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<h3>
Sascha Steinbiss pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/mash">Debian Med / mash</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mash/commit/c24e551d8cc988d7536a767985075dd622ef11be">c24e551d</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2019-10-23T16:39:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.2.2+dfsg</pre>
</li>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#ccf97c63b67930f1487017e1286d34ab3528b2a8">
src/mash/Sketch.cpp
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<li class="file-stats">
<a href="#2ecd5edfb9906ffd092b9b8b4d28f6cb2eed2783">
src/mash/version.h
</a>
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<h4>Changes:</h4>
<li id="ccf97c63b67930f1487017e1286d34ab3528b2a8">
<a href="https://salsa.debian.org/med-team/mash/commit/c24e551d8cc988d7536a767985075dd622ef11be#ccf97c63b67930f1487017e1286d34ab3528b2a8"><strong>src/mash/Sketch.cpp</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">@@ -534,17 +534,19 @@ void addMinHashes(MinHashHeap & minHashHeap, char * seq, uint64_t length, const</td>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="cpp"> <span class="n" style="color: #333;">reverseComplement</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">seqRev</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">);</span></span>
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535
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535
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="cpp"> <span class="p">}</span></span>
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536
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="cpp"> </span>
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539
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<pre style="margin: 0;"> <span id="LC539" 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;">uint64_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;">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmerSize</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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538
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540
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="cpp"> <span class="p">{</span></span>
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539
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541
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// repeatedly skip kmers with bad characters</span></span>
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540
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542
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">bad</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">-<span id="LC543" 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;"><span class="idiff left">uint64_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">i</span></span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">kmerSize</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">kmerSize</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">length</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">kmerSize</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">kmerSize</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">length</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">alphabet</span><span class="p">[</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]]</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// skip to past the bad character</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><span class="idiff left right">++</span></span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// skip to past the bad character</span></span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="cpp"> <span class="n" style="color: #333;">bad</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/mash/commit/c24e551d8cc988d7536a767985075dd622ef11be#2ecd5edfb9906ffd092b9b8b4d28f6cb2eed2783"><strong>src/mash/version.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,4 +4,4 @@</td>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// See the LICENSE.txt file included with this software for license information.</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.2"</span><span class="p">;</span></span></pre>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.2<span class="idiff left right">.2</span>"</span><span class="p">;</span></span></pre>
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