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<h3>
Liubov Chuprikova pushed to branch master
at <a href="https://salsa.debian.org/med-team/ncbi-tools6">Debian Med / ncbi-tools6</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/474ec7bc5c3143d71ae53ead5ba94bdebe96cf46">474ec7bc</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2018-04-12T12:32:51+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopkgtest: improved one test, amended README.test
</pre>
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
debian/README.test
</a>
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/474ec7bc5c3143d71ae53ead5ba94bdebe96cf46#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" 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">@@ -3,6 +3,6 @@ _______________________________________</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="php"></span>
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<td class="diff-line-num new_line" data-linenumber="4" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">execution</span></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="php"></span>
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<td class="diff-line-num old old_line" data-linenumber="6" 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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<td class="diff-line-num new_line old" data-linenumber="6" 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="LC6" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="nx"><span class="idiff left right">ba</span>sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="php"></span>
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<td class="diff-line-num old_line" data-linenumber="8" 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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<td class="diff-line-num new_line" data-linenumber="8" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span></pre>
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<br>
</li>
<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/474ec7bc5c3143d71ae53ead5ba94bdebe96cf46#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" 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="14" 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">@@ -14,6 +14,13 @@ cp /usr/share/ncbi/data/autofix.prt .</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell">cp /usr/share/ncbi/data/UniVec.<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell">gunzip <span class="k" style="font-weight: 600;">*</span>.gz</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">check_GI<span class="o" style="font-weight: 600;">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" 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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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="k" style="font-weight: 600;">while </span><span class="nb" style="color: #0086b3;">read </span>GI<span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-q</span> <span class="nv" style="color: teal;">$GI</span> <span class="nv" style="color: teal;">$1</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"> <span class="k" style="font-weight: 600;">done</span> < <span class="nv" style="color: teal;">$2</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---asn2asn test---'</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -59,6 +66,15 @@ gbk="$(grep -c "^LOCUS " nc0225.gbk)"</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$genes</span> <span class="nt" style="color: navy;">-eq</span> <span class="nv" style="color: teal;">$gbk</span> <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---asn2idx test---'</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell">/usr/bin/asn2idx <span class="nt" style="color: navy;">-p</span> <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: navy;">-x</span> .text < nc0225.text</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> nc0225.idx <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> master.idx <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell">awk <span class="s1" style="color: #d14;">'NR == 1 || NR % 50 == 0 {print $1}'</span> nc0225.idx | sed <span class="s1" style="color: #d14;">'s/\.1//'</span> <span class="o" style="font-weight: 600;">></span> indexed_GIs</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell">check_GI nc0225.text indexed_GIs</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---asn2xml test---'</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="shell">/usr/bin/asn2xml <span class="nt" style="color: navy;">-i</span> nc0225.text <span class="nt" style="color: navy;">-b</span> F <span class="nt" style="color: navy;">-o</span> nc0225.xml</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -100,12 +116,6 @@ end_out="$(grep -c "<Object-id_id>${last_id}</Object-id_id>" dsRNA_viruses.xgs)"</td>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># _insdseqget_ and _idfetch_ testing requires internet connection.</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Comment the lines below to skip the testing.</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="shell"><span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'GI:'</span> nc0225.gbk | head | sed <span class="s1" style="color: #d14;">'s/.*GI://'</span> <span class="o" style="font-weight: 600;">></span> GIs.txt</span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="shell">check_GI<span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="shell"> <span class="k" style="font-weight: 600;">while </span><span class="nb" style="color: #0086b3;">read </span>GI<span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-q</span> <span class="nv" style="color: teal;">$GI</span> <span class="nv" style="color: teal;">$1</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="shell"> <span class="k" style="font-weight: 600;">done</span> < <span class="nv" style="color: teal;">$2</span></span>
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<td class="diff-line-num old old_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</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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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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110
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---insdseqget test---'</span></span>
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111
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##################################################################</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="130" 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="140" 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">@@ -130,11 +140,6 @@ last_out="$(grep ">" vecscreen.output | tail -1 | sed 's/>Vector //' | sed 's/ .</td>
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130
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$last_in</span><span class="o" style="font-weight: 600;">==</span><span class="nv" style="color: teal;">$last_out</span> <span class="o" style="font-weight: 600;">]</span></span>
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131
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="shell"></span>
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="133" 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="LC133" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---asn2idx test---'</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="shell">/usr/bin/asn2idx <span class="nt" style="color: navy;">-p</span> <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: navy;">-x</span> .text < nc0225.text</span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> nc0225.idx <span class="o" style="font-weight: 600;">]</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> master.idx <span class="o" style="font-weight: 600;">]</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="shell"></span>
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138
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---asndisc test---'</span></span>
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139
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="shell">/usr/bin/asndisc <span class="nt" style="color: navy;">-i</span> nc0225.text <span class="nt" style="color: navy;">-a</span> t <span class="nt" style="color: navy;">-o</span> nc0225.disc</span>
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140
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> nc0225.disc <span class="o" style="font-weight: 600;">]</span></span>
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