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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/lighter">Debian Med / lighter</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/lighter/-/commit/57a7a7b5348f19f7c7558e0b28f9337bb25194e4">57a7a7b5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-21T14:47:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix FTBFS
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/lighter/-/commit/bc98dbf2522a4c64d7dd9f2653aebc0413740aef">bc98dbf2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-21T14:47:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix typo
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/lighter/-/commit/796edf359a03203857d89bff3e828fa026301ec0">796edf35</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-21T14:50:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix spelling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/lighter/-/commit/b8c44ba2e4386fbfcf5e4cedb4f116dee1d3ff80">b8c44ba2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-21T14:50:48+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#6291b8126047e99f6f703f1c75aa9277f11d94f5">
debian/lighter.1
</a>
</li>
<li class="file-stats">
<a href="#5293519e0f1f7572f35712263dd33d142533a09b">
<span class="new-file">
+
debian/patches/ftbfs.patch
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</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">
<span class="new-file">
+
debian/patches/spelling.patch
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/lighter/-/compare/806500417d3c3d85be74897c2f3400371f845930...b8c44ba2e4386fbfcf5e4cedb4f116dee1d3ff80#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">lighter (1.1.2-3) unstable; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> [ Helmut Grohne ]</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"> * Fix FTBFS</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Closes: #965228</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Fix spelling</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"> -- Andreas Tille <tille@debian.org> Tue, 21 Jul 2020 14:50:09 +0200</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">lighter (1.1.2-2) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/lighter/-/compare/806500417d3c3d85be74897c2f3400371f845930...b8c44ba2e4386fbfcf5e4cedb4f116dee1d3ff80#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="577" 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="577" 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">@@ -577,7 +577,7 @@ License: MPL-1.1</td>
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<td class="diff-line-num old_line" data-linenumber="577" 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">
577
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<td class="diff-line-num new_line" data-linenumber="577" 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">
577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="plaintext"> shall survive.</span>
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<td class="diff-line-num old_line" data-linenumber="578" 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">
578
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578
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="plaintext"> .</span>
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="plaintext"> 8.2. If You initiate litigation by asserting a patent infringement</span>
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="plaintext"> claim (excluding declatory judgment actions) against Initial Developer</span>
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="plaintext"> claim (excluding decla<span class="idiff left right">ra</span>tory judgment actions) against Initial Developer</span>
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="plaintext"> or a Contributor (the Initial Developer or Contributor against whom</span>
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="plaintext"> You file such action is referred to as "Participant") alleging that:</span>
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="plaintext"> .</span>
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<a href="https://salsa.debian.org/med-team/lighter/-/compare/806500417d3c3d85be74897c2f3400371f845930...b8c44ba2e4386fbfcf5e4cedb4f116dee1d3ff80#6291b8126047e99f6f703f1c75aa9277f11d94f5"><strong>debian/lighter.1</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">@@ -18,7 +18,7 @@ comparable accuracy.</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">.SH OPTIONS:</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">.SS Required parameters:</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">\fB\-r\fR seq_file: seq_file is the path to the sequence file. Can use multiple \fB\-r\fR to specif<span class="idiff left right">i</span>y multiple sequence files</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">\fB\-r\fR seq_file: seq_file is the path to the sequence file. Can use multiple \fB\-r\fR to specify multiple sequence files</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">The file can be fasta and fastq, and can be gzip'ed with extension *.gz.</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">When the input file is *.gz, the corresponding output file will also be gzip'ed.</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">.TP</span>
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<a href="https://salsa.debian.org/med-team/lighter/-/compare/806500417d3c3d85be74897c2f3400371f845930...b8c44ba2e4386fbfcf5e4cedb4f116dee1d3ff80#5293519e0f1f7572f35712263dd33d142533a09b"><strong>debian/patches/ftbfs.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Date: Fri, 17 Jul 2020 22:36:54 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">From: Helmut Grohne <helmut@subdivi.de></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/965228</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Description: lighter fails to build from source, because:</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> main.cpp:26:25: error: narrowing conversion of ‘-1’ from ‘int’ to ‘char’ [-Wnarrowing]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> What happens here is that nucToNum is assigned -1, but it is typed array</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> of char, which happens to be unsigned (on some architectures). It really</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> wants a small signed integer type here (representing numbers between -1</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> and 3). A very simple fix is using signed char (which isn't architecture</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> dependent).</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff">--- lighter-1.1.2.orig/main.cpp</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lighter-1.1.2/main.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> char LIGHTER_VERSION[] = "Lighter v1.1.2" ;</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-char nucToNum[26] = { 0, -1, 1, -1, -1, -1, 2, </span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+signed char nucToNum[26] = { 0, -1, 1, -1, -1, -1, 2, </span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> -1, -1, -1, -1, -1, -1, -1,</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> -1, -1, -1, -1, -1, 3,</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> -1, -1, -1, -1, -1, -1 } ;</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lighter-1.1.2.orig/KmerCode.h</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lighter-1.1.2/KmerCode.h</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -4,7 +4,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> #include <stdio.h></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> #include "utils.h"</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-extern char nucToNum[26] ;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+extern signed char nucToNum[26] ;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> extern char numToNuc[26] ;</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> const int K_BLOCK_NUM = ( MAX_KMER_LENGTH - 1 ) / ( sizeof( uint64_t ) * 4 ) + 1 ;</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lighter-1.1.2.orig/ErrorCorrection.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lighter-1.1.2/ErrorCorrection.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="p">@@ -3,7 +3,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> //#define DEBUG </span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-extern char nucToNum[26] ; </span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+extern signed char nucToNum[26] ; </span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> extern char numToNuc[26] ;</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> extern int MAX_CORRECTION ;</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> extern bool ALLOW_TRIMMING ;</span></pre>
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<a href="https://salsa.debian.org/med-team/lighter/-/compare/806500417d3c3d85be74897c2f3400371f845930...b8c44ba2e4386fbfcf5e4cedb4f116dee1d3ff80#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">hardening.patch</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">ftbfs.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">spelling.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/lighter/-/compare/806500417d3c3d85be74897c2f3400371f845930...b8c44ba2e4386fbfcf5e4cedb4f116dee1d3ff80#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6"><strong>debian/patches/spelling.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Fix spelling</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: Tue, 21 Jul 2020 13:35:04 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/README.md</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -27,7 +27,7 @@</span> Lighter is small and portable, with [pth</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> Usage: ./lighter [OPTIONS]</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> OPTIONS:</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> Required parameters:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -r seq_file: seq_file is the path to the sequence file. Can use multiple -r to specifiy multiple sequence files</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -r seq_file: seq_file is the path to the sequence file. Can use multiple -r to specify multiple sequence files</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> The file can be fasta and fastq, and can be gzip'ed with extension *.gz. </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> When the input file is *.gz, the corresponding output file will also be gzip'ed.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> -k kmer_length genome_size alpha</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/main.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/main.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -58,7 +58,7 @@</span> void PrintHelp()</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> printf( "Usage: ./lighter [OPTIONS]\n"</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> "OPTIONS:\n"</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> "Required parameters:\n"</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "\t-r seq_file: seq_file is the path to the sequence file. Can use multiple -r to specifiy multiple sequence files\n"</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "\t-r seq_file: seq_file is the path to the sequence file. Can use multiple -r to specify multiple sequence files\n"</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> "\t The file can be fasta and fastq, and can be gzip\'ed with extension *.gz.\n" </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> "\t When the input file is *.gz, the corresponding output file will also be gzip\'ed.\n"</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> "\t-k kmer_length genome_size alpha: (see README for information on setting alpha)\n"</span></pre>
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