p">{</span><span class="nv" style="color: teal;">$ofh</span><span class="p">}</span> <span class="s" style="color: #d14;">"$_\n"</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: teal;">$filt</span><span class="p">;</span></span>
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536
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683
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="perl"> <span class="p">}</span></span>
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537
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684
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$k</span> <span class="p">(</span><span class="nv" style="color: teal;">@fhs_to_close</span><span class="p">)</span> <span class="p">{</span> <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: teal;">$k</span><span class="p">);</span> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/centrifuge/commit/f6f7b098137879381ca6b18e3e5ba7c4c327171f#d8f5fe0588502d1a8ca61541057cc297e42bc963"><strong>centrifuge-download</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,10 +11,10 @@ if hash rsync 2>/dev/null; then</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"> <span class="nv" style="color: teal;">DL_MODE</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"rsync"</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">elif </span><span class="nb" style="color: #0086b3;">hash </span>wget 2>/dev/null<span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">DL_PROG</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"wget -N --reject=index.html -qO"</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"> <span class="nv" style="color: teal;">DL_MODE</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"<span class="idiff left right">ftp</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"> <span class="nv" style="color: teal;">DL_MODE</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"<span class="idiff left right">https</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">else </span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">DL_PROG</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"curl -s -o"</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"> <span class="nv" style="color: teal;">DL_MODE</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"<span class="idiff left right">ftp</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"> <span class="nv" style="color: teal;">DL_MODE</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"<span class="idiff left right">https</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span>DL_PROG DL_MODE</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -154,7 +154,7 @@ COMMON OPTIONS</td>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="shell"><span class="s2" style="color: #d14;">WHEN USING database refseq OR genbank:</span></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="shell"><span class="s2" style="color: #d14;"> -d <domain> What domain to download. One or more of </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">ALL_GENOMES</span><span class="p">// /, </span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> (comma separated).</span></span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="shell"><span class="s2" style="color: #d14;"> -a <assembly level> Only download genomes with the specified assembly level. Default: '</span><span class="nv" style="color: teal;">$ASSEMBLY_LEVEL</span><span class="s2" style="color: #d14;">'.</span></span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="shell"><span class="s2" style="color: #d14;"> -a <assembly level> Only download genomes with the specified assembly level. Default: '</span><span class="nv" style="color: teal;">$ASSEMBLY_LEVEL</span><span class="s2" style="color: #d14;">'.<span class="idiff left right"> Use 'Any' for any assembly level.</span></span></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="shell"><span class="s2" style="color: #d14;"> -c <refseq category> Only download genomes in the specified refseq category. Default: any.</span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="shell"><span class="s2" style="color: #d14;"> -t <taxids> Only download the specified taxonomy IDs, comma separated. Default: any.</span></span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="shell"><span class="s2" style="color: #d14;"> -r Download RNA sequences, too.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -262,8 +262,10 @@ SPECIES_TAXID_FIELD=7</td>
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="shell"><span class="nv" style="color: teal;">VERSION_STATUS_FIELD</span><span class="o" style="font-weight: 600;">=</span>11</span>
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263
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="shell"><span class="nv" style="color: teal;">ASSEMBLY_LEVEL_FIELD</span><span class="o" style="font-weight: 600;">=</span>12</span>
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264
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="shell"><span class="nv" style="color: teal;">FTP_PATH_FIELD</span><span class="o" style="font-weight: 600;">=</span>20</span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="shell"><span class="nv" style="color: teal;">FTP_PATH_FIELD2</span><span class="o" style="font-weight: 600;">=</span>21 <span class="c" style="color: #998; font-style: italic;">## Needed for wrongly formatted virus files - hopefully just a temporary fix</span></span>
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265
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="shell"></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="shell"><span class="nv" style="color: teal;">AWK_QUERY</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\$</span><span class="nv" style="color: teal;">$ASSEMBLY_LEVEL_FIELD</span><span class="s2" style="color: #d14;">==</span><span class="se" style="color: #d14;">\"</span><span class="nv" style="color: teal;">$ASSEMBLY_LEVEL</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;"> && </span><span class="se" style="color: #d14;">\$</span><span class="nv" style="color: teal;">$VERSION_STATUS_FIELD</span><span class="s2" style="color: #d14;">==</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">latest</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="shell"><span class="nv" style="color: teal;">AWK_QUERY</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\$</span><span class="nv" style="color: teal;">$VERSION_STATUS_FIELD</span><span class="s2" style="color: #d14;">==</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">latest</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="shell"><span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$ASSEMBLY_LEVEL</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"Any"</span> <span class="o" style="font-weight: 600;">]]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">AWK_QUERY</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$AWK_QUERY</span><span class="s2" style="color: #d14;"> && </span><span class="se" style="color: #d14;">\$</span><span class="nv" style="color: teal;">$ASSEMBLY_LEVEL_FIELD</span><span class="s2" style="color: #d14;">==</span><span class="se" style="color: #d14;">\"</span><span class="nv" style="color: teal;">$ASSEMBLY_LEVEL</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span></span>
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267
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="shell"><span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$REFSEQ_CATEGORY</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">AWK_QUERY</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$AWK_QUERY</span><span class="s2" style="color: #d14;"> && </span><span class="se" style="color: #d14;">\$</span><span class="nv" style="color: teal;">$REFSEQ_CAT_FIELD</span><span class="s2" style="color: #d14;">==</span><span class="se" style="color: #d14;">\"</span><span class="nv" style="color: teal;">$REFSEQ_CATEGORY</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span></span>
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268
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="shell"></span>
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269
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="shell"><span class="nv" style="color: teal;">TAXID</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">TAXID</span><span class="p">//,/|</span><span class="k" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -320,11 +322,22 @@ for DOMAIN in $DOMAINS; do</td>
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="shell"></span>
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321
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="shell"> <span class="nv" style="color: teal;">N_EXPECTED</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">cat</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$ASSEMBLY_SUMMARY_FILE</span><span class="s2" style="color: #d14;">"</span> | wc <span class="nt" style="color: navy;">-l</span><span class="sb" style="color: #d14;">`</span></span>
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322
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="shell"> <span class="o" style="font-weight: 600;">[[</span> <span class="nv" style="color: teal;">$N_EXPECTED</span> <span class="nt" style="color: navy;">-gt</span> 0 <span class="o" style="font-weight: 600;">]]</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">{</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Domain </span><span class="nv" style="color: teal;">$DOMAIN</span><span class="s2" style="color: #d14;"> has no genomes with specified filter."</span> <span class="o" style="font-weight: 600;">></span>&2<span class="p">;</span> <span class="nb" style="color: #0086b3;">exit </span>1<span class="p">;</span> <span class="o" style="font-weight: 600;">}</span></span>
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323
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Downloading </span><span class="nv" style="color: teal;">$N_EXPECTED</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: teal;">$DOMAIN</span><span class="s2" style="color: #d14;"> genomes at assembly level </span><span class="nv" style="color: teal;">$ASSEMBLY_LEVEL</span><span class="s2" style="color: #d14;"> ... (will take a while)"</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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324
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="shell"> cut <span class="nt" style="color: navy;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$TAXID_FIELD</span><span class="s2" style="color: #d14;">,</span><span class="nv" style="color: teal;">$FTP_PATH_FIELD</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$ASSEMBLY_SUMMARY_FILE</span><span class="s2" style="color: #d14;">"</span> | sed <span class="s1" style="color: #d14;">'s#\([^/]*\)$#\1/\1_genomic.fna.gz#'</span> |<span class="se" style="color: #d14;">\</span></span>
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325
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="shell"> tr <span class="s1" style="color: #d14;">'\n'</span> <span class="s1" style="color: #d14;">'\0'</span> | xargs <span class="nt" style="color: navy;">-0</span> <span class="nt" style="color: navy;">-n1</span> <span class="nt" style="color: navy;">-P</span> <span class="nv" style="color: teal;">$N_PROC</span> bash <span class="nt" style="color: navy;">-c</span> <span class="s1" style="color: #d14;">'download_n_process_nofail "$@"'</span> _ | count <span class="nv" style="color: teal;">$N_EXPECTED</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="shell"></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$DOMAIN</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">"viral"</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">## Wrong columns in viral assembly summary files - the path is sometimes in field 20, sometimes 21</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="shell"> cut <span class="nt" style="color: navy;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$TAXID_FIELD</span><span class="s2" style="color: #d14;">,</span><span class="nv" style="color: teal;">$FTP_PATH_FIELD</span><span class="s2" style="color: #d14;">,</span><span class="nv" style="color: teal;">$FTP_PATH_FIELD2</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$ASSEMBLY_SUMMARY_FILE</span><span class="s2" style="color: #d14;">"</span> | <span class="se" style="color: #d14;">\</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="shell"> sed <span class="s1" style="color: #d14;">'s/^\(.*\)\t\(ftp:.*\)\t.*/\1\t\2/;s/^\(.*\)\t.*\t\(ftp:.*\)/\1\t\2/'</span> | <span class="se" style="color: #d14;">\</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="shell"> sed <span class="s1" style="color: #d14;">'s#\([^/]*\)$#\1/\1_genomic.fna.gz#'</span> |<span class="se" style="color: #d14;">\</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="shell"> tr <span class="s1" style="color: #d14;">'\n'</span> <span class="s1" style="color: #d14;">'\0'</span> | xargs <span class="nt" style="color: navy;">-0</span> <span class="nt" style="color: navy;">-n1</span> <span class="nt" style="color: navy;">-P</span> <span class="nv" style="color: teal;">$N_PROC</span> bash <span class="nt" style="color: navy;">-c</span> <span class="s1" style="color: #d14;">'download_n_process_nofail "$@"'</span> _ | count <span class="nv" style="color: teal;">$N_EXPECTED</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Downloading </span><span class="nv" style="color: teal;">$N_EXPECTED</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: teal;">$DOMAIN</span><span class="s2" style="color: #d14;"> genomes at assembly level </span><span class="nv" style="color: teal;">$ASSEMBLY_LEVEL</span><span class="s2" style="color: #d14;"> ... (will take a while)"</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="shell"> cut <span class="nt" style="color: navy;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$TAXID_FIELD</span><span class="s2" style="color: #d14;">,</span><span class="nv" style="color: teal;">$FTP_PATH_FIELD</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$ASSEMBLY_SUMMARY_FILE</span><span class="s2" style="color: #d14;">"</span> | sed <span class="s1" style="color: #d14;">'s#\([^/]*\)$#\1/\1_genomic.fna.gz#'</span> |<span class="se" style="color: #d14;">\</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="shell"> tr <span class="s1" style="color: #d14;">'\n'</span> <span class="s1" style="color: #d14;">'\0'</span> | xargs <span class="nt" style="color: navy;">-0</span> <span class="nt" style="color: navy;">-n1</span> <span class="nt" style="color: navy;">-P</span> <span class="nv" style="color: teal;">$N_PROC</span> bash <span class="nt" style="color: navy;">-c</span> <span class="s1" style="color: #d14;">'download_n_process_nofail "$@"'</span> _ | count <span class="nv" style="color: teal;">$N_EXPECTED</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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326
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337
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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327
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338
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="shell"></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="shell"></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="shell"></span>
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328
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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$DOWNLOAD_RNA</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">"1"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$DOMAIN</span> | egrep <span class="s1" style="color: #d14;">'bacteria|viral|archaea'</span><span class="sb" style="color: #d14;">`</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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329
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342
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Downloadinging rna sequence files"</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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330
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343
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="shell"> cut <span class="nt" style="color: navy;">-f</span> <span class="nv" style="color: teal;">$TAXID_FIELD</span>,<span class="nv" style="color: teal;">$FTP_PATH_FIELD</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$ASSEMBLY_SUMMARY_FILE</span><span class="s2" style="color: #d14;">"</span>| sed <span class="s1" style="color: #d14;">'s#\([^/]*\)$#\1/\1_rna.fna.gz#'</span> |<span class="se" style="color: #d14;">\</span></span>
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<a href="https://salsa.debian.org/med-team/centrifuge/commit/f6f7b098137879381ca6b18e3e5ba7c4c327171f#fd1054bfea308886c08eb1c3c254619085646a47"><strong>centrifuge-kreport</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,12 +9,17 @@</td>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">strict</span><span class="p">;</span></span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">warnings</span><span class="p">;</span></span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Getopt::</span><span class="nv" style="color: teal;">Long</span><span class="p">;</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">File::</span><span class="nv" style="color: teal;">Basename</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">Cwd</span><span class="p">;</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">Cwd</span> <span class="s" style="color: #d14;">'cwd'</span> <span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">Cwd</span> <span class="s" style="color: #d14;">'abs_path'</span> <span class="p">;</span></span>
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12
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="perl"></span>
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13
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$centrifuge_index</span><span class="p">,</span> <span class="nv" style="color: teal;">$min_score</span><span class="p">,</span> <span class="nv" style="color: teal;">$min_length</span><span class="p">);</span></span>
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14
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$only_unique</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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15
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$show_zeros</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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16
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$is_cnts_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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17
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$PROG</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"centrifuge-kreport"</span><span class="p">;</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$CWD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">dirname</span><span class="p">(</span> <span class="nv" style="color: teal;">abs_path</span><span class="p">(</span> <span class="nv" style="color: teal;">$0</span> <span class="p">)</span> <span class="p">)</span> <span class="p">;</span></span>
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18
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="perl"></span>
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19
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="perl"><span class="nv" style="color: teal;">GetOptions</span><span class="p">(</span></span>
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20
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="perl"> <span class="s" style="color: #d14;">"help"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\&</span><span class="nv" style="color: teal;">display_help</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,9 +76,23 @@ if ($is_cnts_table) {</td>
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71
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="perl"> <span class="nv" style="color: teal;">$seq_count</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: teal;">$count</span><span class="p">;</span></span>
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72
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="perl"> <span class="p">}</span></span>
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73
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="perl"><span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="perl"> <span class="o" style="font-weight: 600;"><></span><span class="p">;</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$header</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="sr" style="color: #009926;">/\s+/</span><span class="p">,</span> <span class="nv" style="color: teal;">$header</span> <span class="p">;</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">%headerMap</span> <span class="p">;</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span> <span class="nv" style="color: teal;">@cols</span> <span class="p">)</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="nv" style="color: teal;">$i</span> <span class="p">)</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="perl"> <span class="p">{</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="perl"> <span class="nv" style="color: teal;">$headerMap</span><span class="p">{</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="nv" style="color: teal;">$i</span><span class="p">]</span> <span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$i</span> <span class="p">;</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="perl"> <span class="p">}</span></span>
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75
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><></span><span class="p">)</span> <span class="p">{</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">undef</span><span class="p">,</span><span class="nv" style="color: teal;">$seqID</span><span class="p">,</span><span class="nv" style="color: teal;">$taxid</span><span class="p">,</span><span class="nv" style="color: teal;">$score</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">undef</span><span class="p">,</span> <span class="nv" style="color: teal;">$hitLength</span><span class="p">,</span> <span class="nv" style="color: teal;">$queryLength</span><span class="p">,</span> <span class="nv" style="color: teal;">$numMatches</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="sr" style="color: #009926;">/\t/</span><span class="p">;</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#my (undef,$seqID,$taxid,$score, undef, $hitLength, $queryLength, $numMatches) = split /\t/;</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="sr" style="color: #009926;">/\s+/</span> <span class="p">;</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$seqID</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span> <span class="nv" style="color: teal;">$headerMap</span><span class="p">{</span> <span class="s" style="color: #d14;">"seqID"</span> <span class="p">}</span> <span class="p">]</span> <span class="p">;</span> </span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$taxid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span> <span class="nv" style="color: teal;">$headerMap</span><span class="p">{</span> <span class="s" style="color: #d14;">"taxID"</span> <span class="p">}</span> <span class="p">]</span> <span class="p">;</span> </span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$score</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span> <span class="nv" style="color: teal;">$headerMap</span><span class="p">{</span> <span class="s" style="color: #d14;">"score"</span> <span class="p">}</span> <span class="p">]</span> <span class="p">;</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$hitLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span> <span class="nv" style="color: teal;">$headerMap</span><span class="p">{</span> <span class="s" style="color: #d14;">"hitLength"</span> <span class="p">}</span> <span class="p">]</span> <span class="p">;</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$queryLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span> <span class="nv" style="color: teal;">$headerMap</span><span class="p">{</span> <span class="s" style="color: #d14;">"queryLength"</span> <span class="p">}</span> <span class="p">]</span> <span class="p">;</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$numMatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span> <span class="nv" style="color: teal;">$headerMap</span><span class="p">{</span> <span class="s" style="color: #d14;">"numMatches"</span> <span class="p">}</span> <span class="p">]</span> <span class="p">;</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="perl"></span>
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77
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<td class="diff-line-num new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="perl"> <span class="k" style="font-weight: 600;">next</span> <span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: teal;">$only_unique</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$numMatches</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
78
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<td class="diff-line-num new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="perl"> <span class="k" style="font-weight: 600;">next</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$min_length</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$hitLength</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$min_length</span><span class="p">;</span></span>
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79
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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="perl"> <span class="k" style="font-weight: 600;">next</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$min_score</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$score</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$min_score</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -150,7 +169,7 @@ sub dfs_summation {</td>
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150
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<td class="diff-line-num new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">load_taxonomy</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
151
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<td class="diff-line-num new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
152
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<td class="diff-line-num new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Loading names file ...\n"</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
153
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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">open</span> <span class="nv" style="color: teal;">NAMES</span><span class="p">,</span> <span class="s" style="color: #d14;">"-|"</span><span class="p">,</span> <span class="s" style="color: #d14;">"centrifuge-inspect --name-table $centrifuge_index"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">open</span> <span class="nv" style="color: teal;">NAMES</span><span class="p">,</span> <span class="s" style="color: #d14;">"-|"</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left right">$CWD/</span>centrifuge-inspect --name-table $centrifuge_index"</span></span>
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154
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<td class="diff-line-num new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="perl"> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"$PROG: can't open names file: $!\n"</span><span class="p">;</span></span>
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155
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="sr" style="color: #009926;"><NAMES></span><span class="p">)</span> <span class="p">{</span></span>
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156
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<td class="diff-line-num new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -162,7 +181,7 @@ sub load_taxonomy {</td>
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162
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">close</span> <span class="nv" style="color: teal;">NAMES</span><span class="p">;</span></span>
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163
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
164
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<td class="diff-line-num new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Loading nodes file ...\n"</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
165
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<td class="diff-line-num new_line old" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">open</span> <span class="nv" style="color: teal;">NODES</span><span class="p">,</span> <span class="s" style="color: #d14;">"-|"</span><span class="p">,</span> <span class="s" style="color: #d14;">"centrifuge-inspect --taxonomy-tree $centrifuge_index"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">open</span> <span class="nv" style="color: teal;">NODES</span><span class="p">,</span> <span class="s" style="color: #d14;">"-|"</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left right">$CWD/</span>centrifuge-inspect --taxonomy-tree $centrifuge_index"</span></span>
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166
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<td class="diff-line-num new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="perl"> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"$PROG: can't open nodes file: $!\n"</span><span class="p">;</span></span>
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167
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<td class="diff-line-num new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="sr" style="color: #009926;"><NODES></span><span class="p">)</span> <span class="p">{</span></span>
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168
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<td class="diff-line-num new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/centrifuge/commit/f6f7b098137879381ca6b18e3e5ba7c4c327171f#5e28451c048cf424257052950561e0cae5208bf9"><strong>centrifuge-promote</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env perl</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="perl"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">strict</span> <span class="p">;</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">warnings</span> <span class="p">;</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="perl"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">File::</span><span class="nv" style="color: teal;">Basename</span><span class="p">;</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">Cwd</span><span class="p">;</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">Cwd</span> <span class="s" style="color: #d14;">'cwd'</span> <span class="p">;</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">Cwd</span> <span class="s" style="color: #d14;">'abs_path'</span> <span class="p">;</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="perl"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="perl"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="perl"><span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"Usage: centrifuge-promote.pl centrifuge_index centrifuge_output level > output\n\n"</span><span class="o" style="font-weight: 600;">.</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"> <span class="s" style="color: #d14;">"Promote the taxonomy id to specified level in Centrifuge output.\n"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">@ARGV</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="p">;</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="perl"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$CWD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">dirname</span><span class="p">(</span> <span class="nv" style="color: teal;">abs_path</span><span class="p">(</span> <span class="nv" style="color: teal;">$0</span> <span class="p">)</span> <span class="p">)</span> <span class="p">;</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Go through the index to obtain the taxonomy tree</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">%taxParent</span> <span class="p">;</span> </span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">%taxIdToSeqId</span> <span class="p">;</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">%taxLevel</span> <span class="p">;</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="perl"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$centrifuge_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$ARGV</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="perl"><span class="nb" style="color: #0086b3;">open</span> <span class="nv" style="color: teal;">FP1</span><span class="p">,</span> <span class="s" style="color: #d14;">"-|"</span><span class="p">,</span> <span class="s" style="color: #d14;">"$CWD/centrifuge-inspect --taxonomy-tree $centrifuge_index"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"can't open $!\n"</span> <span class="p">;</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="perl"><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="sr" style="color: #009926;"><FP1></span> <span class="p">)</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="perl"><span class="p">{</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span> <span class="p">;</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="sr" style="color: #009926;">/\t\|\t/</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="perl"> <span class="nv" style="color: teal;">$taxParent</span><span class="p">{</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="perl"> <span class="nv" style="color: teal;">$taxLevel</span><span class="p">{</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="perl"><span class="nb" style="color: #0086b3;">close</span> <span class="nv" style="color: teal;">FP1</span> <span class="p">;</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="perl"><span class="nb" style="color: #0086b3;">open</span> <span class="nv" style="color: teal;">FP1</span><span class="p">,</span> <span class="s" style="color: #d14;">"-|"</span><span class="p">,</span> <span class="s" style="color: #d14;">"$CWD/centrifuge-inspect --conversion-table $centrifuge_index"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"can't open $!\n"</span> <span class="p">;</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="perl"><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="sr" style="color: #009926;"><FP1></span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="perl"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="sr" style="color: #009926;">/\t/</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="perl"> <span class="nv" style="color: teal;">$taxIdToSeqId</span><span class="p">{</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="perl"><span class="nb" style="color: #0086b3;">close</span> <span class="nv" style="color: teal;">FP1</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Go through the output of centrifuge</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$level</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$ARGV</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">PromoteTaxId</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="perl"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$tid</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span> <span class="nv" style="color: teal;">$taxLevel</span><span class="p">{</span> <span class="nv" style="color: teal;">$tid</span> <span class="p">}</span> <span class="p">)</span> <span class="p">)</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$taxLevel</span><span class="p">{</span> <span class="nv" style="color: teal;">$tid</span> <span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="nv" style="color: teal;">$level</span> <span class="p">)</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="perl"> <span class="p">{</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: teal;">$tid</span> <span class="p">;</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="perl"> <span class="p">}</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="perl"> <span class="p">{</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$tid</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="p">;</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: teal;">PromoteTaxId</span><span class="p">(</span> <span class="nv" style="color: teal;">$taxParent</span><span class="p">{</span> <span class="nv" style="color: teal;">$tid</span> <span class="p">}</span> <span class="p">)</span> <span class="p">;</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="perl"> <span class="p">}</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="perl"><span class="p">}</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="perl"></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">OutputPromotedLines</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="perl"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">@</span><span class="p">{</span> <span class="nv" style="color: teal;">$_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">}</span> <span class="p">;</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span> <span class="nv" style="color: teal;">@lines</span> <span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="p">;</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="perl"></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@newLines</span> <span class="p">;</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$i</span> <span class="p">;</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$numMatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">%showedUpTaxId</span> <span class="p">;</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$tab</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sprintf</span><span class="p">(</span> <span class="s" style="color: #d14;">"\t"</span> <span class="p">)</span> <span class="p">;</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span> <span class="nv" style="color: teal;">@lines</span> <span class="p">)</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="nv" style="color: teal;">$i</span> <span class="p">)</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="perl"> <span class="p">{</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="sr" style="color: #009926;">/\t+/</span><span class="p">,</span> <span class="nv" style="color: teal;">$lines</span><span class="p">[</span> <span class="nv" style="color: teal;">$i</span> <span class="p">]</span> <span class="p">;</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$newTid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">PromoteTaxId</span><span class="p">(</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="p">)</span> <span class="p">;</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$newTid</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="perl"> <span class="p">{</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="perl"> <span class="nv" style="color: teal;">$newTid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="p">;</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="perl"> <span class="p">}</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$newLevel</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="p">;</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="perl"> <span class="nv" style="color: teal;">$newLevel</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$taxLevel</span><span class="p">{</span> <span class="nv" style="color: teal;">$newTid</span> <span class="p">}</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$newTid</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$taxLevel</span><span class="p">{</span> <span class="nv" style="color: teal;">$newTid</span> <span class="p">}</span> <span class="p">)</span> <span class="p">;</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="perl"> </span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="perl"> <span class="k" style="font-weight: 600;">next</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$showedUpTaxId</span><span class="p">{</span> <span class="nv" style="color: teal;">$newTid</span> <span class="p">}</span> <span class="p">)</span> <span class="p">;</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="perl"> </span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="perl"> <span class="nv" style="color: teal;">$showedUpTaxId</span><span class="p">{</span> <span class="nv" style="color: teal;">$newTid</span> <span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="p">;</span> </span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="perl"> <span class="o" style="font-weight: 600;">++</span><span class="nv" style="color: teal;">$numMatches</span> <span class="p">;</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="perl"></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="perl"> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$newTid</span> <span class="p">;</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="perl"> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$newLevel</span> <span class="p">;</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="nv" style="color: teal;">@newLines</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">(</span> <span class="nv" style="color: teal;">$tab</span><span class="p">,</span> <span class="nv" style="color: teal;">@cols</span> <span class="p">)</span> <span class="p">;</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="perl"> <span class="p">}</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span> <span class="nv" style="color: teal;">@newLines</span> <span class="p">)</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="nv" style="color: teal;">$i</span> <span class="p">)</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="perl"> <span class="p">{</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="sr" style="color: #009926;">/\t+/</span><span class="p">,</span> <span class="nv" style="color: teal;">$newLines</span><span class="p">[</span><span class="nv" style="color: teal;">$i</span><span class="p">]</span> <span class="p">;</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="perl"> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$numMatches</span> <span class="p">;</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">(</span> <span class="nv" style="color: teal;">$tab</span><span class="p">,</span> <span class="nv" style="color: teal;">@cols</span> <span class="p">),</span> <span class="s" style="color: #d14;">"\n"</span> <span class="p">;</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="perl"> <span class="p">}</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="perl"><span class="p">}</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="perl"><span class="nb" style="color: #0086b3;">open</span> <span class="nv" style="color: teal;">FP1</span><span class="p">,</span> <span class="nv" style="color: teal;">$ARGV</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$header</span> <span class="o" style="font-weight: 600;">=</span> <span class="sr" style="color: #009926;"><FP1></span> <span class="p">;</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$prevReadId</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span> <span class="p">;</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@lines</span> <span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">$header</span> <span class="p">;</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="perl"><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="sr" style="color: #009926;"><FP1></span> <span class="p">)</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="perl"><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span> <span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="sr" style="color: #009926;">/\t/</span> <span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="nv" style="color: teal;">$prevReadId</span> <span class="p">)</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="nv" style="color: teal;">@lines</span><span class="p">,</span> <span class="nv" style="color: teal;">$_</span> <span class="p">;</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="perl"> <span class="p">{</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="perl"> <span class="nv" style="color: teal;">$prevReadId</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$cols</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="perl"> </span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="perl"> <span class="nv" style="color: teal;">OutputPromotedLines</span><span class="p">(</span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">@lines</span> <span class="p">)</span> <span class="p">;</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">undef</span> <span class="nv" style="color: teal;">@lines</span> <span class="p">;</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="nv" style="color: teal;">@lines</span><span class="p">,</span> <span class="nv" style="color: teal;">$_</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="perl"><span class="p">}</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="perl"><span class="nv" style="color: teal;">OutputPromotedLines</span><span class="p">(</span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">@lines</span> <span class="p">)</span> <span class="p">;</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="perl"><span class="nb" style="color: #0086b3;">close</span> <span class="nv" style="color: teal;">FP1</span> <span class="p">;</span></span></pre>
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<a href="https://salsa.debian.org/med-team/centrifuge/commit/f6f7b098137879381ca6b18e3e5ba7c4c327171f#3e44d076ff9b15d146f6db332bac2d871b3f4c64"><strong>centrifuge.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -501,7 +501,7 @@ static void resetOptions() {</td>
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501
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="cpp"> <span class="n" style="color: #333;">col_name_map</span><span class="p">[</span><span class="s" style="color: #d14;">"CIGAR"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PLACEHOLDER</span><span class="p">;</span></span>
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502
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502
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="cpp"> <span class="n" style="color: #333;">col_name_map</span><span class="p">[</span><span class="s" style="color: #d14;">"RNEXT"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SEQ_ID</span><span class="p">;</span></span>
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503
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503
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="cpp"> <span class="n" style="color: #333;">col_name_map</span><span class="p">[</span><span class="s" style="color: #d14;">"PNEXT"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PLACEHOLDER_ZERO</span><span class="p">;</span></span>
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504
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="cpp"> <span class="n" style="color: #333;">col_name_map</span><span class="p">[</span><span class="s" style="color: #d14;">"TLEN"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PLACEHOLDER_ZERO</span><span class="p">;</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="cpp"> <span class="n" style="color: #333;">col_name_map</span><span class="p">[</span><span class="s" style="color: #d14;">"TLEN"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">QUERY_LENGTH</span></span><span class="idiff"> </span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//</span>PLACEHOLDER_ZERO;</span></span>
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505
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505
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="cpp"> <span class="n" style="color: #333;">col_name_map</span><span class="p">[</span><span class="s" style="color: #d14;">"SEQ"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SEQ</span><span class="p">;</span></span>
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506
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506
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="cpp"> <span class="n" style="color: #333;">col_name_map</span><span class="p">[</span><span class="s" style="color: #d14;">"QUAL"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">QUAL</span><span class="p">;</span></span>
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507
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507
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/centrifuge/commit/f6f7b098137879381ca6b18e3e5ba7c4c327171f#4d3778d4c482b69d10dbd5975319cc35b317d046"><strong>classifier.h</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -418,7 +418,10 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="c"> </span>
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">_tree_traverse</span><span class="p">)</span> <span class="p">{</span></span>
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420
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_hitMap</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">khits</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="c"> <span class="n" style="color: #333;">reportUnclassified</span><span class="p">(</span> <span class="n" style="color: #333;">sink</span> <span class="p">)</span> <span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="c"> <span class="p">}</span></span>
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425
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="c"> <span class="p">}</span></span>
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426
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">rank</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -511,7 +514,10 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="c"> <span class="p">}</span></span>
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516
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<pre style="margin: 0;"> <span id="LC516" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">only_host_taxIDs</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">_hitMap</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">khits</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="c"> <span class="n" style="color: #333;">reportUnclassified</span><span class="p">(</span> <span class="n" style="color: #333;">sink</span> <span class="p">)</span> <span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> // boost up the score if the assignment is unique</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -528,7 +534,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="c"> <span class="n" style="color: #333;">max_score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">rdlen</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">15</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">rdlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">15</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">rdlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">15</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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535
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="c"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">reported</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">false</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">;</span></span> </span>
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">gi</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">gi</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">_hitMap</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">gi</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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539
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="c"> <span class="n" style="color: #333;">assert_gt</span><span class="p">(</span><span class="n" style="color: #333;">_hitMap</span><span class="p">[</span><span class="n" style="color: #333;">gi</span><span class="p">].</span><span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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534
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540
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="c"> <span class="n" style="color: #333;">HitCount</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">index_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">hitCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_hitMap</span><span class="p">[</span><span class="n" style="color: #333;">gi</span><span class="p">];</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -555,8 +561,13 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="c"> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">readPositions</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="c"> <span class="n" style="color: #333;">isFw</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="c"> <span class="n" style="color: #333;">sink</span><span class="p">.</span><span class="n" style="color: #333;">report</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">rs</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="c"> <span class="n" style="color: #333;">reported</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span> <span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">reported</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span> <span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="c"> <span class="n" style="color: #333;">reportUnclassified</span><span class="p">(</span> <span class="n" style="color: #333;">sink</span> <span class="p">)</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">getGenomeIdx</span><span class="p">(</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -968,62 +979,73 @@ private:</td>
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<pre style="margin: 0;"> <span id="LC979" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">offset</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC980" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">length</span><span class="p">)</span></span>
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970
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981
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<pre style="margin: 0;"> <span id="LC981" class="line" lang="c"> <span class="p">{</span></span>
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971
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<pre style="margin: 0;">-<span id="LC971" class="line" lang="c"><span class="idiff left right"> </span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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982
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<pre style="margin: 0;">+<span id="LC982" class="line" lang="c"><span class="idiff left right"> </span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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972
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983
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<pre style="margin: 0;"> <span id="LC983" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef LI_DEBUG</span></span>
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973
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<pre style="margin: 0;">-<span id="LC973" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Add "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">taxID</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">partialHitScore</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">weightedHitLen</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Add "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">taxID</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">partialHitScore</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">weightedHitLen</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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974
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985
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<pre style="margin: 0;"> <span id="LC985" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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975
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<pre style="margin: 0;">-<span id="LC975" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TaxonomyPathTable</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pathTable</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ebwt</span><span class="p">.</span><span class="n" style="color: #333;">paths</span><span class="p">();</span></span>
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976
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<pre style="margin: 0;">-<span id="LC976" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">pathTable</span><span class="p">.</span><span class="n" style="color: #333;">getPath</span><span class="p">(</span><span class="n" style="color: #333;">taxID</span><span class="p">,</span> <span class="n" style="color: #333;">_tempPath</span><span class="p">);</span></span>
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977
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<pre style="margin: 0;">-<span id="LC977" class="line" lang="c"><span class="idiff left right"> </span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">rank</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_classification_rank</span><span class="p">;</span></span>
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978
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<pre style="margin: 0;">-<span id="LC978" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rank</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
979
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<td class="diff-line-num new_line old" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC979" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">for</span><span class="p">(;</span> <span class="n" style="color: #333;">rank</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">_tempPath</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">rank</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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980
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<pre style="margin: 0;">-<span id="LC980" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_tempPath</span><span class="p">[</span><span class="n" style="color: #333;">rank</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
981
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<td class="diff-line-num new_line old" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC981" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">taxID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_tempPath</span><span class="p">[</span><span class="n" style="color: #333;">rank</span><span class="p">];</span></span>
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982
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<pre style="margin: 0;">-<span id="LC982" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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983
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<pre style="margin: 0;">-<span id="LC983" class="line" lang="c"><span class="idiff left right"> </span> <span class="p">}</span></span>
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984
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<pre style="margin: 0;">-<span id="LC984" class="line" lang="c"><span class="idiff left right"> </span> <span class="p">}</span></span>
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985
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<pre style="margin: 0;">-<span id="LC985" class="line" lang="c"><span class="idiff left right"> </span> <span class="p">}</span></span>
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986
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<pre style="margin: 0;">-<span id="LC986" class="line" lang="c"><span class="idiff left right"> </span></span>
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987
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<pre style="margin: 0;">-<span id="LC987" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">for</span><span class="p">(;</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hitMap</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
988
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<pre style="margin: 0;">-<span id="LC988" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">same</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
989
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<td class="diff-line-num new_line old" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC989" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rank</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
990
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<td class="diff-line-num new_line old" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC990" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">same</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">uniqueID</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">hitMap</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">].</span><span class="n" style="color: #333;">uniqueID</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
991
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<td class="diff-line-num new_line old" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC991" class="line" lang="c"><span class="idiff left right"> </span> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
992
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<td class="diff-line-num new_line old" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC992" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">same</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">taxID</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">hitMap</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">].</span><span class="n" style="color: #333;">taxID</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
993
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<pre style="margin: 0;">-<span id="LC993" class="line" lang="c"><span class="idiff left right"> </span> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
994
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<td class="diff-line-num new_line old" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC994" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">same</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
995
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<pre style="margin: 0;">-<span id="LC995" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">hitMap</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">].</span><span class="n" style="color: #333;">timeStamp</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">hi</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
996
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<td class="diff-line-num new_line old" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC996" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitMap</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">].</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
997
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<td class="diff-line-num new_line old" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC997" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitMap</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">].</span><span class="n" style="color: #333;">scores</span><span class="p">[</span><span class="n" style="color: #333;">rdi</span><span class="p">][</span><span class="n" style="color: #333;">fwi</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">partialHitScore</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
998
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<td class="diff-line-num new_line old" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC998" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitMap</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">].</span><span class="n" style="color: #333;">summedHitLens</span><span class="p">[</span><span class="n" style="color: #333;">rdi</span><span class="p">][</span><span class="n" style="color: #333;">fwi</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">weightedHitLen</span><span class="p">;</span></span>
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999
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<td class="diff-line-num new_line old" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC999" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitMap</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">].</span><span class="n" style="color: #333;">timeStamp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">hi</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1000
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<pre style="margin: 0;">-<span id="LC1000" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitMap</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">].</span><span class="n" style="color: #333;">readPositions</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1001
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<td class="diff-line-num new_line old" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1001" class="line" lang="c"><span class="idiff left right"> </span> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1002
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<td class="diff-line-num new_line old" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1002" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1003
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<td class="diff-line-num new_line old" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1003" class="line" lang="c"><span class="idiff left right"> </span> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1004
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<td class="diff-line-num new_line old" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1004" class="line" lang="c"><span class="idiff left right"> </span> <span class="p">}</span></span>
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1005
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<td class="diff-line-num new_line old" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1005" class="line" lang="c"><span class="idiff left right"> </span></span>
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<td class="diff-line-num old old_line" data-linenumber="1006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1006
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<td class="diff-line-num new_line old" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1006" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">hitMap</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">considerOnlyIfPreviouslyObserved</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1007" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitMap</span><span class="p">.</span><span class="n" style="color: #333;">expand</span><span class="p">();</span></span>
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1008
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<pre style="margin: 0;">-<span id="LC1008" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">HitCount</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">index_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">hitCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hitMap</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">();</span></span>
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1009
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<pre style="margin: 0;">-<span id="LC1009" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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1010
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<pre style="margin: 0;">-<span id="LC1010" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">uniqueID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uniqueID</span><span class="p">;</span></span>
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1011
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<pre style="margin: 0;">-<span id="LC1011" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1012
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<pre style="margin: 0;">-<span id="LC1012" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">scores</span><span class="p">[</span><span class="n" style="color: #333;">rdi</span><span class="p">][</span><span class="n" style="color: #333;">fwi</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">partialHitScore</span><span class="p">;</span></span>
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1013
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<pre style="margin: 0;">-<span id="LC1013" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">summedHitLens</span><span class="p">[</span><span class="n" style="color: #333;">rdi</span><span class="p">][</span><span class="n" style="color: #333;">fwi</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">weightedHitLen</span><span class="p">;</span></span>
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1014
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<pre style="margin: 0;">-<span id="LC1014" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">timeStamp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">hi</span><span class="p">;</span></span>
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1015
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<pre style="margin: 0;">-<span id="LC1015" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">readPositions</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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1016
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<pre style="margin: 0;">-<span id="LC1016" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">readPositions</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">));</span></span>
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1017
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<pre style="margin: 0;">-<span id="LC1017" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_tempPath</span><span class="p">;</span></span>
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1018
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<pre style="margin: 0;">-<span id="LC1018" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">rank</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rank</span><span class="p">;</span></span>
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1019
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<pre style="margin: 0;">-<span id="LC1019" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">taxID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">taxID</span><span class="p">;</span></span>
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1020
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<pre style="margin: 0;">-<span id="LC1020" class="line" lang="c"><span class="idiff left right"> </span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TaxonomyPathTable</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pathTable</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ebwt</span><span class="p">.</span><span class="n" style="color: #333;">paths</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
987
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">pathTable</span><span class="p">.</span><span class="n" style="color: #333;">getPath</span><span class="p">(</span><span class="n" style="color: #333;">taxID</span><span class="p">,</span> <span class="n" style="color: #333;">_tempPath</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="c"><span class="idiff left right"> </span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">rank</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_classification_rank</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rank</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">for</span><span class="p">(;</span> <span class="n" style="color: #333;">rank</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">_tempPath</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">rank</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
991
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_tempPath</span><span class="p">[</span><span class="n" style="color: #333;">rank</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
992
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">taxID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_tempPath</span><span class="p">[</span><span class="n" style="color: #333;">rank</span><span class="p">];</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
993
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
994
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="c"><span class="idiff left right"> </span> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
995
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="c"><span class="idiff left right"> </span> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
996
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="c"><span class="idiff left right"> </span> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="c"></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
998
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<pre style="margin: 0;">+<span id="LC998" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">for</span><span class="p">(;</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hitMap</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">idx</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
999
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">same</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1000
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rank</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">same</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">uniqueID</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">hitMap</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">].</span><span class="n" style="color: #333;">uniqueID</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="c"><span class="idiff left right"> </span> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">same</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">taxID</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">hitMap</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">].</span><span class="n" style="color: #333;">taxID</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="c"><span class="idiff left right"> </span> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">same</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">hitMap</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">].</span><span class="n" style="color: #333;">timeStamp</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">hi</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitMap</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">].</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitMap</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">].</span><span class="n" style="color: #333;">scores</span><span class="p">[</span><span class="n" style="color: #333;">rdi</span><span class="p">][</span><span class="n" style="color: #333;">fwi</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">partialHitScore</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitMap</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">].</span><span class="n" style="color: #333;">summedHitLens</span><span class="p">[</span><span class="n" style="color: #333;">rdi</span><span class="p">][</span><span class="n" style="color: #333;">fwi</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">weightedHitLen</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitMap</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">].</span><span class="n" style="color: #333;">timeStamp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">hi</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitMap</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">].</span><span class="n" style="color: #333;">readPositions</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="c"><span class="idiff left right"> </span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="c"><span class="idiff left right"> </span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1015
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="c"><span class="idiff left right"> </span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1016
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="c"></span>
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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">hitMap</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">considerOnlyIfPreviouslyObserved</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitMap</span><span class="p">.</span><span class="n" style="color: #333;">expand</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">HitCount</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">index_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">hitCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hitMap</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1021
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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">uniqueID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uniqueID</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">scores</span><span class="p">[</span><span class="n" style="color: #333;">rdi</span><span class="p">][</span><span class="n" style="color: #333;">fwi</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">partialHitScore</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">summedHitLens</span><span class="p">[</span><span class="n" style="color: #333;">rdi</span><span class="p">][</span><span class="n" style="color: #333;">fwi</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">weightedHitLen</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">timeStamp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">hi</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">readPositions</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">readPositions</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1028
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<pre style="margin: 0;">+<span id="LC1028" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_tempPath</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1029
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<pre style="margin: 0;">+<span id="LC1029" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">rank</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rank</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1030
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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="c"><span class="idiff left right"> </span> <span class="n" style="color: #333;">hitCount</span><span class="p">.</span><span class="n" style="color: #333;">taxID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">taxID</span><span class="p">;</span></span>
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1031
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="c"><span class="idiff left right"> </span> <span class="p">}</span></span>
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1021
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1032
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<pre style="margin: 0;"> <span id="LC1032" class="line" lang="c"></span>
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1022
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<td class="diff-line-num new_line old" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1022" class="line" lang="c"><span class="idiff left right"> </span> <span class="c1" style="color: #998; font-style: italic;">//if considerOnlyIfPreviouslyObserved and it was not found, genus Idx size is equal to the genus Map size</span></span>
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1023
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<pre style="margin: 0;">-<span id="LC1023" class="line" lang="c"><span class="idiff left right"> </span> <span class="c1" style="color: #998; font-style: italic;">//assert_lt(genusIdx, genusMap.size());</span></span>
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1024
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<pre style="margin: 0;">-<span id="LC1024" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">idx</span><span class="p">;</span></span>
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1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="c"><span class="idiff left right"> </span> <span class="c1" style="color: #998; font-style: italic;">//if considerOnlyIfPreviouslyObserved and it was not found, genus Idx size is equal to the genus Map size</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1034
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="c"><span class="idiff left right"> </span> <span class="c1" style="color: #998; font-style: italic;">//assert_lt(genusIdx, genusMap.size());</span></span>
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1035
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="c"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">idx</span><span class="p">;</span></span>
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1025
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1036
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<pre style="margin: 0;"> <span id="LC1036" class="line" lang="c"> <span class="p">}</span></span>
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1026
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1037
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<pre style="margin: 0;"> <span id="LC1037" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="1038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1038
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">reportUnclassified</span><span class="p">(</span> <span class="n" style="color: #333;">AlnSinkWrap</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">index_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">sink</span> <span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="c"> <span class="n" style="color: #333;">AlnRes</span> <span class="n" style="color: #333;">rs</span> <span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="c"> <span class="n" style="color: #333;">EList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">dummy</span> <span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="c"> <span class="n" style="color: #333;">dummy</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="p">)</span> <span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="c"> <span class="n" style="color: #333;">rs</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">(</span> <span class="s" style="color: #d14;">"unclassified"</span> <span class="p">),</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">dummy</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span> <span class="p">)</span> <span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="c"> <span class="n" style="color: #333;">sink</span><span class="p">.</span><span class="n" style="color: #333;">report</span><span class="p">(</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">rs</span> <span class="p">)</span> <span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="c"> <span class="p">}</span></span>
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1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="c"></span>
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1047
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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="c"></span>
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1027
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1049
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<pre style="margin: 0;"> <span id="LC1049" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// compare BWTHits by size, ascending, first, then by length, descending</span></span>
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<pre style="margin: 0;"> <span id="LC1050" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// TODO: move this operator into BWTHits if that is the standard way we would like to sort</span></span>
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<pre style="margin: 0;"> <span id="LC1051" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// TODO: this ordering does not necessarily give the best results</span></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="html"><span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"TOC"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="html"><span class="nt" style="color: navy;"><ul></span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#introduction"</span><span class="nt" style="color: navy;">></span>Introduction<span class="nt" style="color: navy;"></a><ul></span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#what-is-centrifuge"</span><span class="nt" style="color: navy;">></span>What is Centrifuge?<span class="nt" style="color: navy;"></a></li></span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="html"><span class="nt" style="color: navy;"></ul></li></span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#obtaining-centrifuge"</span><span class="nt" style="color: navy;">></span>Obtaining Centrifuge<span class="nt" style="color: navy;"></a><ul></span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#building-from-source"</span><span class="nt" style="color: navy;">></span>Building from source<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="html"><span class="nt" style="color: navy;"></ul></li></span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#running-centrifuge"</span><span class="nt" style="color: navy;">></span>Running Centrifuge<span class="nt" style="color: navy;"></a><ul></span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#adding-to-path"</span><span class="nt" style="color: navy;">></span>Adding to PATH<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#before-running-centrifuge"</span><span class="nt" style="color: navy;">></span>Before running Centrifuge<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#database-download-and-index-building"</span><span class="nt" style="color: navy;">></span>Database download and index building<span class="nt" style="color: navy;"></a><ul></span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#building-index-on-all-complete-bacterial-and-viral-genomes"</span><span class="nt" style="color: navy;">></span>Building index on all complete bacterial and viral genomes<span class="nt" style="color: navy;"></a></li></span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#adding-human-or-mouse-genome-to-the-index"</span><span class="nt" style="color: navy;">></span>Adding human or mouse genome to the index<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#nt-database"</span><span class="nt" style="color: navy;">></span>nt database<span class="nt" style="color: navy;"></a></li></span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-classification-output"</span><span class="nt" style="color: navy;">></span>Centrifuge classification output<span class="nt" style="color: navy;"></a></li></span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-summary-output-the-default-filename-is-centrifuge_report.tsv"</span><span class="nt" style="color: navy;">></span>Centrifuge summary output (the default filename is centrifuge_report.tsv)<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#kraken-style-report"</span><span class="nt" style="color: navy;">></span>Kraken-style report<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="html"><span class="nt" style="color: navy;"></ul></li></span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#inspecting-the-centrifuge-index"</span><span class="nt" style="color: navy;">></span>Inspecting the Centrifuge index<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#wrapper"</span><span class="nt" style="color: navy;">></span>Wrapper<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#performance-tuning"</span><span class="nt" style="color: navy;">></span>Performance tuning<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#command-line"</span><span class="nt" style="color: navy;">></span>Command Line<span class="nt" style="color: navy;"></a><ul></span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#usage"</span><span class="nt" style="color: navy;">></span>Usage<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#main-arguments"</span><span class="nt" style="color: navy;">></span>Main arguments<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#options"</span><span class="nt" style="color: navy;">></span>Options<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="html"><span class="nt" style="color: navy;"></ul></li></span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="html"><span class="nt" style="color: navy;"></ul></li></span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#the-centrifuge-build-indexer"</span><span class="nt" style="color: navy;">></span>The <span class="nt" style="color: navy;"><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span> indexer<span class="nt" style="color: navy;"></a><ul></span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#command-line-1"</span><span class="nt" style="color: navy;">></span>Command Line<span class="nt" style="color: navy;"></a><ul></span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#main-arguments-1"</span><span class="nt" style="color: navy;">></span>Main arguments<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#options-1"</span><span class="nt" style="color: navy;">></span>Options<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="html"><span class="nt" style="color: navy;"></ul></li></span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="html"><span class="nt" style="color: navy;"></ul></li></span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#the-centrifuge-inspect-index-inspector"</span><span class="nt" style="color: navy;">></span>The <span class="nt" style="color: navy;"><code></span>centrifuge-inspect<span class="nt" style="color: navy;"></code></span> index inspector<span class="nt" style="color: navy;"></a><ul></span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#command-line-2"</span><span class="nt" style="color: navy;">></span>Command Line<span class="nt" style="color: navy;"></a><ul></span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#main-arguments-2"</span><span class="nt" style="color: navy;">></span>Main arguments<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#options-2"</span><span class="nt" style="color: navy;">></span>Options<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="html"><span class="nt" style="color: navy;"></ul></li></span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#getting-started-with-centrifuge"</span><span class="nt" style="color: navy;">></span>Getting started with Centrifuge<span class="nt" style="color: navy;"></a><ul></span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#indexing-a-reference-genome"</span><span class="nt" style="color: navy;">></span>Indexing a reference genome<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"><!--</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> ! This manual is written in "markdown" format and thus contains some</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> ! distracting formatting clutter. See 'MANUAL' for an easier-to-read version</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> ! of this text document, or see the HTML manual online.</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> ! --></span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="html"><span class="nt" style="color: navy;"><h1</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"introduction"</span><span class="nt" style="color: navy;">></span>Introduction<span class="nt" style="color: navy;"></h1></span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"what-is-centrifuge"</span><span class="nt" style="color: navy;">></span>What is Centrifuge?<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="html"><span class="nt" style="color: navy;"><p><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://www.ccb.jhu.edu/software/centrifuge"</span><span class="nt" style="color: navy;">></span>Centrifuge<span class="nt" style="color: navy;"></a></span> is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (5.8 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at a very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="html"><span class="nt" style="color: navy;"><h1</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"obtaining-centrifuge"</span><span class="nt" style="color: navy;">></span>Obtaining Centrifuge<span class="nt" style="color: navy;"></h1></span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Download Centrifuge and binaries from the Releases sections on the right side. Binaries are available for Intel architectures (<span class="nt" style="color: navy;"><code></span>x86_64<span class="nt" style="color: navy;"></code></span>) running Linux, and Mac OS X.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"building-from-source"</span><span class="nt" style="color: navy;">></span>Building from source<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Building Centrifuge from source requires a GNU-like environment with GCC, GNU Make and other basics. It should be possible to build Centrifuge on most vanilla Linux installations or on a Mac installation with <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://developer.apple.com/xcode/"</span><span class="nt" style="color: navy;">></span>Xcode<span class="nt" style="color: navy;"></a></span> installed. Centrifuge can also be built on Windows using <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://www.cygwin.com/"</span><span class="nt" style="color: navy;">></span>Cygwin<span class="nt" style="color: navy;"></a></span> or <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://www.mingw.org/"</span><span class="nt" style="color: navy;">></span>MinGW<span class="nt" style="color: navy;"></a></span> (MinGW recommended). For a MinGW build the choice of what compiler is to be used is important since this will determine if a 32 or 64 bit code can be successfully compiled using it. If there is a need to generate both 32 and 64 bit on the same machine then a multilib MinGW has to be properly installed. <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://www.mingw.org/wiki/msys"</span><span class="nt" style="color: navy;">></span>MSYS<span class="nt" style="color: navy;"></a></span>, the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://cygwin.com/packages/mingw-zlib/"</span><span class="nt" style="color: navy;">></span>zlib<span class="nt" style="color: navy;"></a></span> library, and depending on architecture <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://sourceware.org/pthreads-win32/"</span><span class="nt" style="color: navy;">></span>pthreads<span class="nt" style="color: navy;"></a></span> library are also required. We are recommending a 64 bit build since it has some clear advantages in real life research problems. In order to simplify the MinGW setup it might be worth investigating popular MinGW personal builds since these are coming already prepared with most of the toolchains needed.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>First, download the [source package] from the Releases secion on the right side. Unzip the file, change to the unzipped directory, and build the Centrifuge tools by running GNU <span class="nt" style="color: navy;"><code></span>make<span class="nt" style="color: navy;"></code></span> (usually with the command <span class="nt" style="color: navy;"><code></span>make<span class="nt" style="color: navy;"></code></span>, but sometimes with <span class="nt" style="color: navy;"><code></span>gmake<span class="nt" style="color: navy;"></code></span>) with no arguments. If building with MinGW, run <span class="nt" style="color: navy;"><code></span>make<span class="nt" style="color: navy;"></code></span> from the MSYS environment.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Centrifuge is using the multithreading software model in order to speed up execution times on SMP architectures where this is possible. On POSIX platforms (like linux, Mac OS, etc) it needs the pthread library. Although it is possible to use pthread library on non-POSIX platform like Windows, due to performance reasons Centrifuge will try to use Windows native multithreading if possible.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>For the support of SRA data access in HISAT2, please download and install the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"https://github.com/ncbi/ngs/wiki/Downloads"</span><span class="nt" style="color: navy;">></span>NCBI-NGS<span class="nt" style="color: navy;"></a></span> toolkit. When running <span class="nt" style="color: navy;"><code></span>make<span class="nt" style="color: navy;"></code></span>, specify additional variables as follow. <span class="nt" style="color: navy;"><code></span>make USE_SRA=1 NCBI_NGS_DIR=/path/to/NCBI-NGS-directory NCBI_VDB_DIR=/path/to/NCBI-NGS-directory<span class="nt" style="color: navy;"></code></span>, where <span class="nt" style="color: navy;"><code></span>NCBI_NGS_DIR<span class="nt" style="color: navy;"></code></span> and <span class="nt" style="color: navy;"><code></span>NCBI_VDB_DIR<span class="nt" style="color: navy;"></code></span> will be used in Makefile for -I and -L compilation options. For example, $(NCBI_NGS_DIR)/include and $(NCBI_NGS_DIR)/lib64 will be used.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="html"><span class="nt" style="color: navy;"><h1</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"running-centrifuge"</span><span class="nt" style="color: navy;">></span>Running Centrifuge<span class="nt" style="color: navy;"></h1></span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"adding-to-path"</span><span class="nt" style="color: navy;">></span>Adding to PATH<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>By adding your new Centrifuge directory to your <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/PATH_(variable)"</span><span class="nt" style="color: navy;">></span>PATH environment variable<span class="nt" style="color: navy;"></a></span>, you ensure that whenever you run <span class="nt" style="color: navy;"><code></span>centrifuge<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>centrifuge-download<span class="nt" style="color: navy;"></code></span> or <span class="nt" style="color: navy;"><code></span>centrifuge-inspect<span class="nt" style="color: navy;"></code></span> from the command line, you will get the version you just installed without having to specify the entire path. This is recommended for most users. To do this, follow your operating system's instructions for adding the directory to your <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/PATH_(variable)"</span><span class="nt" style="color: navy;">></span>PATH<span class="nt" style="color: navy;"></a></span>.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>If you would like to install Centrifuge by copying the Centrifuge executable files to an existing directory in your <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/PATH_(variable)"</span><span class="nt" style="color: navy;">></span>PATH<span class="nt" style="color: navy;"></a></span>, make sure that you copy all the executables, including <span class="nt" style="color: navy;"><code></span>centrifuge<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>centrifuge-class<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>centrifuge-build-bin<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>centrifuge-download<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><code></span>centrifuge-inspect<span class="nt" style="color: navy;"></code></span> and <span class="nt" style="color: navy;"><code></span>centrifuge-inspect-bin<span class="nt" style="color: navy;"></code></span>. Furthermore you need the programs in the scripts/ folder if you opt for genome compression in the database construction.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"before-running-centrifuge"</span><span class="nt" style="color: navy;">></span>Before running Centrifuge<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Classification is considerably different from alignment in that classification is performed on a large set of genomes as opposed to on just one reference genome as in alignment. Currently, an enormous number of complete genomes are available at the GenBank (e.g. <span class="ni" style="color: purple;">></span>4,000 bacterial genomes, <span class="ni" style="color: purple;">></span>10,000 viral genomes, …). These genomes are organized in a taxonomic tree where each genome is located at the bottom of the tree, at the strain or subspecies level. On the taxonomic tree, genomes have ancestors usually situated at the species level, and those ancestors also have ancestors at the genus level and so on up the family level, the order level, class level, phylum, kingdom, and finally at the root level.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Given the gigantic number of genomes available, which continues to expand at a rapid rate, and the development of the taxonomic tree, which continues to evolve with new advancements in research, we have designed Centrifuge to be flexible and general enough to reflect this huge database. We provide several standard indexes that will meet most of users’ needs (see the side panel - Indexes). In our approach our indexes not only include raw genome sequences, but also genome names/sizes and taxonomic trees. This enables users to perform additional analyses on Centrifuge’s classification output without the need to download extra database sources. This also eliminates the potential issue of discrepancy between the indexes we provide and the databases users may otherwise download. We plan to provide a couple of additional standard indexes in the near future, and update the indexes on a regular basis.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>We encourage first time users to take a look at and follow a <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-example"</span><span class="nt" style="color: navy;">><code></span>small example<span class="nt" style="color: navy;"></code></a></span> that illustrates how to build an index, how to run Centrifuge using the index, how to interpret the classification results, and how to extract additional genomic information from the index. For those who choose to build customized indexes, please take a close look at the following description.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"database-download-and-index-building"</span><span class="nt" style="color: navy;">></span>Database download and index building<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Centrifuge indexes can be built with arbritary sequences. Standard choices are all of the complete bacterial and viral genomes, or using the sequences that are part of the BLAST nt database. Centrifuge always needs the nodes.dmp file from the NCBI taxonomy dump to build the taxonomy tree, as well as a sequence ID to taxonomy ID map. The map is a tab-separated file with the sequence ID to taxonomy ID map.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>To download all of the complete archaeal, viral, and bacterial genomes from RefSeq, and build the index:<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Centrifuge indices can be build on arbritary sequences. Usually an ensemble of genomes is used - such as all complete microbial genomes in the RefSeq database, or all sequences in the BLAST nt database.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>To map sequence identifiers to taxonomy IDs, and taxonomy IDs to names and its parents, three files are necessary in addition to the sequence files:<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="html"><span class="nt" style="color: navy;"><ul></span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="html"><span class="nt" style="color: navy;"><li></span>taxonomy tree: typically nodes.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their parents<span class="nt" style="color: navy;"></li></span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="html"><span class="nt" style="color: navy;"><li></span>names file: typically names.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their scientific name<span class="nt" style="color: navy;"></li></span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="html"><span class="nt" style="color: navy;"><li></span>a tab-separated sequence ID to taxonomy ID mapping<span class="nt" style="color: navy;"></li></span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="html"><span class="nt" style="color: navy;"></ul></span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>When using the provided scripts to download the genomes, these files are automatically downloaded or generated. When using a custom taxonomy or sequence files, please refer to the section <span class="nt" style="color: navy;"><code></span>TODO<span class="nt" style="color: navy;"></code></span> to learn more about their format.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="html"><span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"building-index-on-all-complete-bacterial-and-viral-genomes"</span><span class="nt" style="color: navy;">></span>Building index on all complete bacterial and viral genomes<span class="nt" style="color: navy;"></h3></span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Use <span class="nt" style="color: navy;"><code></span>centrifuge-download<span class="nt" style="color: navy;"></code></span> to download genomes from NCBI. The following two commands download the NCBI taxonomy to <span class="nt" style="color: navy;"><code></span>taxonomy/<span class="nt" style="color: navy;"></code></span> in the current directory, and all complete archaeal, bacterial and viral genomes to <span class="nt" style="color: navy;"><code></span>library/<span class="nt" style="color: navy;"></code></span>. Low-complexity regions in the genomes are masked after download (parameter <span class="nt" style="color: navy;"><code></span>-m<span class="nt" style="color: navy;"></code></span>) using blast+'s <span class="nt" style="color: navy;"><code></span>dustmasker<span class="nt" style="color: navy;"></code></span>. <span class="nt" style="color: navy;"><code></span>centrifuge-download<span class="nt" style="color: navy;"></code></span> outputs tab-separated sequence ID to taxonomy ID mappings to standard out, which are required by <span class="nt" style="color: navy;"><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span>.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>centrifuge-download -o taxonomy taxonomy</span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="html">centrifuge-download -o library -m -d <span class="ni" style="color: purple;">"</span>archaea,bacteria,viral<span class="ni" style="color: purple;">"</span> refseq <span class="ni" style="color: purple;">></span> seqid2taxid.map<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>To build the index, first concatenate all downloaded sequences into a single file, and then run <span class="nt" style="color: navy;"><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span>:<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>cat library/*/*.fna <span class="ni" style="color: purple;">></span> input-sequences.fna</span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="html">## build centrifuge index with 4 threads</span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="html">centrifuge-build -p 4 --conversion-table seqid2taxid.map \</span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="html"> --taxonomy-tree taxonomy/nodes.dmp --name-table taxonomy/names.dmp \</span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="html"> input-sequences.fna abv<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>After building the index, all files except the index *.[123].cf files may be removed. If you also want to include the human and/or the mouse genome, add their sequences to the library folder before building the index with one of the following commands:<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>After the index building, all but the *.[123].cf index files may be removed. I.e. the files in the <span class="nt" style="color: navy;"><code></span>library/<span class="nt" style="color: navy;"></code></span> and <span class="nt" style="color: navy;"><code></span>taxonomy/<span class="nt" style="color: navy;"></code></span> directories are no longer needed.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="html"><span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"adding-human-or-mouse-genome-to-the-index"</span><span class="nt" style="color: navy;">></span>Adding human or mouse genome to the index<span class="nt" style="color: navy;"></h3></span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The human and mouse genomes can also be downloaded using <span class="nt" style="color: navy;"><code></span>centrifuge-download<span class="nt" style="color: navy;"></code></span>. They are in the domain <span class="ni" style="color: purple;">"</span>vertebrate_mammalian<span class="ni" style="color: purple;">"</span> (argument <span class="nt" style="color: navy;"><code></span>-d<span class="nt" style="color: navy;"></code></span>), are assembled at the chromosome level (argument <span class="nt" style="color: navy;"><code></span>-a<span class="nt" style="color: navy;"></code></span>) and categorized as reference genomes by RefSeq (<span class="nt" style="color: navy;"><code></span>-c<span class="nt" style="color: navy;"></code></span>). The argument <span class="nt" style="color: navy;"><code></span>-t<span class="nt" style="color: navy;"></code></span> takes a comma-separated list of taxonomy IDs - e.g. <span class="nt" style="color: navy;"><code></span>9606<span class="nt" style="color: navy;"></code></span> for human and <span class="nt" style="color: navy;"><code></span>10090<span class="nt" style="color: navy;"></code></span> for mouse:<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span># download mouse and human reference genomes</span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="html">centrifuge-download -o library -d <span class="ni" style="color: purple;">"</span>vertebrate_mammalian<span class="ni" style="color: purple;">"</span> -a <span class="ni" style="color: purple;">"</span>Chromosome<span class="ni" style="color: purple;">"</span> -t 9606,10090 -c <span class="ni" style="color: purple;">'</span>reference genome<span class="ni" style="color: purple;">'</span> <span class="ni" style="color: purple;">>></span> seqid2taxid.map</span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="html"># only human</span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="html">centrifuge-download -o library -d <span class="ni" style="color: purple;">"</span>vertebrate_mammalian<span class="ni" style="color: purple;">"</span> -a <span class="ni" style="color: purple;">"</span>Chromosome<span class="ni" style="color: purple;">"</span> -t 9606 -c <span class="ni" style="color: purple;">'</span>reference genome<span class="ni" style="color: purple;">'</span> <span class="ni" style="color: purple;">>></span> seqid2taxid.map</span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="html"># only mouse</span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="html">centrifuge-download -o library -d <span class="ni" style="color: purple;">"</span>vertebrate_mammalian<span class="ni" style="color: purple;">"</span> -a <span class="ni" style="color: purple;">"</span>Chromosome<span class="ni" style="color: purple;">"</span> -t 10090 -c <span class="ni" style="color: purple;">'</span>reference genome<span class="ni" style="color: purple;">'</span> <span class="ni" style="color: purple;">>></span> seqid2taxid.map<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="html"><span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"nt-database"</span><span class="nt" style="color: navy;">></span>nt database<span class="nt" style="color: navy;"></h3></span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>NCBI BLAST's nt database contains all spliced non-redundant coding sequences from multiplpe databases, inferred from genommic sequences. Traditionally used with BLAST, a download of the FASTA is provided on the NCBI homepage. Building an index with any database requires the user to creates a sequence ID to taxonomy ID map that can be generated from a GI taxid dump:<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>wget ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nt.gz</span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="html">gunzip nt.gz <span class="ni" style="color: purple;">&&</span> mv -v nt nt.fa</span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="html"># Get mapping file</span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="html">wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz</span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="html">gunzip -c gi_taxid_nucl.dmp.gz | sed <span class="ni" style="color: purple;">'</span>s/^/gi|/<span class="ni" style="color: purple;">'</span> <span class="ni" style="color: purple;">></span> gi_taxid_nucl.map</span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="html"># build index using 16 cores and a small bucket size, which will require less memory</span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="html">centrifuge-build -p 16 --bmax 1342177280 --conversion-table gi_taxid_nucl.map \</span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="html"> --taxonomy-tree taxonomy/nodes.dmp --name-table taxonomy/names.dmp \ </span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="html"> nt.fa nt<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="html"><span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"custom-database"</span><span class="nt" style="color: navy;">></span>Custom database<span class="nt" style="color: navy;"></h3></span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>TODO: Add toy example for nodes.dmp, names.dmp and seqid2taxid.map<span class="nt" style="color: navy;"></p></span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="html"><span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-classification-output"</span><span class="nt" style="color: navy;">></span>Centrifuge classification output<span class="nt" style="color: navy;"></h3></span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The following example shows classification assignments for a read. The assignment output has 8 columns.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>readID seqID taxID score 2ndBestScore hitLength queryLength numMatches</span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="html">1_1 gi|4 9646 4225 0 80 80 1</span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="html">The first column is the read ID from a raw sequencing read (e.g., 1_1 in the example).</span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="html">The second column is the sequence ID of the genomic sequence, where the read is classified (e.g., gi|4).</span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="html">The third column is the taxonomic ID of the genomic sequence in the second column (e.g., 9646).</span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="html">The fourth column is the score for the classification, which is the weighted sum of hits (e.g., 4225)</span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="html">The fifth column is the score for the next best classification (e.g., 0).</span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="html">The sixth column is a pair of two numbers: (1) an approximate number of base pairs of the read that match the genomic sequence and (2) the length of a read or the combined length of mate pairs (e.g., 80 / 80).</span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="html">The seventh column is a pair of two numbers: (1) an approximate number of base pairs of the read that match the genomic sequence and (2) the length of a read or the combined length of mate pairs (e.g., 80 / 80). </span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="html">The eighth column is the number of classifications for this read, indicating how many assignments were made (e.g.,1).<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="html"><span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-summary-output-the-default-filename-is-centrifuge_report.tsv"</span><span class="nt" style="color: navy;">></span>Centrifuge summary output (the default filename is centrifuge_report.tsv)<span class="nt" style="color: navy;"></h3></span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The following example shows a classification summary for each genome or taxonomic unit. The assignment output has 7 columns.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>name taxID taxRank genomeSize numReads numUniqueReads abundance</span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="html">Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis 36870 leaf 703004 5981 5964 0.0152317</span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="html">The first column is the name of a genome, or the name corresponding to a taxonomic ID (the second column) at a rank higher than the strain (e.g., Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis).</span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="html">The second column is the taxonomic ID (e.g., 36870).</span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="html">The third column is the taxonomic rank (e.g., leaf).</span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="html">The fourth column is the length of the genome sequence (e.g., 703004).</span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="html">The fifth column is the number of reads classified to this genomic sequence including multi-classified reads (e.g., 5981).</span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="html">The sixth column is the number of reads uniquely classified to this genomic sequence (e.g., 5964).</span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="html">The seventh column is the proportion of this genome normalized by its genomic length (e.g., 0.0152317).<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>As the GenBank database is incomplete (i.e., many more genomes remain to be identified and added), and reads have sequencing errors, classification programs including Centrifuge often report many false assignments. In order to perform more conservative analyses, users may want to discard assignments for reads having a matching length (8th column in the output of Centrifuge) of 40% or lower. It may be also helpful to use a score (4th column) for filtering out some assignments. Our future research plans include working on developing methods that estimate confidence scores for assignments.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="html"><span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"kraken-style-report"</span><span class="nt" style="color: navy;">></span>Kraken-style report<span class="nt" style="color: navy;"></h3></span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="html"><span class="nt" style="color: navy;"><p><code></span>centrifuge-kreport<span class="nt" style="color: navy;"></code></span> can be used to make a Kraken-style report from the Centrifuge output including taxonomy information:<span class="nt" style="color: navy;"></p></span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="html"><span class="nt" style="color: navy;"><p><code></span>centrifuge-kreport -x <span class="ni" style="color: purple;"><</span>centrifuge index<span class="ni" style="color: purple;">></span> <span class="ni" style="color: purple;"><</span>centrifuge out file<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></p></span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"inspecting-the-centrifuge-index"</span><span class="nt" style="color: navy;">></span>Inspecting the Centrifuge index<span class="nt" style="color: navy;"></h2></span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The index can be inspected with <span class="nt" style="color: navy;"><code></span>centrifuge-inspect<span class="nt" style="color: navy;"></code></span>. To extract raw sequences:<span class="nt" style="color: navy;"></p></span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>centrifuge-inspect <span class="ni" style="color: purple;"><</span>centrifuge index<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Extract the sequence ID to taxonomy ID conversion table from the index<span class="nt" style="color: navy;"></p></span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>centrifuge-inspect --conversion-table <span class="ni" style="color: purple;"><</span>centrifuge index<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Extract the taxonomy tree from the index:<span class="nt" style="color: navy;"></p></span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>centrifuge-inspect --taxonomy-tree <span class="ni" style="color: purple;"><</span>centrifuge index<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Extract the lengths of the sequences from the index (each row has two columns: taxonomic ID and length):<span class="nt" style="color: navy;"></p></span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>centrifuge-inspect --size-table <span class="ni" style="color: purple;"><</span>centrifuge index<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Extract the names from the index (each row has two columns: taxonomic ID and name):<span class="nt" style="color: navy;"></p></span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>centrifuge-inspect --name-table <span class="ni" style="color: purple;"><</span>centrifuge index<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"wrapper"</span><span class="nt" style="color: navy;">></span>Wrapper<span class="nt" style="color: navy;"></h2></span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The <span class="nt" style="color: navy;"><code></span>centrifuge<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span> and <span class="nt" style="color: navy;"><code></span>centrifuge-inspect<span class="nt" style="color: navy;"></code></span> executables are actually wrapper scripts that call binary programs as appropriate. Also, the <span class="nt" style="color: navy;"><code></span>centrifuge<span class="nt" style="color: navy;"></code></span> wrapper provides some key functionality, like the ability to handle compressed inputs, and the functionality for [<span class="nt" style="color: navy;"><code></span>--un<span class="nt" style="color: navy;"></code></span>], [<span class="nt" style="color: navy;"><code></span>--al<span class="nt" style="color: navy;"></code></span>] and related options.<span class="nt" style="color: navy;"></p></span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>It is recommended that you always run the centrifuge wrappers and not run the binaries directly.<span class="nt" style="color: navy;"></p></span></span>
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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"performance-tuning"</span><span class="nt" style="color: navy;">></span>Performance tuning<span class="nt" style="color: navy;"></h2></span></span>
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<td class="diff-line-num old old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="html"><span class="nt" style="color: navy;"><ol</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">"list-style-type: decimal"</span><span class="nt" style="color: navy;">></span></span>
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<td class="diff-line-num old old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="html"><span class="nt" style="color: navy;"><li><p></span>If your computer has multiple processors/cores, use <span class="nt" style="color: navy;"><code></span>-p NTHREADS<span class="nt" style="color: navy;"></code></p></span></span>
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<td class="diff-line-num old old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-p"</span><span class="nt" style="color: navy;">><code></span>-p<span class="nt" style="color: navy;"></code></a></span> option causes Centrifuge to launch a specified number of parallel search threads. Each thread runs on a different processor/core and all threads find alignments in parallel, increasing alignment throughput by approximately a multiple of the number of threads (though in practice, speedup is somewhat worse than linear).<span class="nt" style="color: navy;"></p></li></span></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="html"><span class="nt" style="color: navy;"></ol></span></span>
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"command-line"</span><span class="nt" style="color: navy;">></span>Command Line<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="html"><span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"usage"</span><span class="nt" style="color: navy;">></span>Usage<span class="nt" style="color: navy;"></h3></span></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>centrifuge [options]* -x <span class="ni" style="color: purple;"><</span>centrifuge-idx<span class="ni" style="color: purple;">></span> {-1 <span class="ni" style="color: purple;"><</span>m1<span class="ni" style="color: purple;">></span> -2 <span class="ni" style="color: purple;"><</span>m2<span class="ni" style="color: purple;">></span> | -U <span class="ni" style="color: purple;"><</span>r<span class="ni" style="color: purple;">></span> | --sra-acc <span class="ni" style="color: purple;"><</span>SRA accession number<span class="ni" style="color: purple;">></span>} [--report-file <span class="ni" style="color: purple;"><</span>report file name<span class="ni" style="color: purple;">></span> -S <span class="ni" style="color: purple;"><</span>classification output file name<span class="ni" style="color: purple;">></span>]<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="html"><span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"main-arguments"</span><span class="nt" style="color: navy;">></span>Main arguments<span class="nt" style="color: navy;"></h3></span></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="html"><span class="nt" style="color: navy;"><table><tr><td></span></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-x <span class="ni" style="color: purple;"><</span>centrifuge-idx<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The basename of the index for the reference genomes. The basename is the name of any of the index files up to but not including the final <span class="nt" style="color: navy;"><code></span>.1.cf<span class="nt" style="color: navy;"></code></span> / etc.<span class="nt" style="color: navy;"><br</span> <span class="nt" style="color: navy;">/><code></span>centrifuge<span class="nt" style="color: navy;"></code></span> looks for the specified index first in the current directory, then in the directory specified in the <span class="nt" style="color: navy;"><code></span>CENTRIFUGE_INDEXES<span class="nt" style="color: navy;"></code></span> environment variable.<span class="nt" style="color: navy;"></p></span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-1 <span class="ni" style="color: purple;"><</span>m1<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Comma-separated list of files containing mate 1s (filename usually includes <span class="nt" style="color: navy;"><code></span>_1<span class="nt" style="color: navy;"></code></span>), e.g. <span class="nt" style="color: navy;"><code></span>-1 flyA_1.fq,flyB_1.fq<span class="nt" style="color: navy;"></code></span>. Sequences specified with this option must correspond file-for-file and read-for-read with those specified in <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>m2<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>. Reads may be a mix of different lengths. If <span class="nt" style="color: navy;"><code></span>-<span class="nt" style="color: navy;"></code></span> is specified, <span class="nt" style="color: navy;"><code></span>centrifuge<span class="nt" style="color: navy;"></code></span> will read the mate 1s from the <span class="ni" style="color: purple;">"</span>standard in<span class="ni" style="color: purple;">"</span> or <span class="ni" style="color: purple;">"</span>stdin<span class="ni" style="color: purple;">"</span> filehandle.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-2 <span class="ni" style="color: purple;"><</span>m2<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Comma-separated list of files containing mate 2s (filename usually includes <span class="nt" style="color: navy;"><code></span>_2<span class="nt" style="color: navy;"></code></span>), e.g. <span class="nt" style="color: navy;"><code></span>-2 flyA_2.fq,flyB_2.fq<span class="nt" style="color: navy;"></code></span>. Sequences specified with this option must correspond file-for-file and read-for-read with those specified in <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>m1<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>. Reads may be a mix of different lengths. If <span class="nt" style="color: navy;"><code></span>-<span class="nt" style="color: navy;"></code></span> is specified, <span class="nt" style="color: navy;"><code></span>centrifuge<span class="nt" style="color: navy;"></code></span> will read the mate 2s from the <span class="ni" style="color: purple;">"</span>standard in<span class="ni" style="color: purple;">"</span> or <span class="ni" style="color: purple;">"</span>stdin<span class="ni" style="color: purple;">"</span> filehandle.<span class="nt" style="color: navy;"></p></span></span>
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189
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="html"></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-U <span class="ni" style="color: purple;"><</span>r<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="html"></span>
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<td class="diff-line-num old old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Comma-separated list of files containing unpaired reads to be aligned, e.g. <span class="nt" style="color: navy;"><code></span>lane1.fq,lane2.fq,lane3.fq,lane4.fq<span class="nt" style="color: navy;"></code></span>. Reads may be a mix of different lengths. If <span class="nt" style="color: navy;"><code></span>-<span class="nt" style="color: navy;"></code></span> is specified, <span class="nt" style="color: navy;"><code></span>centrifuge<span class="nt" style="color: navy;"></code></span> gets the reads from the <span class="ni" style="color: purple;">"</span>standard in<span class="ni" style="color: purple;">"</span> or <span class="ni" style="color: purple;">"</span>stdin<span class="ni" style="color: purple;">"</span> filehandle.<span class="nt" style="color: navy;"></p></span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td></span></span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="html"></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--sra-acc <span class="ni" style="color: purple;"><</span>SRA accession number<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="html"></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Comma-separated list of SRA accession numbers, e.g. <span class="nt" style="color: navy;"><code></span>--sra-acc SRR353653,SRR353654<span class="nt" style="color: navy;"></code></span>. Information about read types is available at http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?sp=runinfo<span class="ni" style="color: purple;">&</span>acc=<span class="nt" style="color: navy;"><b></span>sra-acc<span class="nt" style="color: navy;"></b></span><span class="ni" style="color: purple;">&</span>retmode=xml, where <span class="nt" style="color: navy;"><b></span>sra-acc<span class="nt" style="color: navy;"></b></span> is SRA accession number. If users run HISAT2 on a computer cluster, it is recommended to disable SRA-related caching (see the instruction at <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"https://github.com/ncbi/sra-tools/wiki/Toolkit-Configuration"</span><span class="nt" style="color: navy;">></span>SRA-MANUAL<span class="nt" style="color: navy;"></a></span>).<span class="nt" style="color: navy;"></p></span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td></span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-S <span class="ni" style="color: purple;"><</span>filename<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="html"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>File to write classification results to. By default, assignments are written to the <span class="ni" style="color: purple;">"</span>standard out<span class="ni" style="color: purple;">"</span> or <span class="ni" style="color: purple;">"</span>stdout<span class="ni" style="color: purple;">"</span> filehandle (i.e. the console).<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td></span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--report-file <span class="ni" style="color: purple;"><</span>filename<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>File to write a classification summary to (default: centrifuge_report.tsv).<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="html"><span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"options"</span><span class="nt" style="color: navy;">></span>Options<span class="nt" style="color: navy;"></h3></span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="html"><span class="nt" style="color: navy;"><h4</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"input-options"</span><span class="nt" style="color: navy;">></span>Input options<span class="nt" style="color: navy;"></h4></span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="html"><span class="nt" style="color: navy;"><table></span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-q"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-q<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Reads (specified with <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>m1<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>m2<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>s<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>) are FASTQ files. FASTQ files usually have extension <span class="nt" style="color: navy;"><code></span>.fq<span class="nt" style="color: navy;"></code></span> or <span class="nt" style="color: navy;"><code></span>.fastq<span class="nt" style="color: navy;"></code></span>. FASTQ is the default format. See also: <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-options-solexa-quals"</span><span class="nt" style="color: navy;">><code></span>--solexa-quals<span class="nt" style="color: navy;"></code></a></span> and <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-options-int-quals"</span><span class="nt" style="color: navy;">><code></span>--int-quals<span class="nt" style="color: navy;"></code></a></span>.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-qseq"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--qseq<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Reads (specified with <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>m1<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>m2<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>s<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>) are QSEQ files. QSEQ files usually end in <span class="nt" style="color: navy;"><code></span>_qseq.txt<span class="nt" style="color: navy;"></code></span>. See also: <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-options-solexa-quals"</span><span class="nt" style="color: navy;">><code></span>--solexa-quals<span class="nt" style="color: navy;"></code></a></span> and <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-options-int-quals"</span><span class="nt" style="color: navy;">><code></span>--int-quals<span class="nt" style="color: navy;"></code></a></span>.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-f"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-f<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Reads (specified with <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>m1<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>m2<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>s<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>) are FASTA files. FASTA files usually have extension <span class="nt" style="color: navy;"><code></span>.fa<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>.fasta<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>.mfa<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>.fna<span class="nt" style="color: navy;"></code></span> or similar. FASTA files do not have a way of specifying quality values, so when <span class="nt" style="color: navy;"><code></span>-f<span class="nt" style="color: navy;"></code></span> is set, the result is as if <span class="nt" style="color: navy;"><code></span>--ignore-quals<span class="nt" style="color: navy;"></code></span> is also set.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-r"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-r<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Reads (specified with <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>m1<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>m2<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>s<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>) are files with one input sequence per line, without any other information (no read names, no qualities). When <span class="nt" style="color: navy;"><code></span>-r<span class="nt" style="color: navy;"></code></span> is set, the result is as if <span class="nt" style="color: navy;"><code></span>--ignore-quals<span class="nt" style="color: navy;"></code></span> is also set.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-c"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-c<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The read sequences are given on command line. I.e. <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>m1<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>m2<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> and <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>singles<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> are comma-separated lists of reads rather than lists of read files. There is no way to specify read names or qualities, so <span class="nt" style="color: navy;"><code></span>-c<span class="nt" style="color: navy;"></code></span> also implies <span class="nt" style="color: navy;"><code></span>--ignore-quals<span class="nt" style="color: navy;"></code></span>.<span class="nt" style="color: navy;"></p></span></span>
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253
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-s"</span><span class="nt" style="color: navy;">></span></span>
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254
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255
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-s/--skip <span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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257
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258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Skip (i.e. do not align) the first <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> reads or pairs in the input.<span class="nt" style="color: navy;"></p></span></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr></span></span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-u"</span><span class="nt" style="color: navy;">></span></span>
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261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="html"></span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-u/--qupto <span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="html"></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Align the first <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> reads or read pairs from the input (after the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-options-s"</span><span class="nt" style="color: navy;">><code></span>-s<span class="nt" style="color: navy;"></code></span>/<span class="nt" style="color: navy;"><code></span>--skip<span class="nt" style="color: navy;"></code></a></span> reads or pairs have been skipped), then stop. Default: no limit.<span class="nt" style="color: navy;"></p></span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr></span></span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-5"</span><span class="nt" style="color: navy;">></span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="html"></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-5/--trim5 <span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="html"></span>
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272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Trim <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> bases from 5' (left) end of each read before alignment (default: 0).<span class="nt" style="color: navy;"></p></span></span>
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273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr></span></span>
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<td class="diff-line-num old old_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-3"</span><span class="nt" style="color: navy;">></span></span>
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275
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-3/--trim3 <span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Trim <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> bases from 3' (right) end of each read before alignment (default: 0).<span class="nt" style="color: navy;"></p></span></span>
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280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-phred33-quals"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--phred33<span class="nt" style="color: navy;"></code></pre></span></span>
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284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="html"></span>
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285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Input qualities are ASCII chars equal to the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/Phred_quality_score"</span><span class="nt" style="color: navy;">></span>Phred quality<span class="nt" style="color: navy;"></a></span> plus 33. This is also called the <span class="ni" style="color: purple;">"</span>Phred+33<span class="ni" style="color: purple;">"</span> encoding, which is used by the very latest Illumina pipelines.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-phred64-quals"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--phred64<span class="nt" style="color: navy;"></code></pre></span></span>
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291
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292
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Input qualities are ASCII chars equal to the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/Phred_quality_score"</span><span class="nt" style="color: navy;">></span>Phred quality<span class="nt" style="color: navy;"></a></span> plus 64. This is also called the <span class="ni" style="color: purple;">"</span>Phred+64<span class="ni" style="color: purple;">"</span> encoding.<span class="nt" style="color: navy;"></p></span></span>
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293
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294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-solexa-quals"</span><span class="nt" style="color: navy;">></span></span>
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295
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296
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--solexa-quals<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Convert input qualities from <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/Phred_quality_score"</span><span class="nt" style="color: navy;">></span>Solexa<span class="nt" style="color: navy;"></a></span> (which can be negative) to <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/Phred_quality_score"</span><span class="nt" style="color: navy;">></span>Phred<span class="nt" style="color: navy;"></a></span> (which can't). This scheme was used in older Illumina GA Pipeline versions (prior to 1.3). Default: off.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-int-quals"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--int-quals<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Quality values are represented in the read input file as space-separated ASCII integers, e.g., <span class="nt" style="color: navy;"><code></span>40 40 30 40<span class="nt" style="color: navy;"></code></span>..., rather than ASCII characters, e.g., <span class="nt" style="color: navy;"><code></span>II?I<span class="nt" style="color: navy;"></code></span>.... Integers are treated as being on the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/Phred_quality_score"</span><span class="nt" style="color: navy;">></span>Phred quality<span class="nt" style="color: navy;"></a></span> scale unless <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-options-solexa-quals"</span><span class="nt" style="color: navy;">><code></span>--solexa-quals<span class="nt" style="color: navy;"></code></a></span> is also specified. Default: off.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="html"><span class="nt" style="color: navy;"><h4</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"classification"</span><span class="nt" style="color: navy;">></span>Classification<span class="nt" style="color: navy;"></h4></span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-min-hitlen"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--min-hitlen <span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Minimum length of partial hits, which must be greater than 15 (default: 22)<span class="ni" style="color: purple;">"</span><span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-k"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-k <span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>It searches for at most <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> distinct, primary assignments for each read or pair.<span class="nt" style="color: navy;"><br</span> <span class="nt" style="color: navy;">/></span>Primary assignments mean assignments whose assignment score is equal or higher than any other assignments. If there are more primary assignments than this value, the search will merge some of the assignments into a higher taxonomic rank. The assignment score for a paired-end assignment equals the sum of the assignment scores of the individual mates. Default: 5<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-host-taxids"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--host-taxids<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>A comma-separated list of taxonomic IDs that will be preferred in classification procedure. The descendants from these IDs will also be preferred. In case some of a read's assignments correspond to these taxonomic IDs, only those corresponding assignments will be reported.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-exclude-taxids"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--exclude-taxids<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>A comma-separated list of taxonomic IDs that will be excluded in classification procedure. The descendants from these IDs will also be exclude.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">#### Alignment options</span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--n-ceil`]: #centrifuge-options-n-ceil</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> --n-ceil <func></span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">Sets a function governing the maximum number of ambiguous characters (usually</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">`N`s and/or `.`s) allowed in a read as a function of read length. For instance,</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">where x is the read length. See also: [setting function options]. Reads</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">exceeding this ceiling are [filtered out]. Default: `L,0,0.15`.</span></span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[filtered out]: #filtering</span></span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--ignore-quals`]: #centrifuge-options-ignore-quals</span></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> --ignore-quals</span></span>
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376
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"></td><td></span></span>
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377
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">When calculating a mismatch penalty, always consider the quality value at the</span></span>
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379
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">mismatched position to be the highest possible, regardless of the actual value. </span></span>
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380
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">I.e. input is treated as though all quality values are high. This is also the</span></span>
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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">default behavior when the input doesn't specify quality values (e.g. in [`-f`],</span></span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`-r`], or [`-c`] modes).</span></span>
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383
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"><tr><td id="centrifuge-options-nofw"></span></span>
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386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="html"></span>
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387
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--nofw`]: #centrifuge-options-nofw</span></span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="html"></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> --nofw/--norc</span></span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="html"></span>
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391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"></td><td></span></span>
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392
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="html"></span>
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393
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">If `--nofw` is specified, `centrifuge` will not attempt to align unpaired reads to</span></span>
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394
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">the forward (Watson) reference strand. If `--norc` is specified, `centrifuge` will</span></span>
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395
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">not attempt to align unpaired reads against the reverse-complement (Crick)</span></span>
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the</span></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">fragments; i.e. specifying `--nofw` causes `centrifuge` to explore only those</span></span>
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">paired-end configurations corresponding to fragments from the reverse-complement</span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">(Crick) strand. Default: both strands enabled. </span></span>
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"></table></span></span>
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">#### Paired-end options</span></span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"><table></span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"><tr><td id="centrifuge-options-fr"></span></span>
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--fr`/`--rf`/`--ff`]: #centrifuge-options-fr</span></span>
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--fr`]: #centrifuge-options-fr</span></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--rf`]: #centrifuge-options-fr</span></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--ff`]: #centrifuge-options-fr</span></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> --fr/--rf/--ff</span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">The upstream/downstream mate orientations for a valid paired-end alignment</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">against the forward reference strand. E.g., if `--fr` is specified and there is</span></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">a candidate paired-end alignment where mate 1 appears upstream of the reverse</span></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">complement of mate 2 and the fragment length constraints ([`-I`] and [`-X`]) are</span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">met, that alignment is valid. Also, if mate 2 appears upstream of the reverse</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">complement of mate 1 and all other constraints are met, that too is valid.</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">`--rf` likewise requires that an upstream mate1 be reverse-complemented and a</span></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1</span></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate</span></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">for Illumina's Paired-end Sequencing Assay).</span></span>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">--></span></span>
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="html"><span class="nt" style="color: navy;"><h4</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"output-options"</span><span class="nt" style="color: navy;">></span>Output options<span class="nt" style="color: navy;"></h4></span></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-t"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-t/--time<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Print the wall-clock time required to load the index files and align the reads. This is printed to the <span class="ni" style="color: purple;">"</span>standard error<span class="ni" style="color: purple;">"</span> (<span class="ni" style="color: purple;">"</span>stderr<span class="ni" style="color: purple;">"</span>) filehandle. Default: off.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"><!--</span></span>
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"><tr><td id="centrifuge-options-un"></span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--un`]: #centrifuge-options-un</span></span>
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--un-gz`]: #centrifuge-options-un</span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--un-bz2`]: #centrifuge-options-un</span></span>
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> --un <path></span></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> --un-gz <path></span></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> --un-bz2 <path></span></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">Write unpaired reads that fail to align to file at `<path>`. These reads</span></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">correspond to the SAM records with the FLAGS `0x4` bit set and neither the</span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">`0x40` nor `0x80` bits set. If `--un-gz` is specified, output will be gzip</span></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">compressed. If `--un-bz2` is specified, output will be bzip2 compressed. Reads</span></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">written in this way will appear exactly as they did in the input file, without</span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">any modification (same sequence, same name, same quality string, same quality</span></span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">encoding). Reads will not necessarily appear in the same order as they did in</span></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">the input.</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"><tr><td id="centrifuge-options-al"></span></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--al`]: #centrifuge-options-al</span></span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--al-gz`]: #centrifuge-options-al</span></span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--al-bz2`]: #centrifuge-options-al</span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> --al <path></span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> --al-gz <path></span></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> --al-bz2 <path></span></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"></td><td></span></span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">Write unpaired reads that align at least once to file at `<path>`. These reads</span></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">correspond to the SAM records with the FLAGS `0x4`, `0x40`, and `0x80` bits</span></span>
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">unset. If `--al-gz` is specified, output will be gzip compressed. If `--al-bz2`</span></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">is specified, output will be bzip2 compressed. Reads written in this way will</span></span>
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">appear exactly as they did in the input file, without any modification (same</span></span>
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">sequence, same name, same quality string, same quality encoding). Reads will</span></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">not necessarily appear in the same order as they did in the input.</span></span>
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"><tr><td id="centrifuge-options-un-conc"></span></span>
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491
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--un-conc`]: #centrifuge-options-un-conc</span></span>
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492
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--un-conc-gz`]: #centrifuge-options-un-conc</span></span>
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493
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--un-conc-bz2`]: #centrifuge-options-un-conc</span></span>
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494
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495
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> --un-conc <path></span></span>
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496
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> --un-conc-gz <path></span></span>
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497
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> --un-conc-bz2 <path></span></span>
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498
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499
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"></td><td></span></span>
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500
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="html"></span>
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501
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">Write paired-end reads that fail to align concordantly to file(s) at `<path>`.</span></span>
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502
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">These reads correspond to the SAM records with the FLAGS `0x4` bit set and</span></span>
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503
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">either the `0x40` or `0x80` bit set (depending on whether it's mate #1 or #2).</span></span>
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504
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">`.1` and `.2` strings are added to the filename to distinguish which file</span></span>
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505
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">contains mate #1 and mate #2. If a percent symbol, `%`, is used in `<path>`,</span></span>
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506
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">the percent symbol is replaced with `1` or `2` to make the per-mate filenames.</span></span>
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507
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">Otherwise, `.1` or `.2` are added before the final dot in `<path>` to make the</span></span>
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508
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">per-mate filenames. Reads written in this way will appear exactly as they did</span></span>
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509
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">in the input files, without any modification (same sequence, same name, same</span></span>
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510
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">quality string, same quality encoding). Reads will not necessarily appear in</span></span>
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511
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">the same order as they did in the inputs.</span></span>
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512
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="html"></span>
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513
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"></td></tr></span></span>
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514
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"><tr><td id="centrifuge-options-al-conc"></span></span>
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515
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="html"></span>
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516
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--al-conc`]: #centrifuge-options-al-conc</span></span>
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517
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--al-conc-gz`]: #centrifuge-options-al-conc</span></span>
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518
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">[`--al-conc-bz2`]: #centrifuge-options-al-conc</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> --al-conc <path></span></span>
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> --al-conc-gz <path></span></span>
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> --al-conc-bz2 <path></span></span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"></td><td></span></span>
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">Write paired-end reads that align concordantly at least once to file(s) at</span></span>
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">`<path>`. These reads correspond to the SAM records with the FLAGS `0x4` bit</span></span>
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">unset and either the `0x40` or `0x80` bit set (depending on whether it's mate #1</span></span>
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">or #2). `.1` and `.2` strings are added to the filename to distinguish which</span></span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">file contains mate #1 and mate #2. If a percent symbol, `%`, is used in</span></span>
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">`<path>`, the percent symbol is replaced with `1` or `2` to make the per-mate</span></span>
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">filenames. Otherwise, `.1` or `.2` are added before the final dot in `<path>` to</span></span>
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">make the per-mate filenames. Reads written in this way will appear exactly as</span></span>
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">they did in the input files, without any modification (same sequence, same name,</span></span>
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">same quality string, same quality encoding). Reads will not necessarily appear</span></span>
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">in the same order as they did in the inputs.</span></span>
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;">--></span></span>
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-quiet"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--quiet<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Print nothing besides alignments and serious errors.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-met-file"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--met-file <span class="ni" style="color: purple;"><</span>path<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Write <span class="nt" style="color: navy;"><code></span>centrifuge<span class="nt" style="color: navy;"></code></span> metrics to file <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>path<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>. Having alignment metric can be useful for debugging certain problems, especially performance issues. See also: <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-options-met"</span><span class="nt" style="color: navy;">><code></span>--met<span class="nt" style="color: navy;"></code></a></span>. Default: metrics disabled.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-met-stderr"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--met-stderr<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Write <span class="nt" style="color: navy;"><code></span>centrifuge<span class="nt" style="color: navy;"></code></span> metrics to the <span class="ni" style="color: purple;">"</span>standard error<span class="ni" style="color: purple;">"</span> (<span class="ni" style="color: purple;">"</span>stderr<span class="ni" style="color: purple;">"</span>) filehandle. This is not mutually exclusive with <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-options-met-file"</span><span class="nt" style="color: navy;">><code></span>--met-file<span class="nt" style="color: navy;"></code></a></span>. Having alignment metric can be useful for debugging certain problems, especially performance issues. See also: <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-options-met"</span><span class="nt" style="color: navy;">><code></span>--met<span class="nt" style="color: navy;"></code></a></span>. Default: metrics disabled.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-met"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--met <span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Write a new <span class="nt" style="color: navy;"><code></span>centrifuge<span class="nt" style="color: navy;"></code></span> metrics record every <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> seconds. Only matters if either <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-options-met-stderr"</span><span class="nt" style="color: navy;">><code></span>--met-stderr<span class="nt" style="color: navy;"></code></a></span> or <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-options-met-file"</span><span class="nt" style="color: navy;">><code></span>--met-file<span class="nt" style="color: navy;"></code></a></span> are specified. Default: 1.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="html"><span class="nt" style="color: navy;"><h4</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"performance-options"</span><span class="nt" style="color: navy;">></span>Performance options<span class="nt" style="color: navy;"></h4></span></span>
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="html"><span class="nt" style="color: navy;"><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-o"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-o/--offrate <span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Override the offrate of the index with <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>. If <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> is greater than the offrate used to build the index, then some row markings are discarded when the index is read into memory. This reduces the memory footprint of the aligner but requires more time to calculate text offsets. <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> must be greater than the value used to build the index.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-p"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-p/--threads NTHREADS<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Launch <span class="nt" style="color: navy;"><code></span>NTHREADS<span class="nt" style="color: navy;"></code></span> parallel search threads (default: 1). Threads will run on separate processors/cores and synchronize when parsing reads and outputting alignments. Searching for alignments is highly parallel, and speedup is close to linear. Increasing <span class="nt" style="color: navy;"><code></span>-p<span class="nt" style="color: navy;"></code></span> increases Centrifuge's memory footprint. E.g. when aligning to a human genome index, increasing <span class="nt" style="color: navy;"><code></span>-p<span class="nt" style="color: navy;"></code></span> from 1 to 8 increases the memory footprint by a few hundred megabytes. This option is only available if <span class="nt" style="color: navy;"><code></span>bowtie<span class="nt" style="color: navy;"></code></span> is linked with the <span class="nt" style="color: navy;"><code></span>pthreads<span class="nt" style="color: navy;"></code></span> library (i.e. if <span class="nt" style="color: navy;"><code></span>BOWTIE_PTHREADS=0<span class="nt" style="color: navy;"></code></span> is not specified at build time).<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-reorder"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--reorder<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Guarantees that output records are printed in an order corresponding to the order of the reads in the original input file, even when <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-p"</span><span class="nt" style="color: navy;">><code></span>-p<span class="nt" style="color: navy;"></code></a></span> is set greater than 1. Specifying <span class="nt" style="color: navy;"><code></span>--reorder<span class="nt" style="color: navy;"></code></span> and setting <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-p"</span><span class="nt" style="color: navy;">><code></span>-p<span class="nt" style="color: navy;"></code></a></span> greater than 1 causes Centrifuge to run somewhat slower and use somewhat more memory then if <span class="nt" style="color: navy;"><code></span>--reorder<span class="nt" style="color: navy;"></code></span> were not specified. Has no effect if <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-p"</span><span class="nt" style="color: navy;">><code></span>-p<span class="nt" style="color: navy;"></code></a></span> is set to 1, since output order will naturally correspond to input order in that case.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC595" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-mm"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--mm<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC600" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Use memory-mapped I/O to load the index, rather than typical file I/O. Memory-mapping allows many concurrent <span class="nt" style="color: navy;"><code></span>bowtie<span class="nt" style="color: navy;"></code></span> processes on the same computer to share the same memory image of the index (i.e. you pay the memory overhead just once). This facilitates memory-efficient parallelization of <span class="nt" style="color: navy;"><code></span>bowtie<span class="nt" style="color: navy;"></code></span> in situations where using <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-p"</span><span class="nt" style="color: navy;">><code></span>-p<span class="nt" style="color: navy;"></code></a></span> is not possible or not preferable.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC603" class="line" lang="html"><span class="nt" style="color: navy;"><h4</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"other-options"</span><span class="nt" style="color: navy;">></span>Other options<span class="nt" style="color: navy;"></h4></span></span>
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-qc-filter"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC607" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--qc-filter<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Filter out reads for which the QSEQ filter field is non-zero. Only has an effect when read format is <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-options-qseq"</span><span class="nt" style="color: navy;">><code></span>--qseq<span class="nt" style="color: navy;"></code></a></span>. Default: off.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-seed"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC614" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--seed <span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC615" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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<pre style="margin: 0;">-<span id="LC617" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Use <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> as the seed for pseudo-random number generator. Default: 0.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr></span></span>
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<pre style="margin: 0;">-<span id="LC619" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-non-deterministic"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--non-deterministic<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC624" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Normally, Centrifuge re-initializes its pseudo-random generator for each read. It seeds the generator with a number derived from (a) the read name, (b) the nucleotide sequence, (c) the quality sequence, (d) the value of the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-options-seed"</span><span class="nt" style="color: navy;">><code></span>--seed<span class="nt" style="color: navy;"></code></a></span> option. This means that if two reads are identical (same name, same nucleotides, same qualities) Centrifuge will find and report the same classification(s) for both, even if there was ambiguity. When <span class="nt" style="color: navy;"><code></span>--non-deterministic<span class="nt" style="color: navy;"></code></span> is specified, Centrifuge re-initializes its pseudo-random generator for each read using the current time. This means that Centrifuge will not necessarily report the same classification for two identical reads. This is counter-intuitive for some users, but might be more appropriate in situations where the input consists of many identical reads.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-version"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--version<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Print version information and quit.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-options-h"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC635" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-h/--help<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC638" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Print usage information and quit.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="html"><span class="nt" style="color: navy;"><h1</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"the-centrifuge-build-indexer"</span><span class="nt" style="color: navy;">></span>The <span class="nt" style="color: navy;"><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span> indexer<span class="nt" style="color: navy;"></h1></span></span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="html"><span class="nt" style="color: navy;"><p><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span> builds a Centrifuge index from a set of DNA sequences. <span class="nt" style="color: navy;"><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span> outputs a set of 6 files with suffixes <span class="nt" style="color: navy;"><code></span>.1.cf<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>.2.cf<span class="nt" style="color: navy;"></code></span>, and <span class="nt" style="color: navy;"><code></span>.3.cf<span class="nt" style="color: navy;"></code></span>. These files together constitute the index: they are all that is needed to align reads to that reference. The original sequence FASTA files are no longer used by Centrifuge once the index is built.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC644" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Use of Karkkainen's <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://portal.acm.org/citation.cfm?id=1314852"</span><span class="nt" style="color: navy;">></span>blockwise algorithm<span class="nt" style="color: navy;"></a></span> allows <span class="nt" style="color: navy;"><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span> to trade off between running time and memory usage. <span class="nt" style="color: navy;"><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span> has two options governing how it makes this trade: <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-bmax"</span><span class="nt" style="color: navy;">><code></span>--bmax<span class="nt" style="color: navy;"></code></a></span>/<span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-bmaxdivn"</span><span class="nt" style="color: navy;">><code></span>--bmaxdivn<span class="nt" style="color: navy;"></code></a></span>, and <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-dcv"</span><span class="nt" style="color: navy;">><code></span>--dcv<span class="nt" style="color: navy;"></code></a></span>. By default, <span class="nt" style="color: navy;"><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span> will automatically search for the settings that yield the best running time without exhausting memory. This behavior can be disabled using the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-a"</span><span class="nt" style="color: navy;">><code></span>-a<span class="nt" style="color: navy;"></code></span>/<span class="nt" style="color: navy;"><code></span>--noauto<span class="nt" style="color: navy;"></code></a></span> option.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC645" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The indexer provides options pertaining to the <span class="ni" style="color: purple;">"</span>shape<span class="ni" style="color: purple;">"</span> of the index, e.g. <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-o"</span><span class="nt" style="color: navy;">><code></span>--offrate<span class="nt" style="color: navy;"></code></a></span> governs the fraction of <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/Burrows-Wheeler_transform"</span><span class="nt" style="color: navy;">></span>Burrows-Wheeler<span class="nt" style="color: navy;"></a></span> rows that are <span class="ni" style="color: purple;">"</span>marked<span class="ni" style="color: purple;">"</span> (i.e., the density of the suffix-array sample; see the original <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/FM-index"</span><span class="nt" style="color: navy;">></span>FM Index<span class="nt" style="color: navy;"></a></span> paper for details). All of these options are potentially profitable trade-offs depending on the application. They have been set to defaults that are reasonable for most cases according to our experiments. See <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#performance-tuning"</span><span class="nt" style="color: navy;">></span>Performance tuning<span class="nt" style="color: navy;"></a></span> for details.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC646" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The Centrifuge index is based on the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/FM-index"</span><span class="nt" style="color: navy;">></span>FM Index<span class="nt" style="color: navy;"></a></span> of Ferragina and Manzini, which in turn is based on the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/Burrows-Wheeler_transform"</span><span class="nt" style="color: navy;">></span>Burrows-Wheeler<span class="nt" style="color: navy;"></a></span> transform. The algorithm used to build the index is based on the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://portal.acm.org/citation.cfm?id=1314852"</span><span class="nt" style="color: navy;">></span>blockwise algorithm<span class="nt" style="color: navy;"></a></span> of Karkkainen.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC647" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"command-line-1"</span><span class="nt" style="color: navy;">></span>Command Line<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC648" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Usage:<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC649" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>centrifuge-build [options]* --conversion-table <span class="ni" style="color: purple;"><</span>table_in<span class="ni" style="color: purple;">></span> --taxonomy-tree <span class="ni" style="color: purple;"><</span>taxonomy_in<span class="ni" style="color: purple;">></span> --name-table <span class="ni" style="color: purple;"><</span>table_in2<span class="ni" style="color: purple;">></span> <span class="ni" style="color: purple;"><</span>reference_in<span class="ni" style="color: purple;">></span> <span class="ni" style="color: purple;"><</span>cf_base<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC650" class="line" lang="html"><span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"main-arguments-1"</span><span class="nt" style="color: navy;">></span>Main arguments<span class="nt" style="color: navy;"></h3></span></span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span><span class="ni" style="color: purple;"><</span>reference_in<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>A comma-separated list of FASTA files containing the reference sequences to be aligned to, or, if <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-c"</span><span class="nt" style="color: navy;">><code></span>-c<span class="nt" style="color: navy;"></code></a></span> is specified, the sequences themselves. E.g., <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>reference_in<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> might be <span class="nt" style="color: navy;"><code></span>chr1.fa,chr2.fa,chrX.fa,chrY.fa<span class="nt" style="color: navy;"></code></span>, or, if <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-c"</span><span class="nt" style="color: navy;">><code></span>-c<span class="nt" style="color: navy;"></code></a></span> is specified, this might be <span class="nt" style="color: navy;"><code></span>GGTCATCCT,ACGGGTCGT,CCGTTCTATGCGGCTTA<span class="nt" style="color: navy;"></code></span>.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span><span class="ni" style="color: purple;"><</span>cf_base<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The basename of the index files to write. By default, <span class="nt" style="color: navy;"><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span> writes files named <span class="nt" style="color: navy;"><code></span>NAME.1.cf<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>NAME.2.cf<span class="nt" style="color: navy;"></code></span>, and <span class="nt" style="color: navy;"><code></span>NAME.3.cf<span class="nt" style="color: navy;"></code></span>, where <span class="nt" style="color: navy;"><code></span>NAME<span class="nt" style="color: navy;"></code></span> is <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>cf_base<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="html"><span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"options-1"</span><span class="nt" style="color: navy;">></span>Options<span class="nt" style="color: navy;"></h3></span></span>
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The reference input files (specified as <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>reference_in<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>) are FASTA files (usually having extension <span class="nt" style="color: navy;"><code></span>.fa<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>.mfa<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>.fna<span class="nt" style="color: navy;"></code></span> or similar).<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-build-options-c"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-c<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The reference sequences are given on the command line. I.e. <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>reference_in<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> is a comma-separated list of sequences rather than a list of FASTA files.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC679" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-build-options-a"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-a/--noauto<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC684" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Disable the default behavior whereby <span class="nt" style="color: navy;"><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span> automatically selects values for the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-bmax"</span><span class="nt" style="color: navy;">><code></span>--bmax<span class="nt" style="color: navy;"></code></a></span>, <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-dcv"</span><span class="nt" style="color: navy;">><code></span>--dcv<span class="nt" style="color: navy;"></code></a></span> and [<span class="nt" style="color: navy;"><code></span>--packed<span class="nt" style="color: navy;"></code></span>] parameters according to available memory. Instead, user may specify values for those parameters. If memory is exhausted during indexing, an error message will be printed; it is up to the user to try new parameters.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-build-options-p"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC687" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-p/--threads <span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Launch <span class="nt" style="color: navy;"><code></span>NTHREADS<span class="nt" style="color: navy;"></code></span> parallel search threads (default: 1).<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC691" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-build-options-conversion-table"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC693" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--conversion-table <span class="ni" style="color: purple;"><</span>file<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC696" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>List of UIDs (unique ID) and corresponding taxonomic IDs.<span class="nt" style="color: navy;"></p></span></span>
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697
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-build-options-taxonomy-tree"</span><span class="nt" style="color: navy;">></span></span>
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698
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699
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<pre style="margin: 0;">-<span id="LC699" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--taxonomy-tree <span class="ni" style="color: purple;"><</span>file<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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700
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<pre style="margin: 0;">-<span id="LC700" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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701
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<pre style="margin: 0;">-<span id="LC701" class="line" lang="html"></span>
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702
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<pre style="margin: 0;">-<span id="LC702" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Taxonomic tree (e.g. nodes.dmp).<span class="nt" style="color: navy;"></p></span></span>
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703
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<pre style="margin: 0;">-<span id="LC703" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-build-options-name-table"</span><span class="nt" style="color: navy;">></span></span>
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704
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<pre style="margin: 0;">-<span id="LC704" class="line" lang="html"></span>
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705
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<pre style="margin: 0;">-<span id="LC705" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--name-table <span class="ni" style="color: purple;"><</span>file<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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706
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<pre style="margin: 0;">-<span id="LC706" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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707
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708
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<pre style="margin: 0;">-<span id="LC708" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Name table (e.g. names.dmp).<span class="nt" style="color: navy;"></p></span></span>
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709
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<pre style="margin: 0;">-<span id="LC709" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-build-options-taxonomy-tree"</span><span class="nt" style="color: navy;">></span></span>
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710
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711
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<pre style="margin: 0;">-<span id="LC711" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--size-table <span class="ni" style="color: purple;"><</span>file<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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712
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<pre style="margin: 0;">-<span id="LC712" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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713
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<pre style="margin: 0;">-<span id="LC713" class="line" lang="html"></span>
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714
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<pre style="margin: 0;">-<span id="LC714" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>List of taxonomic IDs and lengths of the sequences belonging to the same taxonomic IDs.<span class="nt" style="color: navy;"></p></span></span>
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715
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-build-options-bmax"</span><span class="nt" style="color: navy;">></span></span>
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716
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717
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--bmax <span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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718
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<pre style="margin: 0;">-<span id="LC718" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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719
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720
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<pre style="margin: 0;">-<span id="LC720" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The maximum number of suffixes allowed in a block. Allowing more suffixes per block makes indexing faster, but increases peak memory usage. Setting this option overrides any previous setting for <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-bmax"</span><span class="nt" style="color: navy;">><code></span>--bmax<span class="nt" style="color: navy;"></code></a></span>, or <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-bmaxdivn"</span><span class="nt" style="color: navy;">><code></span>--bmaxdivn<span class="nt" style="color: navy;"></code></a></span>. Default (in terms of the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-bmaxdivn"</span><span class="nt" style="color: navy;">><code></span>--bmaxdivn<span class="nt" style="color: navy;"></code></a></span> parameter) is <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-bmaxdivn"</span><span class="nt" style="color: navy;">><code></span>--bmaxdivn<span class="nt" style="color: navy;"></code></a></span> 4. This is configured automatically by default; use <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-a"</span><span class="nt" style="color: navy;">><code></span>-a<span class="nt" style="color: navy;"></code></span>/<span class="nt" style="color: navy;"><code></span>--noauto<span class="nt" style="color: navy;"></code></a></span> to configure manually.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC721" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-build-options-bmaxdivn"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC722" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC723" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--bmaxdivn <span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC724" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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<pre style="margin: 0;">-<span id="LC725" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC726" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The maximum number of suffixes allowed in a block, expressed as a fraction of the length of the reference. Setting this option overrides any previous setting for <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-bmax"</span><span class="nt" style="color: navy;">><code></span>--bmax<span class="nt" style="color: navy;"></code></a></span>, or <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-bmaxdivn"</span><span class="nt" style="color: navy;">><code></span>--bmaxdivn<span class="nt" style="color: navy;"></code></a></span>. Default: <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-bmaxdivn"</span><span class="nt" style="color: navy;">><code></span>--bmaxdivn<span class="nt" style="color: navy;"></code></a></span> 4. This is configured automatically by default; use <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-a"</span><span class="nt" style="color: navy;">><code></span>-a<span class="nt" style="color: navy;"></code></span>/<span class="nt" style="color: navy;"><code></span>--noauto<span class="nt" style="color: navy;"></code></a></span> to configure manually.<span class="nt" style="color: navy;"></p></span></span>
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727
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<pre style="margin: 0;">-<span id="LC727" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-build-options-dcv"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC728" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC729" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--dcv <span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC730" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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<pre style="margin: 0;">-<span id="LC731" class="line" lang="html"></span>
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732
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Use <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> as the period for the difference-cover sample. A larger period yields less memory overhead, but may make suffix sorting slower, especially if repeats are present. Must be a power of 2 no greater than 4096. Default: 1024. This is configured automatically by default; use <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-a"</span><span class="nt" style="color: navy;">><code></span>-a<span class="nt" style="color: navy;"></code></span>/<span class="nt" style="color: navy;"><code></span>--noauto<span class="nt" style="color: navy;"></code></a></span> to configure manually.<span class="nt" style="color: navy;"></p></span></span>
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733
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<pre style="margin: 0;">-<span id="LC733" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-build-options-nodc"</span><span class="nt" style="color: navy;">></span></span>
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734
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<pre style="margin: 0;">-<span id="LC734" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC735" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--nodc<span class="nt" style="color: navy;"></code></pre></span></span>
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736
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<pre style="margin: 0;">-<span id="LC736" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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737
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<pre style="margin: 0;">-<span id="LC737" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC738" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Disable use of the difference-cover sample. Suffix sorting becomes quadratic-time in the worst case (where the worst case is an extremely repetitive reference). Default: off.<span class="nt" style="color: navy;"></p></span></span>
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739
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<pre style="margin: 0;">-<span id="LC739" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-build-options-o"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC741" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-o/--offrate <span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC744" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>To map alignments back to positions on the reference sequences, it's necessary to annotate (<span class="ni" style="color: purple;">"</span>mark<span class="ni" style="color: purple;">"</span>) some or all of the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/Burrows-Wheeler_transform"</span><span class="nt" style="color: navy;">></span>Burrows-Wheeler<span class="nt" style="color: navy;"></a></span> rows with their corresponding location on the genome. <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-build-options-o"</span><span class="nt" style="color: navy;">><code></span>-o<span class="nt" style="color: navy;"></code></span>/<span class="nt" style="color: navy;"><code></span>--offrate<span class="nt" style="color: navy;"></code></a></span> governs how many rows get marked: the indexer will mark every 2^<span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> rows. Marking more rows makes reference-position lookups faster, but requires more memory to hold the annotations at runtime. The default is 4 (every 16th row is marked; for human genome, annotations occupy about 680 megabytes).<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC747" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-t/--ftabchars <span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC750" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The ftab is the lookup table used to calculate an initial <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/Burrows-Wheeler_transform"</span><span class="nt" style="color: navy;">></span>Burrows-Wheeler<span class="nt" style="color: navy;"></a></span> range with respect to the first <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> characters of the query. A larger <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> yields a larger lookup table but faster query times. The ftab has size 4^(<span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span>+1) bytes. The default setting is 10 (ftab is 4MB).<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC753" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--seed <span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Use <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> as the seed for pseudo-random number generator.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC759" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--kmer-count <span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Use <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> as kmer-size for counting the distinct number of k-mers in the input sequences.<span class="nt" style="color: navy;"></p></span></span>
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763
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<pre style="margin: 0;">-<span id="LC763" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td></span></span>
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764
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<pre style="margin: 0;">-<span id="LC764" class="line" lang="html"></span>
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765
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<pre style="margin: 0;">-<span id="LC765" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-q/--quiet<span class="nt" style="color: navy;"></code></pre></span></span>
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766
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<pre style="margin: 0;">-<span id="LC766" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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767
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<pre style="margin: 0;">-<span id="LC767" class="line" lang="html"></span>
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768
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<pre style="margin: 0;">-<span id="LC768" class="line" lang="html"><span class="nt" style="color: navy;"><p><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span> is verbose by default. With this option <span class="nt" style="color: navy;"><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span> will print only error messages.<span class="nt" style="color: navy;"></p></span></span>
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769
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<pre style="margin: 0;">-<span id="LC769" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td></span></span>
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770
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<pre style="margin: 0;">-<span id="LC770" class="line" lang="html"></span>
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771
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<pre style="margin: 0;">-<span id="LC771" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-h/--help<span class="nt" style="color: navy;"></code></pre></span></span>
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772
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773
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774
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<pre style="margin: 0;">-<span id="LC774" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Print usage information and quit.<span class="nt" style="color: navy;"></p></span></span>
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775
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<pre style="margin: 0;">-<span id="LC775" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td></span></span>
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776
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777
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<pre style="margin: 0;">-<span id="LC777" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--version<span class="nt" style="color: navy;"></code></pre></span></span>
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778
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<pre style="margin: 0;">-<span id="LC778" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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779
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<pre style="margin: 0;">-<span id="LC779" class="line" lang="html"></span>
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780
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<pre style="margin: 0;">-<span id="LC780" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Print version information and quit.<span class="nt" style="color: navy;"></p></span></span>
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781
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<pre style="margin: 0;">-<span id="LC781" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr></table></span></span>
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782
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783
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<pre style="margin: 0;">-<span id="LC783" class="line" lang="html"><span class="nt" style="color: navy;"><h1</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"the-centrifuge-inspect-index-inspector"</span><span class="nt" style="color: navy;">></span>The <span class="nt" style="color: navy;"><code></span>centrifuge-inspect<span class="nt" style="color: navy;"></code></span> index inspector<span class="nt" style="color: navy;"></h1></span></span>
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784
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<pre style="margin: 0;">-<span id="LC784" class="line" lang="html"><span class="nt" style="color: navy;"><p><code></span>centrifuge-inspect<span class="nt" style="color: navy;"></code></span> extracts information from a Centrifuge index about what kind of index it is and what reference sequences were used to build it. When run without any options, the tool will output a FASTA file containing the sequences of the original references (with all non-<span class="nt" style="color: navy;"><code></span>A<span class="nt" style="color: navy;"></code></span>/<span class="nt" style="color: navy;"><code></span>C<span class="nt" style="color: navy;"></code></span>/<span class="nt" style="color: navy;"><code></span>G<span class="nt" style="color: navy;"></code></span>/<span class="nt" style="color: navy;"><code></span>T<span class="nt" style="color: navy;"></code></span> characters converted to <span class="nt" style="color: navy;"><code></span>N<span class="nt" style="color: navy;"></code></span>s). It can also be used to extract just the reference sequence names using the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-inspect-options-n"</span><span class="nt" style="color: navy;">><code></span>-n<span class="nt" style="color: navy;"></code></span>/<span class="nt" style="color: navy;"><code></span>--names<span class="nt" style="color: navy;"></code></a></span> option or a more verbose summary using the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#centrifuge-inspect-options-s"</span><span class="nt" style="color: navy;">><code></span>-s<span class="nt" style="color: navy;"></code></span>/<span class="nt" style="color: navy;"><code></span>--summary<span class="nt" style="color: navy;"></code></a></span> option.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC785" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"command-line-2"</span><span class="nt" style="color: navy;">></span>Command Line<span class="nt" style="color: navy;"></h2></span></span>
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786
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<pre style="margin: 0;">-<span id="LC786" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Usage:<span class="nt" style="color: navy;"></p></span></span>
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787
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<pre style="margin: 0;">-<span id="LC787" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>centrifuge-inspect [options]* <span class="ni" style="color: purple;"><</span>cf_base<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC788" class="line" lang="html"><span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"main-arguments-2"</span><span class="nt" style="color: navy;">></span>Main arguments<span class="nt" style="color: navy;"></h3></span></span>
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789
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<pre style="margin: 0;">-<span id="LC789" class="line" lang="html"><span class="nt" style="color: navy;"><table><tr><td></span></span>
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790
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<pre style="margin: 0;">-<span id="LC790" class="line" lang="html"></span>
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791
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<pre style="margin: 0;">-<span id="LC791" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span><span class="ni" style="color: purple;"><</span>cf_base<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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792
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<pre style="margin: 0;">-<span id="LC792" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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<pre style="margin: 0;">-<span id="LC793" class="line" lang="html"></span>
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794
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<pre style="margin: 0;">-<span id="LC794" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The basename of the index to be inspected. The basename is name of any of the index files but with the <span class="nt" style="color: navy;"><code></span>.X.cf<span class="nt" style="color: navy;"></code></span> suffix omitted. <span class="nt" style="color: navy;"><code></span>centrifuge-inspect<span class="nt" style="color: navy;"></code></span> first looks in the current directory for the index files, then in the directory specified in the <span class="nt" style="color: navy;"><code></span>Centrifuge_INDEXES<span class="nt" style="color: navy;"></code></span> environment variable.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC795" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr></table></span></span>
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<pre style="margin: 0;">-<span id="LC797" class="line" lang="html"><span class="nt" style="color: navy;"><h3</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"options-2"</span><span class="nt" style="color: navy;">></span>Options<span class="nt" style="color: navy;"></h3></span></span>
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798
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<pre style="margin: 0;">-<span id="LC798" class="line" lang="html"><span class="nt" style="color: navy;"><table><tr><td></span></span>
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<pre style="margin: 0;">-<span id="LC800" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-a/--across <span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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801
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<pre style="margin: 0;">-<span id="LC801" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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802
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<pre style="margin: 0;">-<span id="LC802" class="line" lang="html"></span>
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803
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<pre style="margin: 0;">-<span id="LC803" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>When printing FASTA output, output a newline character every <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> bases (default: 60).<span class="nt" style="color: navy;"></p></span></span>
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804
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<pre style="margin: 0;">-<span id="LC804" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-inspect-options-n"</span><span class="nt" style="color: navy;">></span></span>
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805
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<pre style="margin: 0;">-<span id="LC805" class="line" lang="html"></span>
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806
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<pre style="margin: 0;">-<span id="LC806" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-n/--names<span class="nt" style="color: navy;"></code></pre></span></span>
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807
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808
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<pre style="margin: 0;">-<span id="LC808" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC809" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Print reference sequence names, one per line, and quit.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC810" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-inspect-options-s"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">-<span id="LC812" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-s/--summary<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC813" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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<pre style="margin: 0;">-<span id="LC815" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Print a summary that includes information about index settings, as well as the names and lengths of the input sequences. The summary has this format:<span class="nt" style="color: navy;"></p></span></span>
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816
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<pre style="margin: 0;">-<span id="LC816" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>Colorspace <span class="ni" style="color: purple;"><</span>0 or 1<span class="ni" style="color: purple;">></span></span>
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817
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<pre style="margin: 0;">-<span id="LC817" class="line" lang="html">SA-Sample 1 in <span class="ni" style="color: purple;"><</span>sample<span class="ni" style="color: purple;">></span></span>
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818
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<pre style="margin: 0;">-<span id="LC818" class="line" lang="html">FTab-Chars <span class="ni" style="color: purple;"><</span>chars<span class="ni" style="color: purple;">></span></span>
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819
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<pre style="margin: 0;">-<span id="LC819" class="line" lang="html">Sequence-1 <span class="ni" style="color: purple;"><</span>name<span class="ni" style="color: purple;">></span> <span class="ni" style="color: purple;"><</span>len<span class="ni" style="color: purple;">></span></span>
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820
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<pre style="margin: 0;">-<span id="LC820" class="line" lang="html">Sequence-2 <span class="ni" style="color: purple;"><</span>name<span class="ni" style="color: purple;">></span> <span class="ni" style="color: purple;"><</span>len<span class="ni" style="color: purple;">></span></span>
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821
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<pre style="margin: 0;">-<span id="LC821" class="line" lang="html">...</span>
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822
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<pre style="margin: 0;">-<span id="LC822" class="line" lang="html">Sequence-N <span class="ni" style="color: purple;"><</span>name<span class="ni" style="color: purple;">></span> <span class="ni" style="color: purple;"><</span>len<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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823
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<pre style="margin: 0;">-<span id="LC823" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Fields are separated by tabs. Colorspace is always set to 0 for Centrifuge.<span class="nt" style="color: navy;"></p></span></span>
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824
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<pre style="margin: 0;">-<span id="LC824" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-inspect-options-conversion-table"</span><span class="nt" style="color: navy;">></span></span>
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825
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<pre style="margin: 0;">-<span id="LC825" class="line" lang="html"></span>
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826
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<pre style="margin: 0;">-<span id="LC826" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--conversion-table<span class="nt" style="color: navy;"></code></pre></span></span>
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827
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<pre style="margin: 0;">-<span id="LC827" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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828
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<pre style="margin: 0;">-<span id="LC828" class="line" lang="html"></span>
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829
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Print a list of UIDs (unique ID) and corresponding taxonomic IDs.<span class="nt" style="color: navy;"></p></span></span>
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830
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<pre style="margin: 0;">-<span id="LC830" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-inspect-options-taxonomy-tree"</span><span class="nt" style="color: navy;">></span></span>
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831
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<pre style="margin: 0;">-<span id="LC831" class="line" lang="html"></span>
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832
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<pre style="margin: 0;">-<span id="LC832" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--taxonomy-tree<span class="nt" style="color: navy;"></code></pre></span></span>
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833
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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834
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<pre style="margin: 0;">-<span id="LC834" class="line" lang="html"></span>
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835
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<pre style="margin: 0;">-<span id="LC835" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Print taxonomic tree.<span class="nt" style="color: navy;"></p></span></span>
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836
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<pre style="margin: 0;">-<span id="LC836" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-inspect-options-name-table"</span><span class="nt" style="color: navy;">></span></span>
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837
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<pre style="margin: 0;">-<span id="LC837" class="line" lang="html"></span>
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838
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<pre style="margin: 0;">-<span id="LC838" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--name-table<span class="nt" style="color: navy;"></code></pre></span></span>
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839
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<pre style="margin: 0;">-<span id="LC839" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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840
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<pre style="margin: 0;">-<span id="LC840" class="line" lang="html"></span>
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841
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<pre style="margin: 0;">-<span id="LC841" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Print name table.<span class="nt" style="color: navy;"></p></span></span>
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842
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<pre style="margin: 0;">-<span id="LC842" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"centrifuge-inspect-options-taxonomy-tree"</span><span class="nt" style="color: navy;">></span></span>
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843
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<pre style="margin: 0;">-<span id="LC843" class="line" lang="html"></span>
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844
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<pre style="margin: 0;">-<span id="LC844" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--size-table<span class="nt" style="color: navy;"></code></pre></span></span>
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845
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<pre style="margin: 0;">-<span id="LC845" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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846
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<pre style="margin: 0;">-<span id="LC846" class="line" lang="html"></span>
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847
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<pre style="margin: 0;">-<span id="LC847" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Print a list of taxonomic IDs and lengths of the sequences belonging to the same taxonomic IDs.<span class="nt" style="color: navy;"></p></span></span>
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848
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<pre style="margin: 0;">-<span id="LC848" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td></span></span>
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849
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<pre style="margin: 0;">-<span id="LC849" class="line" lang="html"></span>
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850
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<pre style="margin: 0;">-<span id="LC850" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-v/--verbose<span class="nt" style="color: navy;"></code></pre></span></span>
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851
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<pre style="margin: 0;">-<span id="LC851" class="line" lang="html"><span class="nt" style="color: navy;"></td><td></span></span>
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852
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<pre style="margin: 0;">-<span id="LC852" class="line" lang="html"></span>
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853
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<pre style="margin: 0;">-<span id="LC853" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Print verbose output (for debugging).<span class="nt" style="color: navy;"></p></span></span>
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854
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<pre style="margin: 0;">-<span id="LC854" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr><tr><td></span></span>
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855
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<pre style="margin: 0;">-<span id="LC855" class="line" lang="html"></span>
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856
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<pre style="margin: 0;">-<span id="LC856" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--version<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC859" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Print version information and quit.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC862" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>-h/--help<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC865" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Print usage information and quit.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC868" class="line" lang="html"><span class="nt" style="color: navy;"><h1</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"getting-started-with-centrifuge"</span><span class="nt" style="color: navy;">></span>Getting started with Centrifuge<span class="nt" style="color: navy;"></h1></span></span>
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<pre style="margin: 0;">-<span id="LC869" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Centrifuge comes with some example files to get you started. The example files are not scientifically significant; these files will simply let you start running Centrifuge and downstream tools right away.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC870" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>First follow the manual instructions to <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#obtaining-centrifuge"</span><span class="nt" style="color: navy;">></span>obtain Centrifuge<span class="nt" style="color: navy;"></a></span>. Set the <span class="nt" style="color: navy;"><code></span>CENTRIFUGE_HOME<span class="nt" style="color: navy;"></code></span> environment variable to point to the new Centrifuge directory containing the <span class="nt" style="color: navy;"><code></span>centrifuge<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span> and <span class="nt" style="color: navy;"><code></span>centrifuge-inspect<span class="nt" style="color: navy;"></code></span> binaries. This is important, as the <span class="nt" style="color: navy;"><code></span>CENTRIFUGE_HOME<span class="nt" style="color: navy;"></code></span> variable is used in the commands below to refer to that directory.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC871" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"indexing-a-reference-genome"</span><span class="nt" style="color: navy;">></span>Indexing a reference genome<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC872" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>To create an index for two small sequences included with Centrifuge, create a new temporary directory (it doesn't matter where), change into that directory, and run:<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC873" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>$CENTRIFUGE_HOME/centrifuge-build --conversion-table $CENTRIFUGE_HOME/example/reference/gi_to_tid.dmp --taxonomy-tree $CENTRIFUGE_HOME/example/reference/nodes.dmp --name-table $CENTRIFUGE_HOME/example/reference/names.dmp $CENTRIFUGE_HOME/example/reference/test.fa test<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC874" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The command should print many lines of output then quit. When the command completes, the current directory will contain ten new files that all start with <span class="nt" style="color: navy;"><code></span>test<span class="nt" style="color: navy;"></code></span> and end with <span class="nt" style="color: navy;"><code></span>.1.cf<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>.2.cf<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>.3.cf<span class="nt" style="color: navy;"></code></span>. These files constitute the index - you're done!<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC875" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>You can use <span class="nt" style="color: navy;"><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span> to create an index for a set of FASTA files obtained from any source, including sites such as <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://genome.ucsc.edu/cgi-bin/hgGateway"</span><span class="nt" style="color: navy;">></span>UCSC<span class="nt" style="color: navy;"></a></span>, <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://www.ncbi.nlm.nih.gov/sites/genome"</span><span class="nt" style="color: navy;">></span>NCBI<span class="nt" style="color: navy;"></a></span>, and <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://www.ensembl.org/"</span><span class="nt" style="color: navy;">></span>Ensembl<span class="nt" style="color: navy;"></a></span>. When indexing multiple FASTA files, specify all the files using commas to separate file names. For more details on how to create an index with <span class="nt" style="color: navy;"><code></span>centrifuge-build<span class="nt" style="color: navy;"></code></span>, see the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#the-centrifuge-build-indexer"</span><span class="nt" style="color: navy;">></span>manual section on index building<span class="nt" style="color: navy;"></a></span>. You may also want to bypass this process by obtaining a pre-built index.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC876" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"classifying-example-reads"</span><span class="nt" style="color: navy;">></span>Classifying example reads<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC877" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Stay in the directory created in the previous step, which now contains the <span class="nt" style="color: navy;"><code></span>test<span class="nt" style="color: navy;"></code></span> index files. Next, run:<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC878" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>$CENTRIFUGE_HOME/centrifuge -f -x test $CENTRIFUGE_HOME/example/reads/input.fa<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC879" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>This runs the Centrifuge classifier, which classifies a set of unpaired reads to the the genomes using the index generated in the previous step. The classification results are reported to stdout, and a short classification summary is written to centrifuge-species_report.tsv.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC880" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>You will see something like this:<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC881" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>readID seqID taxID score 2ndBestScore hitLength numMatches</span>
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<pre style="margin: 0;">-<span id="LC882" class="line" lang="html">C_1 gi|7 9913 4225 4225 80 2</span>
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<pre style="margin: 0;">-<span id="LC883" class="line" lang="html">C_1 gi|4 9646 4225 4225 80 2</span>
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<pre style="margin: 0;">-<span id="LC884" class="line" lang="html">C_2 gi|4 9646 4225 4225 80 2</span>
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<pre style="margin: 0;">-<span id="LC886" class="line" lang="html">C_3 gi|7 9913 4225 4225 80 2</span>
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<pre style="margin: 0;">-<span id="LC888" class="line" lang="html">C_4 gi|4 9646 4225 4225 80 2</span>
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<pre style="margin: 0;">-<span id="LC890" class="line" lang="html">1_1 gi|4 9646 4225 0 80 1</span>
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<pre style="margin: 0;">-<span id="LC892" class="line" lang="html">2_1 gi|7 9913 4225 0 80 1</span>
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<pre style="margin: 0;">-<span id="LC894" class="line" lang="html">2_3 gi|7 9913 4225 0 80 1</span>
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<pre style="margin: 0;">-<span id="LC895" class="line" lang="html">2_4 gi|7 9913 4225 0 80 1</span>
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<pre style="margin: 0;">-<span id="LC896" class="line" lang="html">2_5 gi|7 9913 4225 0 80 1</span>
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<pre style="margin: 0;">-<span id="LC897" class="line" lang="html">2_6 gi|7 9913 4225 0 80 1<span class="nt" style="color: navy;"></code></pre></span></span></pre>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> <table width="100%"><tr><td>last updated:</td> <td align="right">12/06/2016</td></tr></span>
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"> <td></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed.tar.gz"><i> Bacteria (compressed)</i></a></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed.tar.gz"><i> Bacteria<span class="idiff left right">, Archaea</span> (compressed)</i></a></span>
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56
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"> </td></span>
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57
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"> <td align="right" style="font-size: x-small"></span>
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58
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> <b>4.4 GB</b></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -60,7 +60,7 @@</td>
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60
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61
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61
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"> <td></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz"><i> Bacteria, Viruses, Human (compressed)</i></a></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz"><i> Bacteria, <span class="idiff left right">Archaea, </span>Viruses, Human (compressed)</i></a></span>
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64
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"> </td></span>
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65
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> <td align="right" style="font-size: x-small"></span>
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66
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"> <b>5.4 GB</b></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -68,7 +68,7 @@</td>
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68
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68
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69
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69
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70
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"> <td></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p+h+v.tar.gz"><i> Bacteria, Viruses, Human </i></a></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p+h+v.tar.gz"><i> Bacteria, <span class="idiff left right">Aarchaea, </span>Viruses, Human </i></a></span>
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72
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"> </td></span>
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<td class="diff-line-num old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
73
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"> <td align="right" style="font-size: x-small"></span>
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<td class="diff-line-num old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
74
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<td class="diff-line-num new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"> <b>7.9 GB</b></span>
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<br>
</li>
<li id="aed90a934a04d9a3fa5df8eecf57722bbc05a662">
<a href="https://salsa.debian.org/med-team/centrifuge/commit/f6f7b098137879381ca6b18e3e5ba7c4c327171f#aed90a934a04d9a3fa5df8eecf57722bbc05a662"><strong>indices/Makefile</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,6 +11,7 @@ KEEP_FILES?=0</td>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"><span class="nv" style="color: teal;">get_ref_file_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>addprefix <span class="nv" style="color: teal;">$(REFERENCE_SEQUENCES_DIR)</span>/, <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>addsuffix <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>1<span class="o" style="font-weight: 600;">)</span>, <span class="se" style="color: #d14;">\</span></span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>addprefix all-,<span class="nv" style="color: teal;">$(COMPLETE_GENOMES)</span><span class="o" style="font-weight: 600;">)</span> <span class="se" style="color: #d14;">\</span></span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>addprefix all-,<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>addsuffix <span class="nt" style="color: navy;">-chromosome_level</span>,<span class="nv" style="color: teal;">$(CHROMOSOME_LEVEL_GENOMES)</span><span class="o" style="font-weight: 600;">))</span> <span class="se" style="color: #d14;">\</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>addprefix all-,<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>addsuffix <span class="nt" style="color: navy;">-any_level</span>,<span class="nv" style="color: teal;">$(ANY_LEVEL_GENOMES)</span><span class="o" style="font-weight: 600;">))</span> <span class="se" style="color: #d14;">\</span></span>
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14
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>addprefix mammalian-reference-,<span class="nv" style="color: teal;">$(MAMMALIAN_TAXIDS)</span><span class="o" style="font-weight: 600;">)</span> <span class="se" style="color: #d14;">\</span></span>
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15
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>addprefix all-compressed-,<span class="nv" style="color: teal;">$(COMPLETE_GENOMES_COMPRESSED)</span><span class="o" style="font-weight: 600;">)</span> <span class="se" style="color: #d14;">\</span></span>
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16
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: teal;">$(INCLUDE_CONTAMINANTS)</span>,contaminants<span class="o" style="font-weight: 600;">)))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -43,6 +44,10 @@ STANDARD TARGETS:</td>
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43
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">p+h+v</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">As</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">above,</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">but</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">with</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">uncompressed</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">bacterial</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">genomes</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">p+v</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="make"></span>
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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">v</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="make"></span>
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46
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<td class="diff-line-num new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">Alternatively,</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">a</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">IDX_NAME</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">and</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">one</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">or</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">more</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">genomes</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">may</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">be</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">specified</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">as</span></span>
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47
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<td class="diff-line-num new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">options</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">to</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">build</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">a</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">custom</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">database.</span></span>
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48
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="make"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,12 +66,12 @@ EXAMPLES:</td>
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61
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="make"></span>
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62
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<td class="diff-line-num new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># same as:</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">make</span> <span class="nv" style="color: teal;">COMPLETE_GENOMES</span><span class="o" style="font-weight: 600;">=</span>archaea <span class="nv" style="color: teal;">COMPLETE_GENOMES_COMPRESSED</span><span class="o" style="font-weight: 600;">=</span>bacteria <span class="nv" style="color: teal;">IDX_NAME</span><span class="o" style="font-weight: 600;">=</span>p_compressed</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="make"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># Make an index with just the human genome</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">make</span> <span class="nv" style="color: teal;">IDX_NAME</span><span class="o" style="font-weight: 600;">=</span>h <span class="nv" style="color: teal;">MAMMALIAN_TAXIDS</span><span class="o" style="font-weight: 600;">=</span>9606</span>
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># All archaeal genomes and contaminant sequences from UniVec and EmVec</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">make</span> <span class="nv" style="color: teal;">IDX_NAME</span><span class="o" style="font-weight: 600;">=</span>a <span class="nv" style="color: teal;">COMPLETE_GENOMES</span><span class="o" style="font-weight: 600;">=</span>archaea <span class="nv" style="color: teal;">INCLUDE_CONTAMINANTS</span><span class="o" style="font-weight: 600;">=</span>1<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">make</span> <span class="nv" style="color: teal;">IDX_NAME</span><span class="o" style="font-weight: 600;">=</span>a <span class="nv" style="color: teal;">COMPLETE_GENOMES</span><span class="o" style="font-weight: 600;">=</span>archaea <span class="nv" style="color: teal;">INCLUDE_CONTAMINANTS</span><span class="o" style="font-weight: 600;">=</span>1</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endef</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="make"><span class="k" style="font-weight: 600;">export</span> <span class="nv" style="color: teal;">USAGE</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -74,30 +79,42 @@ export USAGE</td>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">###################################################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifndef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">IDX_NAME</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$$</span><span class="s2" style="color: #d14;">USAGE"</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="make"><span class="nv" style="color: teal;">IDX_NAME</span><span class="o" style="font-weight: 600;">?=</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> basename <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> dirname <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>abspath <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>lastword <span class="nv" style="color: teal;">$(MAKEFILE_LIST)))))</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="make"><span class="nv" style="color: teal;">INDICES</span><span class="o" style="font-weight: 600;">=</span>p+h+v p_compressed p_compressed+h+v refseq_microbial refseq_full nt</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="make"><span class="nv" style="color: teal;">INDICES</span><span class="o" style="font-weight: 600;">=</span>p+h+v p<span class="idiff left right">+v v p p</span>_compressed p_compressed+h+v refseq_microbial refseq_full nt</span>
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83
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="make"></span>
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84
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<td class="diff-line-num new_line old" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="make"><span class="nl">p+h+v</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export COMPLETE_GENOMES:=archaea bacteria viral</span></span>
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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="make"><span class="nl">p+h+v</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export ANY_LEVEL_GENOMES:=viral</span></span>
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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="make"><span class="nl">p+h+v</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export COMPLETE_GENOMES:=archaea bacteria</span></span>
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85
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<td class="diff-line-num new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="make"><span class="nl">p+h+v</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export MAMMALIAN_TAXIDS:=9606</span></span>
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86
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<td class="diff-line-num new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="make"><span class="nl">p+h+v</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export INCLUDE_CONTAMINANTS:=1</span></span>
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87
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<td class="diff-line-num new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="make"><span class="nl">p+h+v</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export IDX_NAME:=p+h+v</span></span>
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88
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="make"></span>
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89
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<td class="diff-line-num new_line old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="make"><span class="nl">p_compressed</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export COMPLETE_GENOMES:=</span></span>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="make"><span class="nl">p+v</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export ANY_LEVEL_GENOMES:=viral</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="make"><span class="nl">p+v</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export COMPLETE_GENOMES:=archaea bacteria</span></span>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="make"><span class="nl">p+v</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export INCLUDE_CONTAMINANTS:=1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="make"><span class="nl">p+v</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export IDX_NAME:=p+v</span></span>
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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="make"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="make"><span class="nl">v</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export ANY_LEVEL_GENOMES:=viral</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="make"><span class="nl">v</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export IDX_NAME:=v</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="make"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="make"><span class="nl">p</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export COMPLETE_GENOMES:=archaea bacteria</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="make"><span class="nl">p</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export IDX_NAME:=p</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="make"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
90
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<td class="diff-line-num new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="make"><span class="nl">p_compressed</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export COMPLETE_GENOMES_COMPRESSED:=archaea bacteria</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
91
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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="make"><span class="nl">p_compressed</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export IDX_NAME:=p_compressed</span></span>
</pre>
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92
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="make"></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="make"><span class="nl">p_compressed+h+v</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export <span class="idiff left right">COMPLETE</span>_GENOMES:=viral</span></span>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="make"><span class="nl">p_compressed+h+v</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export <span class="idiff left right">ANY_LEVEL</span>_GENOMES:=viral</span></span>
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94
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<td class="diff-line-num new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="make"><span class="nl">p_compressed+h+v</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export COMPLETE_GENOMES_COMPRESSED:=archaea bacteria</span></span>
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95
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="make"><span class="nl">p_compressed+h+v</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export MAMMALIAN_TAXIDS:=9606</span></span>
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96
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="make"><span class="nl">p_compressed+h+v</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export INCLUDE_CONTAMINANTS:=1</span></span>
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97
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="make"><span class="nl">p_compressed+h+v</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export IDX_NAME:=p_compressed+h+v</span></span>
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98
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="make"></span>
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99
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<td class="diff-line-num new_line old" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="make"><span class="nl">refseq_microbial</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export COMPLETE_GENOMES:=archaea bacteria fungi protozoa<span class="idiff left right"> viral</span></span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="make"><span class="nl">refseq_microbial</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export COMPLETE_GENOMES:=archaea bacteria fungi protozoa</span></span>
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100
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<td class="diff-line-num new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="make"><span class="nl">refseq_microbial</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export CHROMOSOME_LEVEL_GENOMES:=$(COMPLETE_GENOMES)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="make"><span class="nl">refseq_microbial</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export ANY_LEVEL_GENOMES:=viral</span></span>
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101
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">##refseq_microbial: export SMALL_GENOMES:=mitochondrion plasmid plastid # TODO</span></span>
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102
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<td class="diff-line-num new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="make"><span class="nl">refseq_microbial</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export MAMMALIAN_TAXIDS:=9606 10090</span></span>
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<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
103
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="make"><span class="nl">refseq_microbial</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export INCLUDE_CONTAMINANTS:=1</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -106,6 +123,7 @@ refseq_microbial: export CF_BUILD_OPTS+=--ftabchars 14</td>
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106
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="make"></span>
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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
107
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<td class="diff-line-num new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="make"><span class="nl">refseq_full</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export COMPLETE_GENOMES:=archaea bacteria fungi invertebrate plant protozoa vertebrate_mammalian vertebrate_other viral</span></span>
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<td class="diff-line-num old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
108
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<td class="diff-line-num new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="make"><span class="nl">refseq_full</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export CHROMOSOME_LEVEL_GENOMES:=$(COMPLETE_GENOMES)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="make"><span class="nl">refseq_full</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export ANY_LEVEL_GENOMES:=viral</span></span>
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<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
109
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<td class="diff-line-num new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="make"><span class="nl">refseq_full</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export SMALL_GENOMES:=mitochondrion plasmid plastid</span></span>
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110
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<td class="diff-line-num new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="make"><span class="nl">refseq_full</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export MAMMALIAN_TAXIDS:=9606 10090</span></span>
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<td class="diff-line-num old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
111
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<td class="diff-line-num new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="make"><span class="nl">refseq_full</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">export INCLUDE_CONTAMINANTS:=1</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -125,7 +143,7 @@ DONT_DUSTMASK=</td>
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125
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="make"><span class="nv" style="color: teal;">TAXONOMY_DOWNLOAD_OPTS</span><span class="o" style="font-weight: 600;">?=</span></span>
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126
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<td class="diff-line-num new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="make"><span class="nv" style="color: teal;">REFERENCE_SEQUENCES</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>call get_ref_file_names,.fna<span class="o" style="font-weight: 600;">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
127
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<td class="diff-line-num new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="make"><span class="nv" style="color: teal;">TAXID_MAPS</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>call get_ref_file_names,<span class="nv" style="color: teal;">$(TAXID_SUFFIX)</span><span class="o" style="font-weight: 600;">)</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="make"><span class="nv" style="color: teal;">CF_BUILD_OPTS</span><span class="o" style="font-weight: 600;">?=</span><span class="idiff left right"> </span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="make"><span class="nv" style="color: teal;">CF_BUILD_OPTS</span><span class="o" style="font-weight: 600;">?=</span></span>
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129
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<td class="diff-line-num new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="make"></span>
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130
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<td class="diff-line-num new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(nt,$(IDX_NAME))</span></span>
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131
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<td class="diff-line-num new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($(strip</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DONT_DUSTMASK)),)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -196,7 +214,7 @@ $(REFERENCE_SEQUENCES_DIR)/mammalian-reference-%.fna: | $(REFERENCE_SEQUENCES_DI</td>
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196
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<td class="diff-line-num new_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="make"> <span class="p">@</span><span class="o" style="font-weight: 600;">[[</span> <span class="nt" style="color: navy;">-d</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span> <span class="o" style="font-weight: 600;">]]</span> <span class="o" style="font-weight: 600;">&&</span> rm <span class="nt" style="color: navy;">-rf</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span><span class="p">;</span> mkdir <span class="nt" style="color: navy;">-p</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span></span>
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<td class="diff-line-num old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
197
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<td class="diff-line-num new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="make"> centrifuge-download <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span> <span class="nt" style="color: navy;">-d</span> <span class="s2" style="color: #d14;">"vertebrate_mammalian"</span> <span class="nt" style="color: navy;">-a</span> <span class="s2" style="color: #d14;">"Chromosome"</span> <span class="nt" style="color: navy;">-t</span> <span class="nv" style="color: teal;">$*</span> <span class="nt" style="color: navy;">-c</span> <span class="s1" style="color: #d14;">'reference genome'</span> <span class="nt" style="color: navy;">-P</span> <span class="nv" style="color: teal;">$(THREADS)</span> refseq <span class="o" style="font-weight: 600;">></span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
198
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<td class="diff-line-num new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="make"> <span class="nv" style="color: teal;">$(TMP_DIR)</span>/<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %.fna,%<span class="nv" style="color: teal;">$(TAXID_SUFFIX)</span>, <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>notdir <span class="nv" style="color: teal;">$@</span><span class="o" style="font-weight: 600;">))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
199
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<td class="diff-line-num new_line old" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">cat</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$(TMP_DIR)</span></span><span class="idiff">/vertebrate_mammalian/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff right">.fna</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$@</span>.tmp <span class="o" style="font-weight: 600;">&&</span> mv <span class="nv" style="color: teal;">$@</span>.tmp <span class="nv" style="color: teal;">$@</span></span>
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<td class="diff-line-num new old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="make"> <span class="idiff left">find </span><span class="nv" style="color: teal;"><span class="idiff">$(TMP_DIR)</span></span><span class="idiff">/vertebrate_mammalian </span><span class="nt" style="color: navy;"><span class="idiff">-name</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"*.fna"</span></span><span class="idiff"> | xargs </span><span class="nb" style="color: #0086b3;"><span class="idiff right">cat</span></span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$@</span>.tmp <span class="o" style="font-weight: 600;">&&</span> mv <span class="nv" style="color: teal;">$@</span>.tmp <span class="nv" style="color: teal;">$@</span></span>
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200
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<td class="diff-line-num new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="make"> mv <span class="nv" style="color: teal;">$(TMP_DIR)</span>/<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %.fna,%<span class="nv" style="color: teal;">$(TAXID_SUFFIX)</span>,<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>notdir <span class="nv" style="color: teal;">$@</span><span class="o" style="font-weight: 600;">))</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %.fna,%<span class="nv" style="color: teal;">$(TAXID_SUFFIX)</span>,<span class="nv" style="color: teal;">$@</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
201
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<td class="diff-line-num new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
219
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(1,$(KEEP_FILES))</span></span>
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<td class="diff-line-num old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
202
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<td class="diff-line-num new_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
220
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">[[</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-d</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DL_DIR)/vertebrate_mammalian</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">]]</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">||</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">mkdir</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-p</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DL_DIR)/vertebrate_mammalian</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -219,12 +237,12 @@ else</td>
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">rm</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-rf</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(TMP_DIR)</span></span>
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220
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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221
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239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="make"></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="make"><span class="nl">$(REFERENCE_SEQUENCES_DIR)/all-%.fna</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">| $(REFERENCE_SEQUENCES_DIR) .dustmasker-ok</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="make"><span class="nl">$(REFERENCE_SEQUENCES_DIR)/all-%<span class="idiff left right">-chromosome_level</span>.fna</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">| $(REFERENCE_SEQUENCES_DIR) .dustmasker-ok</span></span>
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223
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="make"> <span class="o" style="font-weight: 600;">[[</span> <span class="nt" style="color: navy;">-d</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span> <span class="o" style="font-weight: 600;">]]</span> <span class="o" style="font-weight: 600;">&&</span> rm <span class="nt" style="color: navy;">-rf</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span><span class="p">;</span> mkdir <span class="nt" style="color: navy;">-p</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span></span>
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224
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo </span>Downloading and dust-masking <span class="nv" style="color: teal;">$*</span></span>
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225
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="make"> centrifuge-download <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span> <span class="nv" style="color: teal;">$(CF_DOWNLOAD_OPTS)</span> <span class="nt" style="color: navy;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$*</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-P</span> <span class="nv" style="color: teal;">$(THREADS)</span> refseq <span class="o" style="font-weight: 600;">></span> <span class="se" style="color: #d14;">\</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="make"> centrifuge-download <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span> <span class="nv" style="color: teal;">$(CF_DOWNLOAD_OPTS)</span> <span class="nt" style="color: navy;">-<span class="idiff left">a</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"Chromosome"</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff right">-</span>d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$*</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-P</span> <span class="nv" style="color: teal;">$(THREADS)</span> refseq <span class="o" style="font-weight: 600;">></span> <span class="se" style="color: #d14;">\</span></span>
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226
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="make"> <span class="nv" style="color: teal;">$(TMP_DIR)</span>/<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %.fna,%<span class="nv" style="color: teal;">$(TAXID_SUFFIX)</span>,<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>notdir <span class="nv" style="color: teal;">$@</span><span class="o" style="font-weight: 600;">))</span></span>
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227
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">cat</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$(TMP_DIR)</span></span><span class="idiff">/</span><span class="nv" style="color: teal;"><span class="idiff">$*</span></span><span class="idiff">/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff right">.fna</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$@</span>.tmp <span class="o" style="font-weight: 600;">&&</span> mv <span class="nv" style="color: teal;">$@</span>.tmp <span class="nv" style="color: teal;">$@</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="make"> <span class="idiff left">find </span><span class="nv" style="color: teal;"><span class="idiff">$(TMP_DIR)</span></span><span class="idiff">/</span><span class="nv" style="color: teal;"><span class="idiff">$*</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-name</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"*.fna"</span></span><span class="idiff"> | xargs </span><span class="nb" style="color: #0086b3;"><span class="idiff right">cat</span></span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$@</span>.tmp <span class="o" style="font-weight: 600;">&&</span> mv <span class="nv" style="color: teal;">$@</span>.tmp <span class="nv" style="color: teal;">$@</span></span>
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228
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<td class="diff-line-num new_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="make"> mv <span class="nv" style="color: teal;">$(TMP_DIR)</span>/<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %.fna,%<span class="nv" style="color: teal;">$(TAXID_SUFFIX)</span>,<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>notdir <span class="nv" style="color: teal;">$@</span><span class="o" style="font-weight: 600;">))</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %.fna,%<span class="nv" style="color: teal;">$(TAXID_SUFFIX)</span>,<span class="nv" style="color: teal;">$@</span><span class="o" style="font-weight: 600;">)</span></span>
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229
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(1,$(KEEP_FILES))</span></span>
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230
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<td class="diff-line-num new_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">[[</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-d</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DL_DIR)/$*</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">]]</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">||</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">mkdir</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-p</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DL_DIR)/$*</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -233,12 +251,12 @@ else</td>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">rm</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-rf</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(TMP_DIR)</span></span>
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234
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252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="make"></span>
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236
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="make"><span class="nl">$(REFERENCE_SEQUENCES_DIR)/all-%-<span class="idiff left right">chromosome</span>_level.fna</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">| $(REFERENCE_SEQUENCES_DIR) .dustmasker-ok</span></span>
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<td class="diff-line-num new old_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="make"><span class="nl">$(REFERENCE_SEQUENCES_DIR)/all-%-<span class="idiff left right">any</span>_level.fna</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">| $(REFERENCE_SEQUENCES_DIR) .dustmasker-ok</span></span>
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237
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="make"> <span class="o" style="font-weight: 600;">[[</span> <span class="nt" style="color: navy;">-d</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span> <span class="o" style="font-weight: 600;">]]</span> <span class="o" style="font-weight: 600;">&&</span> rm <span class="nt" style="color: navy;">-rf</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span><span class="p">;</span> mkdir <span class="nt" style="color: navy;">-p</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span></span>
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238
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<td class="diff-line-num new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo </span>Downloading and dust-masking <span class="nv" style="color: teal;">$*</span></span>
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<td class="diff-line-num old old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
239
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<td class="diff-line-num new_line old" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="make"> centrifuge-download <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span> <span class="nv" style="color: teal;">$(CF_DOWNLOAD_OPTS)</span> <span class="nt" style="color: navy;">-a</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">Chromosome</span>"</span> <span class="nt" style="color: navy;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$*</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-P</span> <span class="nv" style="color: teal;">$(THREADS)</span> refseq <span class="o" style="font-weight: 600;">></span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="make"> centrifuge-download <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span> <span class="nv" style="color: teal;">$(CF_DOWNLOAD_OPTS)</span> <span class="nt" style="color: navy;">-a</span> <span class="s2" style="color: #d14;">"<span class="idiff left right">Any</span>"</span> <span class="nt" style="color: navy;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$*</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-P</span> <span class="nv" style="color: teal;">$(THREADS)</span> refseq <span class="o" style="font-weight: 600;">></span> <span class="se" style="color: #d14;">\</span></span>
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240
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<td class="diff-line-num new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="make"> <span class="nv" style="color: teal;">$(TMP_DIR)</span>/<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %.fna,%<span class="nv" style="color: teal;">$(TAXID_SUFFIX)</span>,<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>notdir <span class="nv" style="color: teal;">$@</span><span class="o" style="font-weight: 600;">))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
241
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">cat</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$(TMP_DIR)</span></span><span class="idiff">/</span><span class="nv" style="color: teal;"><span class="idiff">$*</span></span><span class="idiff">/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff right">.fna</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$@</span>.tmp <span class="o" style="font-weight: 600;">&&</span> mv <span class="nv" style="color: teal;">$@</span>.tmp <span class="nv" style="color: teal;">$@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="make"> <span class="idiff left">find </span><span class="nv" style="color: teal;"><span class="idiff">$(TMP_DIR)</span></span><span class="idiff">/</span><span class="nv" style="color: teal;"><span class="idiff">$*</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-name</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"*.fna"</span></span><span class="idiff"> | xargs </span><span class="nb" style="color: #0086b3;"><span class="idiff right">cat</span></span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$@</span>.tmp <span class="o" style="font-weight: 600;">&&</span> mv <span class="nv" style="color: teal;">$@</span>.tmp <span class="nv" style="color: teal;">$@</span></span>
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242
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<td class="diff-line-num new_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="make"> mv <span class="nv" style="color: teal;">$(TMP_DIR)</span>/<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %.fna,%<span class="nv" style="color: teal;">$(TAXID_SUFFIX)</span>,<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>notdir <span class="nv" style="color: teal;">$@</span><span class="o" style="font-weight: 600;">))</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %.fna,%<span class="nv" style="color: teal;">$(TAXID_SUFFIX)</span>,<span class="nv" style="color: teal;">$@</span><span class="o" style="font-weight: 600;">)</span></span>
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243
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(1,$(KEEP_FILES))</span></span>
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244
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<td class="diff-line-num new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">[[</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-d</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DL_DIR)/$*</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">]]</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">||</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">mkdir</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-p</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DL_DIR)/$*</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -247,12 +265,24 @@ else</td>
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247
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">rm</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-rf</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(TMP_DIR)</span></span>
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248
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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249
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="make"></span>
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250
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="make"></span>
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="make"><span class="nl">$(REFERENCE_SEQUENCES_DIR)/all-%.fna</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">| $(REFERENCE_SEQUENCES_DIR) .dustmasker-ok</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="make"> <span class="o" style="font-weight: 600;">[[</span> <span class="nt" style="color: navy;">-d</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span> <span class="o" style="font-weight: 600;">]]</span> <span class="o" style="font-weight: 600;">&&</span> rm <span class="nt" style="color: navy;">-rf</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span><span class="p">;</span> mkdir <span class="nt" style="color: navy;">-p</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo </span>Downloading and dust-masking <span class="nv" style="color: teal;">$*</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="make"> centrifuge-download <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span> <span class="nv" style="color: teal;">$(CF_DOWNLOAD_OPTS)</span> <span class="nt" style="color: navy;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$*</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-P</span> <span class="nv" style="color: teal;">$(THREADS)</span> refseq <span class="o" style="font-weight: 600;">></span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="make"> <span class="nv" style="color: teal;">$(TMP_DIR)</span>/<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %.fna,%<span class="nv" style="color: teal;">$(TAXID_SUFFIX)</span>,<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>notdir <span class="nv" style="color: teal;">$@</span><span class="o" style="font-weight: 600;">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="make"> find <span class="nv" style="color: teal;">$(TMP_DIR)</span>/<span class="nv" style="color: teal;">$*</span> <span class="nt" style="color: navy;">-name</span> <span class="s2" style="color: #d14;">"*.fna"</span> | xargs <span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$@</span>.tmp <span class="o" style="font-weight: 600;">&&</span> mv <span class="nv" style="color: teal;">$@</span>.tmp <span class="nv" style="color: teal;">$@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="make"> mv <span class="nv" style="color: teal;">$(TMP_DIR)</span>/<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %.fna,%<span class="nv" style="color: teal;">$(TAXID_SUFFIX)</span>,<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>notdir <span class="nv" style="color: teal;">$@</span><span class="o" style="font-weight: 600;">))</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %.fna,%<span class="nv" style="color: teal;">$(TAXID_SUFFIX)</span>,<span class="nv" style="color: teal;">$@</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(1,$(KEEP_FILES))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">[[</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-d</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DL_DIR)/$*</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">]]</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">||</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">mkdir</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-p</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DL_DIR)/$*</span></span>
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<td class="diff-line-num new new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">mv</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(TMP_DIR)/$*/*</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DL_DIR)/$*</span></span>
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<td class="diff-line-num new new_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">rm</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-rf</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(TMP_DIR)</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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251
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<td class="diff-line-num new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="make"></span>
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252
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="make"><span class="nl">$(REFERENCE_SEQUENCES_DIR)/contaminants.fna</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">| $(REFERENCE_SEQUENCES_DIR)</span></span>
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253
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<td class="diff-line-num new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="make"> <span class="o" style="font-weight: 600;">[[</span> <span class="nt" style="color: navy;">-d</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span> <span class="o" style="font-weight: 600;">]]</span> <span class="o" style="font-weight: 600;">&&</span> rm <span class="nt" style="color: navy;">-rf</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span><span class="p">;</span> mkdir <span class="nt" style="color: navy;">-p</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span></span>
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254
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<td class="diff-line-num new_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="make"> centrifuge-download <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$(TMP_DIR)</span> contaminants <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$(TMP_DIR)</span>/<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %.fna,%<span class="nv" style="color: teal;">$(TAXID_SUFFIX)</span>,<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>notdir <span class="nv" style="color: teal;">$@</span><span class="o" style="font-weight: 600;">))</span></span>
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255
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<td class="diff-line-num new_line old" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">cat</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$(TMP_DIR)</span></span><span class="idiff">/contaminants/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff right">.fna</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$@</span>.tmp <span class="o" style="font-weight: 600;">&&</span> mv <span class="nv" style="color: teal;">$@</span>.tmp <span class="nv" style="color: teal;">$@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="make"> <span class="idiff left">find </span><span class="nv" style="color: teal;"><span class="idiff">$(TMP_DIR)</span></span><span class="idiff">/contaminants </span><span class="nt" style="color: navy;"><span class="idiff">-name</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"*.fna"</span></span><span class="idiff"> | xargs </span><span class="nb" style="color: #0086b3;"><span class="idiff right">cat</span></span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$@</span>.tmp <span class="o" style="font-weight: 600;">&&</span> mv <span class="nv" style="color: teal;">$@</span>.tmp <span class="nv" style="color: teal;">$@</span></span>
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256
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="make"> mv <span class="nv" style="color: teal;">$(TMP_DIR)</span>/<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %.fna,%<span class="nv" style="color: teal;">$(TAXID_SUFFIX)</span>,<span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>notdir <span class="nv" style="color: teal;">$@</span><span class="o" style="font-weight: 600;">))</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %.fna,%<span class="nv" style="color: teal;">$(TAXID_SUFFIX)</span>,<span class="nv" style="color: teal;">$@</span><span class="o" style="font-weight: 600;">)</span></span>
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257
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(1,$(KEEP_FILES))</span></span>
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258
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<td class="diff-line-num new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">[[</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-d</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DL_DIR)/contaminants</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">]]</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">||</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">mkdir</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-p</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DL_DIR)/contaminants</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -268,7 +298,7 @@ ifeq ($(strip $(DONT_DUSTMASK)),)</td>
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<td class="diff-line-num old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
268
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<td class="diff-line-num new_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(error</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">dustmasker</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">program</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">does</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">not</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">exist.</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">Install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">NCBI</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">blast+,</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">or</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">set</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">option</span> <span class="nv" style="color: teal;">DONT_DUSTMASK</span><span class="o" style="font-weight: 600;">=</span>1<span class="o" style="font-weight: 600;">)</span></span>
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269
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299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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270
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300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="make"><span class="idiff left right"> </span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="make"></span>
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272
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="make"></span>
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273
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="make"><span class="nl">taxonomy/names.dmp</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">taxonomy/nodes.dmp</span></span>
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274
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="make"><span class="nl">taxonomy/nodes.dmp</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">| .path-ok</span></span>
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