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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/mapsembler2">Debian Med / mapsembler2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapsembler2/-/commit/f85e208078b8eef72259a80bb3b46c375a29fe5d">f85e2080</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-07-02T23:58:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: updated uploader address
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapsembler2/-/commit/eab15b8d531ef1bae3f409eb8e401e344d4108a3">eab15b8d</a></strong>
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<span>by Étienne Mollier</span>
<i>at 2021-07-02T23:59:38+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: standard version 4.5.1
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<li>
<strong><a href="https://salsa.debian.org/med-team/mapsembler2/-/commit/b683a5eb1872a4f411dfa2090410d1de7f7e3e61">b683a5eb</a></strong>
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<span>by Étienne Mollier</span>
<i>at 2021-07-03T00:08:58+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/mans/mapsembler2_kissreads.1
fix typo-in-manual-page
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</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapsembler2/-/commit/5cfb5a8745f89d0759a16a0bd43f336f0279cfff">5cfb5a87</a></strong>
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<span>by Étienne Mollier</span>
<i>at 2021-07-03T00:10:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">spelling.patch: fix spelling-error-in-binary
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapsembler2/-/commit/df74cc12f18b06e63bc2832ba3a0fee34d71afa8">df74cc12</a></strong>
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<span>by Étienne Mollier</span>
<i>at 2021-07-03T00:11:44+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update changelog
</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#5d1be87f17e070a1304e79e50d9a4e89a1a6f07f">
debian/mans/mapsembler2_kissreads.1
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<li class="file-stats">
<a href="#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">
debian/patches/spelling.patch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/mapsembler2/-/compare/94228d2f106c29f11b5b619cba9d7bae9573d971...df74cc12f18b06e63bc2832ba3a0fee34d71afa8#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">mapsembler2 (2.2.4+dfsg1-4) UNRELEASED; urgency=medium</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"> * d/salsa-ci.yml: disable i386 build and reprotest in Salsa CI</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * d/control: updated uploader address</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * d/control: standard version 4.5.1</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * d/mans/mapsembler2_kissreads.1: fix typo-in-manual-page</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * spelling.patch: fix spelling-error-in-binary</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Étienne Mollier <e<span class="idiff left">tienne.</span>mollier@<span class="idiff">mailoo</span>.org> S<span class="idiff">un, 21 Feb</span> 2021 <span class="idiff">15:25</span>:4<span class="idiff">5</span> +0<span class="idiff right">1</span>00</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Étienne Mollier <emollier@<span class="idiff left">debian</span>.org> S<span class="idiff">at, 03 Jul</span> 2021 <span class="idiff">00:10</span>:4<span class="idiff">3</span> +0<span class="idiff right">2</span>00</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">mapsembler2 (2.2.4+dfsg1-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/mapsembler2/-/compare/94228d2f106c29f11b5b619cba9d7bae9573d971...df74cc12f18b06e63bc2832ba3a0fee34d71afa8#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -2,7 +2,7 @@ Source: mapsembler2</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Olivier Sallou <osallou@debian.org>,</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> Étienne Mollier <e<span class="idiff left">tienne.</span>mollier@<span class="idiff right">mailoo</span>.org></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Étienne Mollier <emollier@<span class="idiff left right">debian</span>.org></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libhdf5-dev,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libcppunit-dev,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libboost-dev</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/mapsembler2</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/mapsembler2.git</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Homepage: http://colibread.inria.fr/mapsembler2/</span>
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<a href="https://salsa.debian.org/med-team/mapsembler2/-/compare/94228d2f106c29f11b5b619cba9d7bae9573d971...df74cc12f18b06e63bc2832ba3a0fee34d71afa8#5d1be87f17e070a1304e79e50d9a4e89a1a6f07f"><strong>debian/mans/mapsembler2_kissreads.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">@@ -34,7 +34,7 @@ Any other situation (s not coherent with any): couple non read coherent, not out</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">\fB\-n\fR the input file (toCheck.fasta) is a kissnp output (incompatible with \fB\-I\fR option)</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">in this case: 1/ only the upper characters are considered (no mapping done on the extensions) and 2/ the central position (where the SNP occurs) is strictly mapped, no subsitution is authorized on this position.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">in this case: 1/ only the upper characters are considered (no mapping done on the extensions) and 2/ the central position (where the SNP occurs) is strictly mapped, no subs<span class="idiff left right">t</span>itution is authorized on this position.</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">\fB\-I\fR the input file (toCheck.fasta) is an Intl output (incompatible with \fB\-n\fR option)</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">.HP</span>
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<a href="https://salsa.debian.org/med-team/mapsembler2/-/compare/94228d2f106c29f11b5b619cba9d7bae9573d971...df74cc12f18b06e63bc2832ba3a0fee34d71afa8#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6"><strong>debian/patches/spelling.patch</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">@@ -2,9 +2,9 @@ Description: Fix spelling</td>
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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: Wed, 10 Oct 2018 12:49:34 +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">--- <span class="idiff left right">a</span>/kissreads_graph/KissReadsGraph.cpp</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;">+++ <span class="idiff left right">b</span>/kissreads_graph/KissReadsGraph.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -35,7 +35,7 @@</span><span class="idiff left right"> void print_usage_and_exit(char * name){</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- <span class="idiff left right">mapsembler2.orig</span>/kissreads_graph/KissReadsGraph.cpp</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;">+++ <span class="idiff left right">mapsembler2</span>/kissreads_graph/KissReadsGraph.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -35,7 +35,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> fprintf (stderr, "With option \"-t modify\": outputs the same simplified graph:\n");</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> fprintf (stderr, "\t removing low covered edges and nodes (less that min_coverage)\n");</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> fprintf (stderr, "\t then phasing simple non branching paths\n");</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,9 +13,9 @@ Last-Update: Wed, 10 Oct 2018 12:49:34 +0200</td>
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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"> </span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> fprintf (stderr, "\nMANDATORY\n");</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;">--- <span class="idiff left right">a</span>/mapsembler2_extend/IterativeExtensions.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;">+++ <span class="idiff left right">b</span>/mapsembler2_extend/IterativeExtensions.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="p">@@ -178,7 +178,7 @@</span><span class="idiff left right"> void IterativeExtensions::construct_line</span></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;">--- <span class="idiff left right">mapsembler2.orig</span>/mapsembler2_extend/IterativeExtensions.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;">+++ <span class="idiff left right">mapsembler2</span>/mapsembler2_extend/IterativeExtensions.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -178,7 +178,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> revcomp_sequence(kmer_seq,sizeKmer);</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> if (debug)</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,7 +24,7 @@ Last-Update: Wed, 10 Oct 2018 12:49:34 +0200</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> // right extension</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> int len_right = traversal->traverse(kmer,right_traversal,strand);</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="p">@@ -397,7 +397,7 @@</span><span class="idiff left right"> void IterativeExtensions::construct_line</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -397,7 +397,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> revcomp_sequence(kmer_seq,sizeKmer);</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> if (debug)</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,3 +33,14 @@ Last-Update: Wed, 10 Oct 2018 12:49:34 +0200</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> // right extension</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> int len_right = traversal->traverse(kmer,right_traversal,strand);</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;">--- mapsembler2.orig/kissreads/src/kissReads.c</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;">+++ mapsembler2/kissreads/src/kissReads.c</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="p">@@ -93,7 +93,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> fprintf (stderr, "\t -u file_name: write unread-coherent outputs. Default: standard output \n");</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> #ifndef INPUT_FROM_KISSPLICE</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> fprintf (stderr, "\t -n the input file (toCheck.fasta) is a kissnp output (incompatible with -I option) \n");</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;">- fprintf (stderr, "\t\t in this case: 1/ only the upper characters are considered (no mapping done on the extensions) and 2/ the central position (where the SNP occurs) is strictly mapped, no subsitution is authorized on this position.\n");</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf (stderr, "\t\t in this case: 1/ only the upper characters are considered (no mapping done on the extensions) and 2/ the central position (where the SNP occurs) is strictly mapped, no substitution is authorized on this position.\n");</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> fprintf (stderr, "\t -I the input file (toCheck.fasta) is an Intl output (incompatible with -n option) \n");</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> #endif // not INPUT_FROM_KISSPLICE</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> fprintf (stderr, "\t -i index_stride (int value). This is a heuristic for limiting the memory footprint. Instead of indexing each kmer of the sequences contained into the toCheck.fasta, kissreads indexes kmers occurring each \"index_stride\" position. Default = 1 (no heuristic)\n");</span></pre>
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