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<h3>
Michael R. Crusoe pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/lambda-align">Debian Med / lambda-align</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/lambda-align/commit/142f48e49a0036a7836f9afdd24d666432a6c95e">142f48e4</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2018-02-17T09:30:44-08:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.3</pre>
</li>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7be417b8ea0a866946b052f8b0de545ebdaf48b3">
src/holders.hpp
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<li class="file-stats">
<a href="#7552499545cad9fe761b98d5142c0e067cda8faf">
src/options.hpp
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<h4>Changes:</h4>
<li id="7be417b8ea0a866946b052f8b0de545ebdaf48b3">
<a href="https://salsa.debian.org/med-team/lambda-align/commit/142f48e49a0036a7836f9afdd24d666432a6c95e#7be417b8ea0a866946b052f8b0de545ebdaf48b3"><strong>src/holders.hpp</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">@@ -385,7 +385,16 @@ public:</td>
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="cpp"> <span class="n" style="color: #333;">ArrayGaps</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TAlignRow1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Gaps</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">Infix</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">Value</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TGlobalHolder</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TTransSubjSeqs</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Type</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Type</span><span class="p">,</span></span>
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387
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp"> <span class="n" style="color: #333;">ArrayGaps</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TDPContext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DPContext</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">Value</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TGlobalHolder</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TScoreScheme</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Type</span><span class="p">,</span> <span class="n" style="color: #333;">TScoreExtension</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="388" 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">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if (SEQAN_VERSION_MINOR < 4)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="389" 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">
389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TDPContext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DPContext</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">Value</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TGlobalHolder</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TScoreScheme</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Type</span><span class="p">,</span> <span class="n" style="color: #333;">TScoreExtension</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="390" 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">
390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="391" 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">
391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TCellValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="392" 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">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TDPCell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DPCell_</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TCellValue</span><span class="p">,</span> <span class="n" style="color: #333;">TScoreExtension</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="393" 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">
393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TTraceValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TraceBitMap_</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TCellValue</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">Type</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="394" 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">
394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TScoreHost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TDPCell</span><span class="p">,</span> <span class="n" style="color: #333;">Alloc</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">OverAligned</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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<td class="diff-line-num new new_line" data-linenumber="395" 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">
395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TTraceHost</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TTraceValue</span><span class="p">,</span> <span class="n" style="color: #333;">Alloc</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">OverAligned</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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<td class="diff-line-num new new_line" data-linenumber="396" 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">
396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TDPContext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DPContext</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TDPCell</span><span class="p">,</span> <span class="n" style="color: #333;">TTraceValue</span><span class="p">,</span> <span class="n" style="color: #333;">TScoreHost</span><span class="p">,</span> <span class="n" style="color: #333;">TTraceHost</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="397" 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">
397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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389
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">TAliExtContext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AliExtContext_</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TAlignRow0</span><span class="p">,</span> <span class="n" style="color: #333;">TAlignRow1</span><span class="p">,</span> <span class="n" style="color: #333;">TDPContext</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>
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390
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="cpp"> <span class="n" style="color: #333;">TAliExtContext</span> <span class="n" style="color: #333;">alignContext</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/lambda-align/commit/142f48e49a0036a7836f9afdd24d666432a6c95e#7552499545cad9fe761b98d5142c0e067cda8faf"><strong>src/options.hpp</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">@@ -420,14 +420,14 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)</td>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Query sequences."</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="cpp"> <span class="n" style="color: #333;">ArgParseArgument</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INPUT_FILE</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="cpp"> <span class="s" style="color: #d14;">"IN"</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="cpp"> <span class="n" style="color: #333;">setValidValues</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"query"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">toCString</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">concat</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">getFileExtensions</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">SeqFileIn</span></span><span class="p"><span class="idiff">()),</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff right">' '</span></span><span class="p">)));</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="cpp"> <span class="n" style="color: #333;">setValidValues</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"query"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">getFileExtensions</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">SeqFileIn</span></span><span class="p"><span class="idiff right">(</span>)));</span></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="cpp"> <span class="n" style="color: #333;">setRequired</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"q"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="cpp"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"d"</span><span class="p">,</span> <span class="s" style="color: #d14;">"database"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="cpp"> <span class="s" style="color: #d14;">"Path to original database sequences (a precomputed index with .sa or .fm needs to exist!)."</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="cpp"> <span class="n" style="color: #333;">ArgParseArgument</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INPUT_FILE</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="cpp"> <span class="s" style="color: #d14;">"IN"</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="cpp"> <span class="n" style="color: #333;">setValidValues</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"database"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">toCString</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">concat</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">getFileExtensions</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">SeqFileIn</span></span><span class="p"><span class="idiff">()),</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff right">' '</span></span><span class="p">)));</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp"> <span class="n" style="color: #333;">setValidValues</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"database"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">getFileExtensions</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">SeqFileIn</span></span><span class="p"><span class="idiff right">(</span>)));</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp"> <span class="n" style="color: #333;">setRequired</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"d"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="cpp"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"di"</span><span class="p">,</span> <span class="s" style="color: #d14;">"db-index-type"</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1048" 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">@@ -1048,7 +1048,7 @@ parseCommandLine(LambdaIndexerOptions & options, int argc, char const ** argv)</td>
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<pre style="margin: 0;"> <span id="LC1048" class="line" lang="cpp"> <span class="n" style="color: #333;">ArgParseArgument</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">INPUT_FILE</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1049" class="line" lang="cpp"> <span class="s" style="color: #d14;">"IN"</span><span class="p">));</span></span>
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1050
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<pre style="margin: 0;"> <span id="LC1050" class="line" lang="cpp"> <span class="n" style="color: #333;">setRequired</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"database"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1051" 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">
1051
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<pre style="margin: 0;">-<span id="LC1051" class="line" lang="cpp"> <span class="n" style="color: #333;">setValidValues</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"database"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">toCString</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">concat</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">getFileExtensions</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">SeqFileIn</span></span><span class="p"><span class="idiff">()),</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff right">' '</span></span><span class="p">)));</span></span>
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="cpp"> <span class="n" style="color: #333;">setValidValues</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="s" style="color: #d14;">"database"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">getFileExtensions</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">SeqFileIn</span></span><span class="p"><span class="idiff right">(</span>)));</span></span>
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1052
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1052
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<pre style="margin: 0;"> <span id="LC1052" class="line" lang="cpp"></span>
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1053
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<pre style="margin: 0;"> <span id="LC1053" class="line" lang="cpp"> <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">ArgParseOption</span><span class="p">(</span><span class="s" style="color: #d14;">"s"</span><span class="p">,</span></span>
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1054
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1054
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<pre style="margin: 0;"> <span id="LC1054" class="line" lang="cpp"> <span class="s" style="color: #d14;">"segfile"</span><span class="p">,</span></span>
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