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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/discosnp">Debian Med / discosnp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/ef34ffabea022081d11452bc35bb3acfd7431a13">ef34ffab</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-23T11:47:23Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix script pathes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/2df769f4bb7a8a67957c27bf2f3308573599f745">2df769f4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-23T11:48:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Missing ','
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/aab7a5f7a4e2ceb59429ed84a636a8bc23c77a44">aab7a5f7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-23T11:51:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Manpages also for scripts
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/ce3fa0c208708eec924ed72478fb6c8534d21a18">ce3fa0c2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-23T14:16:55Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Python3 helper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/6ea2a7f2d35ebe285858386db7b60200bd85f3b4">6ea2a7f2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-23T14:17:28Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Spelling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/692c4dc57753ca0253a9362e32544369c53a968f">692c4dc5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-23T14:18:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not install jenkins input
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/e7416185bd3005b89225bda144dc883fb9aa749a">e7416185</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-23T14:20:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update README.Debian
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/07f5d2cb0fb54af867b23bdea426d695224f1325">07f5d2cb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-23T14:21:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Leave the readme that describes the scripts next to the scripts
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/02b39a77c2fe5a8a576c8c6c65e794d5c7e1becf">02b39a77</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-23T14:23:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Script is actually bash not sh
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/0cf6149373acc44bc0459a6daeca6496d15cdd79">0cf61493</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-23T14:34:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Depends: gatb-core
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/65c393ea968209195e9ccc26e2df5671a0cf22ba">65c393ea</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-23T14:38:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapt to script dir
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/170cb0efae0fec9f81eb7ebb1d08e5ca743d96fa">170cb0ef</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-23T14:41:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapt test scripts to Debian PATH
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/e0afd99ece280e53c3b5632da8d625e52a0fdf89">e0afd99e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-23T14:55:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add missing dh-python
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/acbf9449bcd8484f4a2e0e4b79ff521984a9508b">acbf9449</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-23T14:55:44Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtest
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/0e5fbfc77c387d1fdd60cfc9c705a965c5b5f64b">0e5fbfc7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-23T14:56:29Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Document how the package can be tested.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/242c4a8e9ff3e572618304cba47916d586431b14">242c4a8e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-23T15:05:26Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Some scripts have remaining Python2 syntax
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/fdd10ba6d4bb3259db4a7d90eec552e0d56184da">fdd10ba6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-23T15:28:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Run all scripts trough 2to3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/9ea19bd4b311bfa1f46a197890ab55f503cc1be7">9ea19bd4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-23T15:34:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix autopkttest
</pre>
</li>
</ul>
<h4>22 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
<span class="new-file">
+
debian/README.Debian
</span>
</a>
</li>
<li class="file-stats">
<a href="#ce41ab26d6ca0c6353c9135eca14c8b5003b7bdc">
<span class="deleted-file">
−
debian/README.debian
</span>
</a>
</li>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<span class="new-file">
+
debian/README.test
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
debian/createmanpages
</a>
</li>
<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
</a>
</li>
<li class="file-stats">
<a href="#efc7fe57b5983b0283c6410fceef7e74f687aeb5">
debian/lintian-overrides
</a>
</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
debian/manpages
</a>
</li>
<li class="file-stats">
<a href="#ea147271d56397c0e4c4c76a3f656b35c4da5646">
debian/kissnp2.1
→
debian/mans/kissnp2.1
</a>
</li>
<li class="file-stats">
<a href="#e9a147728402c4b51000f57231d701405324f72e">
debian/kissreads2.1
→
debian/mans/kissreads2.1
</a>
</li>
<li class="file-stats">
<a href="#5108385b2a1d6bdc41ea7b8c19339f1b20b04b8f">
<span class="new-file">
+
debian/mans/run_discoSnp++.sh.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#a5098d59b3f01a472b3b99623527dace07e65dce">
<span class="new-file">
+
debian/mans/run_discoSnpRad.sh.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
<span class="new-file">
+
debian/patches/2to3.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#abfb1a54765fa4da90cfea86c619e421f0868366">
<span class="new-file">
+
debian/patches/adapt_test_scripts.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#7109d0c90a06eb64dda982f6f112fbe5ff0ca751">
<span class="new-file">
+
debian/patches/fix_scripts.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bf2967f2e5d775c66983431a1a3d3a2edf5b7227">
debian/patches/path_to_readme_file_names.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
</span>
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong></a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
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<td class="diff-line-num new new_line" data-linenumber="1" 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">
1
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">discosnp for DEBIAN</span>
</pre>
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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">
2
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<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">
3
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
</pre>
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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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Please note that several scripts which are in the upstream distribution</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="5" 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">
5
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">can be found in</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="6" 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">
6
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> /usr/share/discosnp/scripts and</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> /usr/share/discosnp/scripts_RAD</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sat, 20 Oct 2018 10:56:58 +0200</span></pre>
</td>
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</table>
<br>
</li>
<li id="ce41ab26d6ca0c6353c9135eca14c8b5003b7bdc">
<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#ce41ab26d6ca0c6353c9135eca14c8b5003b7bdc"><strong>debian/README.debian</strong>
deleted
</a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">discosnp for DEBIAN</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"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">No man page is available but to get help, just type: kissreads or kissnp2</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Output analysis scripts are:</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> discoSnp_to_genotypes</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> discoSnp_to_cvs</span>
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9
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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">type any on command line to get help.</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"> -- Olivier Sallou <osallou@debian.org> Mon, 13 Jan 2014 10:55:29 +0100</span>
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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">This tools is superseded by DiscoSnp++ (see</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> http://colibread.inria.fr/software/discosnp/</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 14 Nov 2017 09:41:19 +0100</span></pre>
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<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="k" style="font-weight: 600;">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span></pre>
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<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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">@@ -10,6 +10,8 @@ discosnp (2.3.0-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Remove trailing whitespace in debian/copyright</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Build-Depends: libboost-dev, libgatbcore-dev, libhdf5-dev, zlib1g-dev</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Fix dh_install</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Depends: gatb-core</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Add autopkgtest</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sat, 20 Oct 2018 10:56:58 +0200</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#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">@@ -5,6 +5,7 @@ Uploaders: Olivier Sallou <osallou@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 12~),</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> cmake,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libgatbcore-dev (>= 1.4.1+git20180206.6f8fce8~),</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libboost-dev,</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">@@ -19,9 +20,9 @@ Package: discosnp</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> ${shlibs:Depends},</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> ${python3:Depends}</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> python3</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"><span class="idiff left right">Recommends:</span> gatb-core</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> ${python3:Depends}<span class="idiff left right">,</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> python3<span class="idiff left right">,</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"><span class="idiff left right"> </span> gatb-core</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Description: discovering Single Nucleotide Polymorphism from raw set(s) of reads</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> Software discoSnp is designed for discovering Single Nucleotide</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation</span>
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<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -364,7 +364,7 @@ License: CeCILL</td>
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="plaintext"> terms and conditions of such technical assistance, and/or such</span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="plaintext"> maintenance, shall then be set forth in a separate instrument. Only the</span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="plaintext"> Licensor offering said maintenance and/or technical assistance services</span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="plaintext"> shall incur liability therefor.</span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext"> shall incur liability therefor<span class="idiff left right">e</span>.</span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="plaintext"> 7.2. Similarly, any or all Licensor shall be entitled to offer to its</span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="plaintext"> Licensees, under its own responsibility, a warranty, that shall only be</span>
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<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"><span class="nv" style="color: teal;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: teal;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian<span class="idiff left right">/mans</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: navy;">-p</span> <span class="nv" style="color: teal;">$MANDIR</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="nv" style="color: teal;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></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">@@ -24,6 +24,18 @@ help2man --no-info --no-discard-stderr --help-option=" -help" \</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"> <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span>run_discoSnp++.sh</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell">help2man <span class="nt" style="color: navy;">--no-info</span> <span class="nt" style="color: navy;">--no-discard-stderr</span> <span class="nt" style="color: navy;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"> <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"pipelining kissnp2 and kissreads for calling SNPs and small indels from NGS reads without the need of a reference genome"</span> <span class="se" style="color: #d14;">\</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"> <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span>run_discoSnpRad.sh</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell">help2man <span class="nt" style="color: navy;">--no-info</span> <span class="nt" style="color: navy;">--no-discard-stderr</span> <span class="nt" style="color: navy;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"> <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"pipelining kissnp2 and kissreads and clustering per locus for calling SNPs and small indels from RAD-seq data without the need of a reference genome"</span> <span class="se" style="color: #d14;">\</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"> <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"></span>
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27
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>
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28
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"></span>
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29
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: teal;">EOT</span></span>
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<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</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">README*</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">doc/*</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">test</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">debian/tests/run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">debian/README.test</span></pre>
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<li id="efc7fe57b5983b0283c6410fceef7e74f687aeb5">
<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#efc7fe57b5983b0283c6410fceef7e74f687aeb5"><strong>debian/lintian-overrides</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># see https://lists.debian.org/debian-med/2018/06/msg00043.html</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">discosnp: script-with-language-extension usr/bin/run_discoSnp++.sh</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">discosnp: script-with-language-extension usr/bin/run_discoSnpRad.sh</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"># The doc is where it belongs to</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">discosnp: package-contains-documentation-outside-usr-share-doc usr/share/discosnp/scripts_RAD/README.md</span></pre>
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<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/<span class="idiff left right">mans/</span>*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#ea147271d56397c0e4c4c76a3f656b35c4da5646"><strong>debian/kissnp2.1</strong>
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<strong>debian/mans/kissnp2.1</strong>
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<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#e9a147728402c4b51000f57231d701405324f72e"><strong>debian/kissreads2.1</strong>
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<strong>debian/mans/kissreads2.1</strong>
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<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#5108385b2a1d6bdc41ea7b8c19339f1b20b04b8f"><strong>debian/mans/run_discoSnp++.sh.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH RUN_DISCOSNP++.SH "1" "January 2019" "run_discoSnp++.sh 2.3.0" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">run_discoSnp++.sh \- pipelining kissnp2 and kissreads for calling SNPs and small indels from NGS reads without the need of a reference genome</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B run_discoSnp++.sh</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,-r read_file_of_files \/\fR[\fI\,OPTIONS\/\fR]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">run_discoSnp++.sh, a pipelining kissnp2 and kissreads for calling SNPs and small indels from NGS reads without the need of a reference genome</span>
</pre>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Version 2.3.X</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">MANDATORY:</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-r\fR read_file_of_files</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Example: \fB\-r\fR bank.fof with bank.fof containing the two lines</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">data_sample/reads_sequence1.fasta</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">data_sample/reads_sequence2.fasta.gz</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">DISCOSNP++ OPTIONS:</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.IP</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-g\fR: reuse a previously created graph (.h5 file) with same prefix and same k and c parameters.</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-b\fR value.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">0: forbid variants for which any of the two paths is branching (high precision, lowers the recall in complex genomes). Default value</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">1: (smart branching) forbid SNPs for which the two paths are branching (e.g. the two paths can be created either with a 'A' or a 'C' at the same position</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">2: No limitation on branching (lowers the precision, high recall)</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-s\fR value. In b2 mode only: maximal number of symmetrical croasroads traversed while trying to close a bubble. Default: no limit</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">\fB\-D\fR value. discoSnp++ will search for deletions of size from 1 to D included. Default=100</span>
</pre>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">\fB\-a\fR value. Maximal size of ambiguity of INDELs. INDELS whose ambiguity is higher than this value are not output [default '20']</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-P\fR value. discoSnp++ will search up to P SNPs in a unique bubble. Default=1</span>
</pre>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">\fB\-p\fR prefix. All out files will start with this prefix. Default="discoRes"</span>
</pre>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">\fB\-l\fR: remove low complexity bubbles</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">\fB\-k\fR value. Set the length of used kmers. Must fit the compiled value. Default=31</span>
</pre>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">\fB\-t\fR: extend found polymorphisms with unitigs \- Forced usage when using discoSnpRad</span>
</pre>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">\fB\-T\fR: extend found polymorphisms with contigs</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">\fB\-c\fR value. Set the minimal coverage per read set: Used by kissnp2 (don't use kmers with lower coverage) and kissreads (read coherency threshold). This coverage can be automatically detected per read set or specified per read set, see the documentation. Default=auto</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">\fB\-C\fR value. Set the maximal coverage for each read set: Used by kissnp2 (don't use kmers with higher coverage). Default=2^31\-1</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">\fB\-d\fR value. Set the number of authorized substitutions used while mapping reads on found SNPs (kissreads). Default=1</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">\fB\-n\fR: do not compute the genotypes</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">\fB\-u\fR: max number of used threads</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">\fB\-v\fR: verbose 0 (avoids progress output) or 1 (enables progress output) \fB\-\-\fR default=1.</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">REFERENCE GENOME AND/OR VCF CREATION OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">\fB\-G\fR: reference genome file (fasta, fastq, gzipped or nor). In absence of this file the VCF created by VCF_creator won't contain mapping related results.</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">\fB\-R\fR: use the reference file also in the variant calling, not only for mapping results</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">\fB\-B\fR: bwa path. e.g. \fI\,/home/me/my_programs/bwa\-0.7\/\fP.12/ (note that bwa must be pre\-compiled)</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">Optional unless option \fB\-G\fR used and bwa is not in the binary path.</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">\fB\-M\fR: Maximal number of mapping errors during BWA mapping phase.</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">Useless unless mapping on reference genome is required (option \fB\-G\fR). Default=4.</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">\fB\-h\fR: Prints this message and exist</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">\fB\-e\fR: map SNP predictions on reference genome with their extensions. \- Forced usage when using discoSnpRad</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">Any further question: read the readme file or contact us via the Biostar forum: https://www.biostars.org/t/discosnp/</span>
</pre>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="a5098d59b3f01a472b3b99623527dace07e65dce">
<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#a5098d59b3f01a472b3b99623527dace07e65dce"><strong>debian/mans/run_discoSnpRad.sh.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH RUN_DISCOSNPRAD.SH "1" "January 2019" "run_discoSnpRad.sh 2.3.0" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">run_discoSnpRad.sh \- pipelining kissnp2 and kissreads and clustering per locus for calling SNPs and small indels from RAD-seq data without the need of a reference genome</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B run_discoSnpRad.sh</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,-r read_file_of_files \/\fR[\fI\,OPTIONS\/\fR]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">run_discoSnpRad.sh, pipelining kissnp2 and kissreads and clustering per locus for calling SNPs and small indels from RAD\-seq data without the need of a reference genome</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Version 2.3.X</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">MANDATORY:</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-r\fR read_file_of_files</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Example: \fB\-r\fR bank.fof with bank.fof containing the two lines</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">data_sample/reads_sequence1.fasta</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">data_sample/reads_sequence2.fasta.gz</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-S\fR **absolute** path to short_read_connector directory, containing the short_read_connector.sh'' file.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">\fB\-Note1\fR: short read connector must be compiled.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-Note2\fR: if this option is missing, discoSnpRad will still however provide a fasta file containing SNPs and INDELS, that won't be clustered by locus</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.IP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">DISCOSNPRAD OPTIONS:</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-g\fR: reuse a previously created graph (.h5 file) with same prefix and same k and c parameters.</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">\fB\-b\fR value.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">1: (smart branching) forbid SNPs for which the two paths are branching (e.g. the two paths can be created either with a 'A' or a 'C' at the same position Default value</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">2: No limitation on branching (lowers the precision, high recall)</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-s\fR value. In b2 mode only: maximal number of symmetrical croasroads traversed while trying to close a bubble. Default: no limit</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">\fB\-D\fR value. discoSnpRad will search for deletions of size from 1 to D included. Default=100</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">\fB\-a\fR value. Maximal size of ambiguity of INDELs. INDELS whose ambiguity is higher than this value are not output [default '20']</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">\fB\-P\fR value. discoSnpRad will search up to P SNPs in a unique bubble. Default=5</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">\fB\-p\fR prefix. All out files will start with this prefix. Default="discoRad"</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">\fB\-l\fR: remove low complexity bubbles</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">\fB\-k\fR value. Set the length of used kmers. Must fit the compiled value. Default=31</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">\fB\-c\fR value. Set the minimal coverage per read set: Used by kissnp2 (don't use kmers with lower coverage) and kissreads (read coherency threshold). This coverage can be automatically detected per read set or specified per read set, see the documentation. Default=auto</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">\fB\-C\fR value. Set the maximal coverage for each read set: Used by kissnp2 (don't use kmers with higher coverage). Default=2^31\-1</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">\fB\-d\fR value. Set the number of authorized substitutions used while mapping reads on found SNPs (kissreads). Default=1</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">\fB\-u\fR: max number of used threads</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">\fB\-v\fR: verbose 0 (avoids progress output) or 1 (enables progress output) \fB\-\-\fR default=1.</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">\fB\-h\fR: Prints this message and exist</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">Any further question: read the readme file or contact us via the Biostar forum: https://www.biostars.org/t/discosnp/</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Mon, 21 Jan 2019 09:01:19 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Result of 2to3</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/filter_out_using_MAF.py</span></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/scripts/filter_out_using_MAF.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2,8 +2,8 @@ import sys</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> import gzip</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> if len(sys.argv)<3:</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;">- print "This tool filters out discoSnp prediction having a minor allele frequency lower than a provided threshold for ALL datasets."</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "python filter_out_using_MAF.py \".fa from discoSnp\" \"MAF threshold\""</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("This tool filters out discoSnp prediction having a minor allele frequency lower than a provided threshold for ALL datasets.")</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("python filter_out_using_MAF.py \".fa from discoSnp\" \"MAF threshold\"")</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> sys.exit()</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </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"><span class="gu" style="color: #800080; font-weight: 600;">@@ -52,7 +52,7 @@ while True:</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> break</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 to_output:</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;">- print (comment1,path1,comment2,path2,)</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;">+ print((comment1,path1,comment2,path2,))</span></span>
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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"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts_RAD/1SNP_by_cluster.py</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts_RAD/1SNP_by_cluster.py</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -88,5 +88,5 @@ vcf_file=sys.argv[1]</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> dict, nb_SNP_before, nb_SNP_after = store_info(vcf_file)</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> output_newvcf(vcf_file, dict)</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print("nb SNP before : " + str(nb_SNP_before))</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print("nb SNP after : " + str(nb_SNP_after))</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print(("nb SNP before : " + str(nb_SNP_before)))</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print(("nb SNP after : " + str(nb_SNP_after)))</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts_RAD/filter_paralogs.py</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts_RAD/filter_paralogs.py</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -100,4 +100,4 @@ dict, nb_cluster_tot = store_info(vcf_fi</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> clusters_to_keep, nb_clusters_kept = discard_clusters(dict, y)</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> output_newvcf(vcf_file, clusters_to_keep)</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print(str(nb_clusters_kept) + " on " + str(nb_cluster_tot) + " clusters had less than " + str(y*100) + "% of SNP with less than " + str(x*100) + "% heterygous genotypes") </span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print((str(nb_clusters_kept) + " on " + str(nb_cluster_tot) + " clusters had less than " + str(y*100) + "% of SNP with less than " + str(x*100) + "% heterygous genotypes")) </span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts_RAD/filter_vcf_by_indiv_cov_and_max_missing.py</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts_RAD/filter_vcf_by_indiv_cov_and_max_missing.py</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -17,25 +17,25 @@ import getopt</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> def usage():</span>
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> '''Usage'''</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="51" 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">
51
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "-----------------------------------------------------------------------------"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="52" 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">
52
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print sys.argv[0]," : vcf filter"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="53" 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">
53
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "-----------------------------------------------------------------------------"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="54" 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">
54
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "usage: ",sys.argv[0]," -i vcf_file -o output_file [-c min_cov -m max_missing -s]"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="55" 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">
55
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -i: input vcf file"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="56" 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">
56
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -o: output vcf file"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="57" 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">
57
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -m: max missing genotype proportion to keep a variant (between 0 and 1, def = 1)"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="58" 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">
58
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -c: min coverage to call a genotype (int, def=0)"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="59" 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">
59
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " -s: snp only (def= all variants)"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="60" 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">
60
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "-----------------------------------------------------------------------------"</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="61" 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">
61
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("-----------------------------------------------------------------------------")</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="62" 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">
62
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(sys.argv[0]," : vcf filter")</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="63" 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">
63
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("-----------------------------------------------------------------------------")</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="64" 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">
64
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("usage: ",sys.argv[0]," -i vcf_file -o output_file [-c min_cov -m max_missing -s]")</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="65" 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">
65
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -i: input vcf file")</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="66" 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">
66
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -o: output vcf file")</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="67" 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">
67
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -m: max missing genotype proportion to keep a variant (between 0 and 1, def = 1)")</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="68" 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">
68
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -c: min coverage to call a genotype (int, def=0)")</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="69" 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">
69
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" -s: snp only (def= all variants)")</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="70" 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">
70
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("-----------------------------------------------------------------------------")</span></span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="71" 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">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> sys.exit(2)</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="72" 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">
72
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="73" 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">
73
</td>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="74" 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">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> def main():</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> try:</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> opts, args = getopt.getopt(sys.argv[1:], "i:o:c:m:s", ["in=", "out=","cov=","miss=","snp-only"])</span>
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<td class="diff-line-num new new_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except getopt.GetoptError, err:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except getopt.GetoptError as err:</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> # print help information and exit:</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print str(err) # will print something like "option -a not recognized"</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(str(err)) # will print something like "option -a not recognized"</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> usage()</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> sys.exit(2)</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> </span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -60,7 +60,7 @@ def main():</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> assert False, "unhandled option"</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> </span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> if input_file == 0 or output_file == 0:</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Missing arguments"</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Missing arguments")</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> usage()</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> sys.exit(2)</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> else:</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/ClassVCF_creator.py</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/ClassVCF_creator.py</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -177,7 +177,7 @@ class VARIANT():</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> #--------------------------------------------------------------------------------------------------------------------------- </span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> def RetrievePolymorphismFromHeader(self):</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> '''Gets from the dicoAllele all the positions, and the nucleotides for each variant '''</span>
</pre>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for key,(posD,ntUp,ntLow) in self.dicoAllele.items(): #Goes through the dictionary of parsed header</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for key,(posD,ntUp,ntLow) in list(self.dicoAllele.items()): #Goes through the dictionary of parsed header</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> self.upper_path.listPosForward.append(int(posD)+1)</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> self.lower_path.listPosForward.append(int(posD)+1)</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> self.upper_path.listPosReverse.append(len(self.upper_path.seq)-int(posD))</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -390,12 +390,12 @@ class VARIANT():</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> if IDVariantUp != IDVariantLow:</span>
</pre>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> if bitwiseFlag & 2048 : #Checks if it's a supplementary alignment</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> print("Supplementary alignment:")</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print(self.upper_path.listSam)</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((self.upper_path.listSam))</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> return (2) </span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> else :</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> print("WARNING two consecutive lines do not store the same variant id: ")</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print(self.upper_path.listSam)</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print(self.lower_path.listSam)</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((self.upper_path.listSam))</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((self.lower_path.listSam))</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> return (1)</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> </span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> else:</span>
</pre>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -438,7 +438,7 @@ class PATH():</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> </span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> def RetrieveXA(self,VCFObject):</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> VCFObject.XA=""</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for position,(NM,cigarcode) in self.dicoMappingPos.items():</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for position,(NM,cigarcode) in list(self.dicoMappingPos.items()):</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> if cigarcode!="":</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> VCFObject.XA+=str(position)+","</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> if VCFObject.XA:</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -852,7 +852,7 @@ class INDEL(VARIANT):</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> else:</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> self.longestSequenceForward=self.ReverseComplement(self.upper_path.seq)</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> self.longestSequenceReverse=self.upper_path.seq</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for key,(posD,ind,amb) in self.dicoAllele.items():#Goes through the dictionary of parsed header</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for key,(posD,ind,amb) in list(self.dicoAllele.items()):#Goes through the dictionary of parsed header</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> #In case of forward strand mapped</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> #we return the disco indel + the lefmost nucleotide before the indel (by taking into account the ambiguity</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> self.upper_path.listPosForward.append(int(posD)-int(amb))</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1230,8 +1230,8 @@ class VCFFIELD():</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> error+=1</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> if error>0:</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> print(" !!! Line where the error occured !!!")</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print(VARIANT.upper_path.listSam)</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print(VARIANT.lower_path.listSam)</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((VARIANT.upper_path.listSam))</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((VARIANT.lower_path.listSam))</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> else : return (error) </span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> </span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="150" 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">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/discoSnp++_to_csv.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="151" 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">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/discoSnp++_to_csv.py</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -64,7 +64,7 @@ while 1:</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> i+=1</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> sys.stdout.write( com2_tab[i][:-1]+",")</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="156" 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">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print (data1_2,)</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((data1_2,))</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> </span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> </span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> </span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/filterOnBestDP_multiple_variant_at_same_pos.py</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/filterOnBestDP_multiple_variant_at_same_pos.py</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -25,7 +25,7 @@ while True:</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> line = vcf_for_igv.readline()</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> if not line: break</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> if line.startswith("#"): #We just print the header</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print (line.rstrip())</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((line.rstrip()))</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> continue</span>
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<td class="diff-line-num new new_line" data-linenumber="170" 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">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> list_line_same_pos.append(line) #list with all the lines </span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> pos=int(line.split("\t")[1]) </span>
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<td class="diff-line-num new new_line" data-linenumber="172" 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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -61,9 +61,9 @@ while True:</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> DP_max=DP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> compt+=1</span>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> if to_output:</span>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print (line_to_print.rstrip())</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((line_to_print.rstrip()))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> elif line_to_print :</span>
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<td class="diff-line-num new new_line" data-linenumber="179" 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">
179
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print (line_to_print.rstrip())</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="180" 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">
180
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((line_to_print.rstrip()))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="181" 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">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> if out:break </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="182" 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">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> vcf_for_igv.close() </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="183" 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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="184" 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">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/filter_out_using_ratio_of_covered_files.py</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="185" 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">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/filter_out_using_ratio_of_covered_files.py</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="186" 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">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -53,7 +53,7 @@ while True:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="187" 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">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> if coverage_high[i]>=minimal_coverage or coverage_low[i]>=minimal_coverage: number_of_covered_sets+=1</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="189" 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">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> if 100*number_of_covered_sets/float(number_of_read_sets)>=ratio_threshold:</span>
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<td class="diff-line-num new new_line" data-linenumber="190" 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">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print (comment1,path1,comment2,path2,)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="191" 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">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((comment1,path1,comment2,path2,))</span></span>
</pre>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> </span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> </span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> </span>
</pre>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/functionObjectVCF_creator.py</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="196" 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">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/functionObjectVCF_creator.py</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="197" 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">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -191,25 +191,25 @@ def CheckAtDistanceXBestHits(upper_path,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="198" 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">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> best_up=1024</span>
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<td class="diff-line-num new new_line" data-linenumber="199" 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">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> if int(upper_path.mappingPosition)==0 and int(lower_path.mappingPosition)==0:#Checks if paths are unmappped</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> return(".")</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for position,(nbMismatch,cigarcode) in posUp.items(): </span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for position,(nbMismatch,cigarcode) in list(posUp.items()): </span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> if nbMismatch<best_up:</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> best_up=nbMismatch</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> </span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> # get the best mapping distance for lower path </span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"> best_low=1024</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for position,(nbMismatch,cigarcode) in posLow.items(): </span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for position,(nbMismatch,cigarcode) in list(posLow.items()): </span></span>
</pre>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> if nbMismatch<best_low:</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> best_low=nbMismatch</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> </span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> # get the union of the mapping position at the best mapping positions</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> position_set = set()</span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for position,(nbMismatch,cigarcode) in posUp.items():</span></span>
</pre>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for position,(nbMismatch,cigarcode) in list(posUp.items()):</span></span>
</pre>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> if nbMismatch == best_up:</span>
</pre>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> position_set.add(position)</span>
</pre>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> if len(position_set) > 1: </span>
</pre>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"> return("MULTIPLE")</span>
</pre>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> </span>
</pre>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for position,(nbMismatch,cigarcode) in posLow.items():</span></span>
</pre>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for position,(nbMismatch,cigarcode) in list(posLow.items()):</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> if nbMismatch == best_low:</span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> position_set.add(position)</span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> if len(position_set) > 1: </span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/one2zeroBased_vcf.py</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/one2zeroBased_vcf.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="229" 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">
229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10,7 +10,7 @@ VCFfile=open("VCFone2zeroBAsed.vcf","w")</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> </span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> for line in file:</span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> if "#" == line[0]: </span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print (line,)</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((line,))</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> continue</span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"> line=line.rstrip('\n')</span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> #SNP_higher_path_3 117 3 C G . . Ty=SNP;Rk=1.00000;UL=86;UR=261;CL=.;CR=.;C1=124,0;C2=0,134 GT:DP:PL 0/0:124:10,378,2484 1/1:134:2684,408,10</span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/VCF_creator.py</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/VCF_creator.py</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -75,7 +75,7 @@ for opt, arg in opts :</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> listName[1]=listName[1].replace("_", " ")</span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> stream_file=open(fileName,'r')</span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> else : </span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("!! No file :" +str(arg)+"!!")</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("!! No file :" +str(arg)+"!!"))</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> sys.exit(2) </span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> elif opt in ("-o","--output"):</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> if arg!=None:</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -91,7 +91,7 @@ for opt, arg in opts :</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> print("!! No filtered sam output !!")</span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"> sys.exit(2) </span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> else:</span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Unkwnown option {} ".format(opt))</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Unkwnown option {} ".format(opt)))</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"> usage()</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"> sys.exit(2)</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> </span></pre>
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<li id="abfb1a54765fa4da90cfea86c619e421f0868366">
<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#abfb1a54765fa4da90cfea86c619e421f0868366"><strong>debian/patches/adapt_test_scripts.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Mon, 21 Jan 2019 09:01:19 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Adapt test scripts to Debian PATH</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/simple_test.sh</span></span>
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6
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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/test/simple_test.sh</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,6 +1,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> #!/bin/bash</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-../run_discoSnp++.sh -r fof.txt -T</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+run_discoSnp++.sh -r fof.txt -T</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> diff discoRes_k_31_c_auto_D_100_P_1_b_0_coherent.fa ref_discoRes_k_31_c_auto_D_100_P_1_b_0_coherent.fa</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> if [ $? -ne 0 ] ; then</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/large_test/local_large_test.sh</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/large_test/local_large_test.sh</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2,7 +2,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> #####################</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> # Default option run: </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"><span class="gd" style="color: #000; background-color: #fdd;">-../../run_discoSnp++.sh -r fof.txt -T</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+run_discoSnp++.sh -r fof.txt -T</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> if [ $? -ne 0 ] ; then</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> echo "*** Default option FAILURE:"</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> echo "*** discoSnp failure"</span></pre>
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<li id="7109d0c90a06eb64dda982f6f112fbe5ff0ca751">
<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#7109d0c90a06eb64dda982f6f112fbe5ff0ca751"><strong>debian/patches/fix_scripts.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Mon, 21 Jan 2019 09:01:19 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Add missing shebang line</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="gd" style="color: #000; background-color: #fdd;">--- a/scripts_RAD/discoRAD_finalization.sh</span></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/scripts_RAD/discoRAD_finalization.sh</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,3 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> # REQUIRES:</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> ## short_read_connector: instaleld and compiled: https://github.com/GATB/short_read_connector</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> ## quick_hierarchical_clustering compiled: </span></pre>
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<li id="bf2967f2e5d775c66983431a1a3d3a2edf5b7227">
<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#bf2967f2e5d775c66983431a1a3d3a2edf5b7227"><strong>debian/patches/path_to_readme_file_names.patch</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="34" 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="34" 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">@@ -34,6 +34,23 @@ Description: There is no point in delivering read_file_names in /usr/bin</td>
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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"> useref=""</span>
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> genome=""</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -463,14 +463,14 @@ echo -e "\t#############################</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> T="$(date +%s)"</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> if [ -f "$src_file" ]; then</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cmd="$EDIR/scripts_RAD/discoRAD_finalization.sh ${kissprefix}_coherent.fa $short_read_connector_path" </span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd="/usr/share/discosnp/scripts_RAD/discoRAD_finalization.sh ${kissprefix}_coherent.fa $short_read_connector_path" </span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> echo $cmd</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> $cmd</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> T="$(($(date +%s)-T))"</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> echo "RAD clustering per locus time in seconds: ${T}"</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> else</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> echo "IF YOU WANT TO CLUSTERIZE RESULTS, RUN: "</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo " $EDIR/scripts_RAD/discoRAD_finalization.sh ${kissprefix}_coherent.fa short_read_connector_path"</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo " /usr/share/discosnp/scripts_RAD/discoRAD_finalization.sh ${kissprefix}_coherent.fa short_read_connector_path"</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> echo " With short_read_connector_path indicating the directory containing short_read_connector.sh command "</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> fi</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> </span>
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37
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/run_discoSnp++.sh</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/run_discoSnp++.sh</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -54,7 +54,7 @@ paired=""</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,6 +78,24 @@ Description: There is no point in delivering read_file_names in /usr/bin</td>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="diff"> </span>
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="diff"> useref=""</span>
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63
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="diff"> genome=""</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -491,7 +491,7 @@ echo -e "\t#################### CREATE V</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> echo -e "\t###############################################################"</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> </span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> if [ -z "$genome" ]; then # NO reference genome use, vcf creator mode 1</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- vcfCreatorCmd="$EDIR/scripts/run_VCF_creator.sh -p ${kissprefix}_coherent.fa -o ${kissprefix}_coherent.vcf"</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ vcfCreatorCmd="/usr/share/discosnp/scripts/run_VCF_creator.sh -p ${kissprefix}_coherent.fa -o ${kissprefix}_coherent.vcf"</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> echo $vcfCreatorCmd</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> $vcfCreatorCmd</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> if [ $? -ne 0 ]</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -500,7 +500,7 @@ if [ -z "$genome" ]; then # NO referenc</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> exit 1</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> fi</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> else # A Reference genome is provided, vcf creator mode 2</span>
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<td class="diff-line-num new new_line" data-linenumber="94" 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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- vcfCreatorCmd="$EDIR/scripts/run_VCF_creator.sh $bwa_path_option -G $genome $bwa_path_option -p ${kissprefix}_coherent.fa -o ${kissprefix}_coherent.vcf -I $option_cores_post_analysis $e"</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ vcfCreatorCmd="/usr/share/discosnp/scripts/run_VCF_creator.sh $bwa_path_option -G $genome $bwa_path_option -p ${kissprefix}_coherent.fa -o ${kissprefix}_coherent.vcf -I $option_cores_post_analysis $e"</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> echo $vcfCreatorCmd</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> $vcfCreatorCmd</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> </span>
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64
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts_RAD/discoRAD_finalization.sh</span></span>
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65
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts_RAD/discoRAD_finalization.sh</span></span>
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66
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -61,7 +61,7 @@ cmd="${short_read_connector_directory}/s</span></span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -2,3 +2,6 @@ use_debian_packaged_gatb-core.patch</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">no_install_to_wrong_dir.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">path_to_readme_file_names.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">spelling.patch</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">fix_scripts.patch</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">adapt_test_scripts.patch</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">2to3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -7,13 +7,14 @@ include /usr/share/dpkg/default.mk</td>
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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"></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"> dh $@</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> dh $@<span class="idiff left right"> --with python3</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> mkdir -p debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> mv debian/$(DEB_SOURCE)/usr/bin/read_file_names debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> mv debian/$(DEB_SOURCE)/usr/bin/quick_hierarchical_clustering debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> for pl in `grep -Rl -e '#![[:space:]]*/bin/python' -e '#![[:space:]]*python' debian/*/usr/*` ; do \</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> rm -rf debian/$(DEB_SOURCE)/usr/share/discosnp/scripts/jenkins</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> for pl in `grep -Rl -e '#![[:space:]]*/bin/python' -e '#![[:space:]]*/usr/bin/env *python' debian/*/usr/*` ; do \</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> sed -i '1s?^#!.*python?#!/usr/bin/python3?' $${pl} ; \</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> done</span></pre>
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<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/discosnp/compare/c63c254996fc9d8b17ccad008e264cbc6c459cdc...9ea19bd4b311bfa1f46a197890ab55f503cc1be7#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: teal;">pkg</span><span class="o" style="font-weight: 600;">=</span>discosnp</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: navy;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: navy;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: navy;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span>/test/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip </span>ref_discoRes_k_31_c_auto_D_100_P_1_b_0_coherent<span class="k" style="font-weight: 600;">*</span>.gz</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">chmod</span> +x simple_test.sh</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">./simple_test.sh</span></pre>
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