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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/last-align">Debian Med / last-align</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/e070a325a2355129a990c43d957ba77e7bc86c10">e070a325</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-12-19T16:19:02+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1168</pre>
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<h4>4 changed files:</h4>
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<a href="#57bf262130f956caf76c405086f0815caf4e0a89">
ChangeLog.txt
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<a href="#5e55dbeefff2057b414960d9467d183920e31b8a">
src/Alignment.cc
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<a href="#a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a">
src/lastal.cc
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<a href="#69737f84c540417aafef4e696f66adcc9f92fa66">
src/version.hh
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<h4>Changes:</h4>
<li id="57bf262130f956caf76c405086f0815caf4e0a89">
<a href="https://salsa.debian.org/med-team/last-align/-/commit/e070a325a2355129a990c43d957ba77e7bc86c10#57bf262130f956caf76c405086f0815caf4e0a89"><strong>ChangeLog.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2020-12-15 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * src/Alignment.cc, src/lastal.cc, test/last-test.out, test/last-</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> test.sh:</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> New frameshifts: fix print precision of score</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> [abed5cbf2f29] [tip]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">2020-12-11 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * src/GeneticCode.cc, src/GeneticCode.hh, src/lastal.cc, test/last-</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> test.out, test/last-test.sh:</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> Better rep-masking for codons & new frameshifts</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> [c1fbf7da4f68]<span class="idiff left right"> [tip]</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> [c1fbf7da4f68]</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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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">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> * src/GappedXdropAlignerFrame.cc, src/GeneticCode.cc,</span>
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<td class="diff-line-num old_line" data-linenumber="9" 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="LC16" class="line" lang="plaintext"> src/GeneticCode.hh, src/lastal.cc:</span>
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<li id="5e55dbeefff2057b414960d9467d183920e31b8a">
<a href="https://salsa.debian.org/med-team/last-align/-/commit/e070a325a2355129a990c43d957ba77e7bc86c10#5e55dbeefff2057b414960d9467d183920e31b8a"><strong>src/Alignment.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -51,12 +51,7 @@ void Alignment::makeXdrop( Aligners &aligners, bool isGreedy,</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Alphabet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span> <span class="n" style="color: #333;">AlignmentExtras</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">extras</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">gamma</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">outputType</span> <span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gap</span><span class="p">.</span><span class="n" style="color: #333;">isNewFrameshifts</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">fullScore</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 class="c1" style="color: #998; font-style: italic;">// means that "score" is (non-integer) fullScore</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">fullScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">gap</span><span class="p">.</span><span class="n" style="color: #333;">isNewFrameshifts</span><span class="p">())</span> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">fullScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">7</span> <span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span> <span class="n" style="color: #333;">seed</span><span class="p">.</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// makes things easier to understand</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/e070a325a2355129a990c43d957ba77e7bc86c10#a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a"><strong>src/lastal.cc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="808" 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="808" 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">@@ -808,8 +808,7 @@ void alignFinish( LastAligner& aligner, const AlignmentPot& gappedAlns,</td>
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<pre style="margin: 0;"> <span id="LC808" class="line" lang="cpp"> <span class="p">}</span></span>
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809
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<pre style="margin: 0;"> <span id="LC809" class="line" lang="cpp"> <span class="n" style="color: #333;">centroid</span><span class="p">.</span><span class="n" style="color: #333;">setPssm</span><span class="p">(</span><span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">queryLen</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">temperature</span><span class="p">,</span></span>
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810
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810
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="cpp"> <span class="n" style="color: #333;">matrices</span><span class="p">.</span><span class="n" style="color: #333;">oneQualExp</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">j</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC811" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC812" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="cpp"> <span class="n" style="color: #333;">centroid</span><span class="p">.</span><span class="n" style="color: #333;">setScoreMatrix</span><span class="p">(</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">temperature</span> <span class="p">);</span></span>
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814
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="cpp"> <span class="p">}</span></span>
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814
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="cpp"> <span class="n" style="color: #333;">centroid</span><span class="p">.</span><span class="n" style="color: #333;">setOutputType</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="816" 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">@@ -817,12 +816,12 @@ void alignFinish( LastAligner& aligner, const AlignmentPot& gappedAlns,</td>
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817
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816
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC817" class="line" lang="cpp"> <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;">i</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;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gappedAlns</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;">i</span> <span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aln</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gappedAlns</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="cpp"> <span class="n" style="color: #333;">AlignmentExtras</span> <span class="n" style="color: #333;">extras</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isFullScoreThreshold</span><span class="p">())</span> <span class="n" style="color: #333;">extras</span><span class="p">.</span><span class="n" style="color: #333;">fullScore</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 class="c1" style="color: #998; font-style: italic;">// score is fullScore</span></span>
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<pre style="margin: 0;"> <span id="LC821" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span> <span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC821" class="line" lang="cpp"> <span class="n" style="color: #333;">writeAlignment</span><span class="p">(</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">aln</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span> <span class="p">);</span></span>
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822
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<pre style="margin: 0;">-<span id="LC822" class="line" lang="cpp"> <span class="p">}</span></span>
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823
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<pre style="margin: 0;">-<span id="LC823" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// calculate match probabilities:</span></span>
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="cpp"> <span class="n" style="color: #333;">writeAlignment</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">aln</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span><span class="p">,</span> <span class="n" style="color: #333;">extras</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// calculate match probabilities:</span></span>
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<pre style="margin: 0;"> <span id="LC824" class="line" lang="cpp"> <span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">probAln</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC825" class="line" lang="cpp"> <span class="n" style="color: #333;">AlignmentExtras</span> <span class="n" style="color: #333;">extras</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC825" class="line" lang="cpp"> <span class="n" style="color: #333;">probAln</span><span class="p">.</span><span class="n" style="color: #333;">seed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">seed</span><span class="p">;</span></span>
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827
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<pre style="margin: 0;"> <span id="LC826" class="line" lang="cpp"> <span class="n" style="color: #333;">probAln</span><span class="p">.</span><span class="n" style="color: #333;">makeXdrop</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">engines</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isGreedy</span><span class="p">,</span></span>
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828
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827
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">globality</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">m</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="830" 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="829" 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">@@ -830,8 +829,8 @@ void alignFinish( LastAligner& aligner, const AlignmentPot& gappedAlns,</td>
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830
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829
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<pre style="margin: 0;"> <span id="LC829" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">.</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">lambda</span><span class="p">(),</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">,</span></span>
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830
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<pre style="margin: 0;"> <span id="LC830" class="line" lang="cpp"> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">frameSize</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">dis</span><span class="p">.</span><span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">,</span></span>
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831
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="cpp"> <span class="n" style="color: #333;">extras</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">gamma</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">aln</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</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="n" style="color: #333;"><span class="idiff">INF</span></span><span class="idiff right"> </span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC834" class="line" lang="cpp"> <span class="n" style="color: #333;">writeAlignment</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">aligner</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">probAln</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">queryNum</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">querySeq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">extras</span></span><span class="idiff right"> </span><span class="p">);</span></span>
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832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">aln</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</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="n" style="color: #333;"><span class="idiff right">INF</span></span><span class="p">);</span></span>
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833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="cpp"> <span class="n" style="color: #333;">writeAlignment</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">aligner</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">probAln</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">queryNum</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">querySeq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">extras</span></span><span class="p">);</span></span>
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835
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834
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<pre style="margin: 0;"> <span id="LC834" class="line" lang="cpp"> <span class="p">}</span></span>
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836
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835
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="cpp"> <span class="p">}</span></span>
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837
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836
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1128" 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="1127" 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">@@ -1128,7 +1127,7 @@ void readIndex( const std::string& baseName, indexT seqCount ) {</td>
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1128
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1127
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<pre style="margin: 0;"> <span id="LC1127" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">numOfIndexes</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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1129
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1128
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<pre style="margin: 0;"> <span id="LC1128" class="line" lang="cpp"> <span class="n" style="color: #333;">suffixArrays</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">].</span><span class="n" style="color: #333;">fromFiles</span><span class="p">(</span><span class="n" style="color: #333;">baseName</span> <span class="o" style="font-weight: 600;">+</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">(</span><span class="sc" style="color: #d14;">'a'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">x</span><span class="p">),</span> <span class="n" style="color: #333;">isCaseSensitiveSeeds</span><span class="p">,</span></span>
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1130
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1129
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<pre style="margin: 0;"> <span id="LC1129" class="line" lang="cpp"> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span><span class="p">);</span></span>
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1131
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<pre style="margin: 0;">-<span id="LC1131" class="line" lang="cpp"> <span class="p">}</span><span class="k" style="font-weight: 600;"><span class="idiff left right">else</span></span><span class="p">{</span></span>
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1130
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<pre style="margin: 0;">+<span id="LC1130" class="line" lang="cpp"> <span class="p">}</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff right"> </span><span class="p">{</span></span>
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1132
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1131
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<pre style="margin: 0;"> <span id="LC1131" class="line" lang="cpp"> <span class="n" style="color: #333;">suffixArrays</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">].</span><span class="n" style="color: #333;">fromFiles</span><span class="p">(</span><span class="n" style="color: #333;">baseName</span><span class="p">,</span> <span class="n" style="color: #333;">isCaseSensitiveSeeds</span><span class="p">,</span></span>
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1133
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1132
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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="cpp"> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span><span class="p">);</span></span>
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1134
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1133
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<pre style="margin: 0;"> <span id="LC1133" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1221" 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="1220" 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">@@ -1221,8 +1220,7 @@ void writeHeader( countT refSequences, countT refLetters, std::ostream& out ){</td>
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1221
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1220
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<pre style="margin: 0;"> <span id="LC1220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;">// we just want hit counts</span></span>
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1222
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1221
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<pre style="margin: 0;"> <span id="LC1221" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"# length</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">count</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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1223
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1222
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<pre style="margin: 0;"> <span id="LC1222" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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1224
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<pre style="margin: 0;">-<span id="LC1224" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1225" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// we want alignments</span></span>
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1223
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<pre style="margin: 0;">+<span id="LC1223" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// we want alignments</span></span>
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1226
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1224
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<pre style="margin: 0;"> <span id="LC1224" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">inputFormat</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pssm</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">matrixFile</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="p">){</span></span>
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1227
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1225
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<pre style="margin: 0;"> <span id="LC1225" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// we're not reading PSSMs, or we bothered to specify a matrix file</span></span>
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1228
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1226
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<pre style="margin: 0;"> <span id="LC1226" class="line" lang="cpp"> <span class="n" style="color: #333;">scoreMatrix</span><span class="p">.</span><span class="n" style="color: #333;">writeCommented</span><span class="p">(</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1382" 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="1380" 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">@@ -1382,7 +1380,7 @@ void lastal( int argc, char** argv ){</td>
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1382
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1380
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<pre style="margin: 0;"> <span id="LC1380" class="line" lang="cpp"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isKeepLowercase</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">maskLowercase</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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<td class="diff-line-num old_line" data-linenumber="1383" 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">
1383
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1381
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<pre style="margin: 0;"> <span id="LC1381" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">isFinished</span><span class="p">()</span> <span class="p">){</span></span>
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<td class="diff-line-num old_line" data-linenumber="1384" 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">
1384
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1382
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<pre style="margin: 0;"> <span id="LC1382" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">sequenceCount</span><span class="p">;</span></span>
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1385
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<pre style="margin: 0;">-<span id="LC1385" class="line" lang="cpp"> <span class="p">}</span><span class="k" style="font-weight: 600;"><span class="idiff left right">else</span></span><span class="p">{</span></span>
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1383
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<pre style="margin: 0;">+<span id="LC1383" class="line" lang="cpp"> <span class="p">}</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff right"> </span><span class="p">{</span></span>
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1386
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<pre style="margin: 0;"> <span id="LC1384" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// this enables downstream parsers to read one batch at a time:</span></span>
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1387
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<pre style="margin: 0;"> <span id="LC1385" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"# batch "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">queryBatchCount</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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1388
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1386
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<pre style="margin: 0;"> <span id="LC1386" class="line" lang="cpp"> <span class="n" style="color: #333;">scanAllVolumes</span><span class="p">(</span> <span class="n" style="color: #333;">volumes</span><span class="p">,</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"116<span class="idiff left right">7</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"116<span class="idiff left right">8</span>"</span></span></pre>
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