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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bamkit">Debian Med / bamkit</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bamkit/-/commit/658e9ec482359fef6dc063794879d33bec04b46b">658e9ec4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-01T21:52:24+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use 2to3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bamkit/-/commit/9d4ddd09a12da13b209b7b06d4ae37fbd0ce052b">9d4ddd09</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-01T21:53:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">No test for the moment
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bamkit/-/commit/d8fac94e28c153607a01f086a00eb51157ee4f1e">d8fac94e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-01T22:03:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use python scripts as links
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bamkit/-/commit/fbe2497195abd1060c69dcf00fe56558cd93d154">fbe24971</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-01T22:16:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpages
</pre>
</li>
</ul>
<h4>18 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<span class="deleted-file">
−
debian/README.test
</span>
</a>
</li>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
<span class="new-file">
+
debian/createmanpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
debian/install
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<li class="file-stats">
<a href="#efc7fe57b5983b0283c6410fceef7e74f687aeb5">
<span class="deleted-file">
−
debian/lintian-overrides
</span>
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</li>
<li class="file-stats">
<a href="#fecfc979d8195fa6ea489055f8e5ba81a97d3964">
<span class="new-file">
+
debian/man/bamcleanheader.py.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#fc227a2c5b7bf91d63129a6f214eada4931aed92">
<span class="new-file">
+
debian/man/bamfilterrg.py.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#23cebe08bbe0c9ce83d35dd6e3d0e523e34b5db6">
<span class="new-file">
+
debian/man/bamfixflags.py.1
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<li class="file-stats">
<a href="#5be701f0aa0de700f7a9b842efeaf1cb65f9b233">
<span class="new-file">
+
debian/man/bamgroupreads.py.1
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<li class="file-stats">
<a href="#c2e36d8c656071347253900a81c5cf0f7e173911">
<span class="new-file">
+
debian/man/bamheadrg.py.1
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</li>
<li class="file-stats">
<a href="#4e0b000ce70272b0cbb3b9307023536351cb7056">
<span class="new-file">
+
debian/man/bamlibs.py.1
</span>
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</li>
<li class="file-stats">
<a href="#54b2328e07acf7a9588bbd91e4d8b4c7272b84c4">
<span class="new-file">
+
debian/man/bamtofastq.py.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
<span class="new-file">
+
debian/manpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
<span class="new-file">
+
debian/patches/2to3.patch
</span>
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</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<span class="new-file">
+
debian/patches/series
</span>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="deleted-file">
−
debian/tests/control
</span>
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="deleted-file">
−
debian/tests/run-unit-test
</span>
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong>
deleted
</a>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<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="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="o" style="font-weight: 600;">.</span></span>
</pre>
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2
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<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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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC3" class="line" lang="php"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
5
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="php"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC7" class="line" lang="php"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
8
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<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>
</td>
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<br>
</li>
<li id="ebcf9854ee19af4b7bf8405b283789c18769680f">
<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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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
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian/man</span>
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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
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$MANDIR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">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 $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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<td class="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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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">NAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Description:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Description: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Package:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Package: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: #008080;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span><span class="se" style="color: #d14;">\</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>bamcleanheader.py</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" --help"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"remove illegal and malformed fields from a BAM file's header"</span> <span class="se" style="color: #d14;">\</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>bamfilterrg.py</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" --help"</span> <span class="se" style="color: #d14;">\</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"filter readgroup(s) from a BAM file"</span> <span class="se" style="color: #d14;">\</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">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 class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>bamfixflags.py</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" --help"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="30" 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">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"filter readgroup(s) from a BAM file"</span> <span class="se" style="color: #d14;">\</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>bamgroupreads.py</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" --help"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="36" 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">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Group BAM file by read IDs without sorting"</span> <span class="se" style="color: #d14;">\</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">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 class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>bamheadrg.py</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" --help"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="42" 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">
42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Inject readgroup info"</span> <span class="se" style="color: #d14;">\</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>bamlibs.py</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" --help"</span> <span class="se" style="color: #d14;">\</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"output comma delimited string of read group IDs for each library"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>bamtofastq.py</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" --help"</span> <span class="se" style="color: #d14;">\</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Convert a coordinate sorted BAM file to FASTQ"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$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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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC60" 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: #008080;">EOT</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"><span class="sh" style="color: #d14;">The following web page might be helpful in doing so:</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">*.py usr/<span class="idiff left right">bin</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">*.py usr/<span class="idiff left right">share/bamkit</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">sectosupp usr/bin</span></pre>
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<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154#efc7fe57b5983b0283c6410fceef7e74f687aeb5"><strong>debian/lintian-overrides</strong>
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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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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">bamkit: script-with-language-extension usr/bin/*.*</span></pre>
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<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154#fecfc979d8195fa6ea489055f8e5ba81a97d3964"><strong>debian/man/bamcleanheader.py.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 1.47.15.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH BAMCLEANHEADER.PY "1" "June 2020" "bamcleanheader.py 0.0.1+git20170413.ccd079d" "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">bamcleanheader.py \- remove illegal and malformed fields from a BAM file's header</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 bamcleanheader.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\-h] [\-S] [input [input ...]]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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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">remove illegal and malformed fields from a BAM file's header</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.SS "positional arguments:"</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">input</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">SAM/BAM file to inject header lines into. If '\-' or absent then defaults to stdin.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.SS "optional arguments:"</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">\fB\-h\fR, \fB\-\-help\fR</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">show this help message and exit</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, \fB\-\-is_sam\fR</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">input is SAM</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="fc227a2c5b7bf91d63129a6f214eada4931aed92">
<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154#fc227a2c5b7bf91d63129a6f214eada4931aed92"><strong>debian/man/bamfilterrg.py.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 1.47.15.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH BAMFILTERRG.PY "1" "June 2020" "bamfilterrg.py 0.0.1+git20170413.ccd079d" "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">bamfilterrg.py \- filter readgroup(s) from a BAM file</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 bamfilterrg.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\-h] [\-i BAM] [\-r STR] [\-n INT] [\-S] [\-b] [\-u]</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">filter readgroup(s) from a BAM file</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.SS "optional arguments:"</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">show this help message and exit</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-i\fR BAM, \fB\-\-input\fR BAM</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Input BAM file</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">\fB\-r\fR STR, \fB\-\-readgroup\fR STR</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Read group(s) to extract (comma separated)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-n\fR INT</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Output first n alignments and quit</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">\fB\-S\fR</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Input is SAM format</span>
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<td class="diff-line-num new new_line" data-linenumber="27" 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">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.TP</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">\fB\-b\fR</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Output BAM format</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">\fB\-u\fR</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Output uncompressed BAM format (implies \fB\-b\fR)</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="23cebe08bbe0c9ce83d35dd6e3d0e523e34b5db6">
<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154#23cebe08bbe0c9ce83d35dd6e3d0e523e34b5db6"><strong>debian/man/bamfixflags.py.1</strong></a>
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1
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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 1.47.15.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH BAMFIXFLAGS.PY "1" "June 2020" "bamfixflags.py 0.0.1+git20170413.ccd079d" "User Commands"</span>
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3
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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">bamfixflags.py \- filter readgroup(s) from a BAM file</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 bamfixflags.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\-h] [\-i BAM] \fB\-l\fR FILE [\-n INT] [\-S] [\-b] [\-u]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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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">filter readgroup(s) from a BAM file</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.SS "optional arguments:"</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">show this help message and exit</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-i\fR BAM, \fB\-\-input\fR BAM</span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Input BAM file</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="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">\fB\-l\fR FILE, \fB\-\-lib_info\fR FILE</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">SVTyper JSON file of library information</span>
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<td class="diff-line-num new new_line" data-linenumber="21" 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">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.TP</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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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-n\fR INT</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Output first n alignments and quit</span>
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<td class="diff-line-num new new_line" data-linenumber="24" 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">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.TP</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="25" 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">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">\fB\-S\fR</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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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Input is SAM format</span>
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<td class="diff-line-num new new_line" data-linenumber="27" 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">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.TP</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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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">\fB\-b\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="29" 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">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Output BAM format</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.TP</span>
</pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">\fB\-u\fR</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="32" 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">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Output uncompressed BAM format (implies \fB\-b\fR)</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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</li>
<li id="5be701f0aa0de700f7a9b842efeaf1cb65f9b233">
<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154#5be701f0aa0de700f7a9b842efeaf1cb65f9b233"><strong>debian/man/bamgroupreads.py.1</strong></a>
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1
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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 1.47.15.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH BAMGROUPREADS.PY "1" "June 2020" "bamgroupreads.py 0.0.1+git20170413.ccd079d" "User Commands"</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">bamgroupreads.py \- Group BAM file by read IDs without sorting</span>
</pre>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
</pre>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B bamgroupreads.py</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\-h] [\-i BAM] [\-r STR] [\-d] [\-f] [\-S] [\-b] [\-u] [\-M]</span>
</pre>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
</pre>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Group BAM file by read IDs without sorting</span>
</pre>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH OPTIONS</span>
</pre>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.SS "optional arguments:"</span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="13" 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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">show this help message and exit</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-i\fR BAM, \fB\-\-input\fR BAM</span>
</pre>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Input BAM file</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</span>
</pre>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">\fB\-r\fR STR, \fB\-\-readgroup\fR STR</span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Read group(s) to extract (comma separated)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="21" 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">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="22" 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">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-d\fR, \fB\-\-reset_dups\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="23" 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">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Reset duplicate flags</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="24" 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">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.TP</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="25" 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">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">\fB\-f\fR, \fB\-\-fix_flags\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="26" 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">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Fix mate flags for secondary reads</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="27" 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">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="28" 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">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">\fB\-S\fR</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="29" 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">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Input is SAM format</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="30" 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">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.TP</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="31" 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">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">\fB\-b\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="32" 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">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Output BAM format</span>
</pre>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">\fB\-u\fR</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Output uncompressed BAM format (implies \fB\-b\fR)</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">\fB\-M\fR</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">split reads are flagged as secondary, not supplementary. For compatibility with legacy BWA\-MEM "\-M" flag</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="c2e36d8c656071347253900a81c5cf0f7e173911">
<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154#c2e36d8c656071347253900a81c5cf0f7e173911"><strong>debian/man/bamheadrg.py.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 1.47.15.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH BAMHEADRG.PY "1" "June 2020" "bamheadrg.py 0.0.1+git20170413.ccd079d" "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">bamheadrg.py \- Inject readgroup info</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 bamheadrg.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\-h] [\-r READGROUP] \fB\-d\fR DONOR [\-S] [recipient]</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">Inject readgroup info</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.SS "positional arguments:"</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">recipient</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">SAM file to inject header lines into. If '\-' or absent then defaults to stdin.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.SS "optional arguments:"</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">\fB\-h\fR, \fB\-\-help\fR</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">show this help message and exit</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-r\fR READGROUP, \fB\-\-readgroup\fR READGROUP</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Read group(s) to extract (comma separated)</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.TP</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-d\fR DONOR, \fB\-\-donor\fR DONOR</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Donor BAM/SAM file to extract read group info</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-S\fR, \fB\-\-donor_is_sam\fR</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Donor file is SAM</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="4e0b000ce70272b0cbb3b9307023536351cb7056">
<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154#4e0b000ce70272b0cbb3b9307023536351cb7056"><strong>debian/man/bamlibs.py.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 1.47.15.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH BAMLIBS.PY "1" "June 2020" "bamlibs.py 0.0.1+git20170413.ccd079d" "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">bamlibs.py \- output comma delimited string of read group IDs for each library</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 bamlibs.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\-h] [\-S] [input]</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">output comma delimited string of read group IDs for each library</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.SS "positional arguments:"</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
</pre>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">input</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">SAM/BAM file to inject header lines into. If '\-' or absent then defaults to stdin.</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.SS "optional arguments:"</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.TP</span>
</pre>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">show this help message and exit</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-S\fR, \fB\-\-is_sam\fR</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">input is SAM</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="54b2328e07acf7a9588bbd91e4d8b4c7272b84c4">
<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154#54b2328e07acf7a9588bbd91e4d8b4c7272b84c4"><strong>debian/man/bamtofastq.py.1</strong></a>
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1
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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 1.47.15.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH BAMTOFASTQ.PY "1" "June 2020" "bamtofastq.py 0.0.1+git20170413.ccd079d" "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">bamtofastq.py \- Convert a coordinate sorted BAM file to FASTQ</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B bamtofastq.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\-h] [\-r STR] [\-n] [\-S] [\-H FILE] [BAM [BAM ...]]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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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">Convert a coordinate sorted BAM file to FASTQ</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">(ignores unpaired reads)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.SS "positional arguments:"</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">BAM</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Input BAM file(s). If absent then defaults to stdin.</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.SS "optional arguments:"</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">show this help message and exit</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
</pre>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">\fB\-r\fR STR, \fB\-\-readgroup\fR STR</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Read group(s) to extract (comma separated)</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">\fB\-n\fR, \fB\-\-rename\fR</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Rename reads</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.TP</span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">\fB\-S\fR, \fB\-\-is_sam\fR</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Input is SAM format</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">\fB\-H\fR FILE, \fB\-\-header\fR FILE</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Write BAM header to file</span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.SH AUTHOR</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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</li>
<li id="68e0b13744e158347bfd74ebaaca667435f07d14">
<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154#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/man/*.1</span></pre>
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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 26 May 2020 15:07:58 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Use 2to3 t port to Python3</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/bamcleanheader.py</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/bamcleanheader.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> import argparse, sys</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> from argparse import RawTextHelpFormatter</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">@@ -107,11 +107,11 @@</span> def bam_clean(bam, is_sam, header_only):</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> # out_bam = pysam.Samfile('-', 'w', template=in_bam)</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 class="gd" style="color: #000; background-color: #fdd;">- print get_clean_header(in_bam)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(get_clean_header(in_bam))</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> if not header_only:</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> for al in in_bam:</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 al</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(al)</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"> # # this code leads to pipeing errors</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> # if not header_only:</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -140,6 +140,6 @@</span> def main():</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> if __name__ == '__main__':</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> try:</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> sys.exit(main())</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except IOError, e:</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except IOError as e:</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> if e.errno != 32: # ignore SIGPIPE</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> raise</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bamfilterrg.py</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bamfilterrg.py</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> </span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> # for tgi cluster:</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> #/gapp/x64linux/opt/pythonbrew/venvs/Python-2.7.6/gemini/bin/python</span>
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<td class="diff-line-num new new_line" data-linenumber="43" 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">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="p">@@ -125,7 +125,7 @@</span> def main():</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> if __name__ == "__main__":</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> try:</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> sys.exit(main())</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except IOError, e:</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except IOError as e:</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> if e.errno != 32: # ignore SIGPIPE</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> raise</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> </span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bamfixflags.py</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bamfixflags.py</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> # for tgi cluster:</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> #/gapp/x64linux/opt/pythonbrew/venvs/Python-2.7.6/gemini/bin/python</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="p">@@ -121,16 +121,16 @@</span> def bamfixflags(bamfile,</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> for sample in lib_info:</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> # print lib_info[sample]['libraryArray'][0]</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> for lib in lib_info[sample]['libraryArray']:</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- lib_hist = {int(k):int(v) for k,v in lib['histogram'].items()}</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ lib_hist = {int(k):int(v) for k,v in list(lib['histogram'].items())}</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> p25 = percentile(lib_hist, 25)</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> p75 = percentile(lib_hist, 75)</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> lib_mean = mean(lib_hist)</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> lib_sd = stdev(lib_hist)</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'p25', p25</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'p75', p75</span></span>
</pre>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'mean', lib_mean</span></span>
</pre>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'sd', lib_sd</span></span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('p25', p25)</span></span>
</pre>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('p75', p75)</span></span>
</pre>
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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="gi" style="color: #000; background-color: #dfd;">+ print('mean', lib_mean)</span></span>
</pre>
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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;">+ print('sd', lib_sd)</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> </span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> low = int(p25 - mapping_bound * (p75 - p25) + .499)</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> high = int(p75 + mapping_bound * (p75 - p25) + .499)</span>
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<td class="diff-line-num new new_line" data-linenumber="82" 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">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="p">@@ -171,49 +171,49 @@</span> def bamfixflags(bamfile,</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> else:</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> out_bam = pysam.Samfile('-', 'wh', template=in_bam)</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> </span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print proper</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(proper)</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> for al in in_bam:</span>
</pre>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> # out_bam.write(al)</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print al</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(al)</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> </span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> if al.is_supplementary:</span>
</pre>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> pass</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> </span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> elif al.is_unmapped or al.mate_is_unmapped:</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> if al.is_proper_pair:</span>
</pre>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'mismarked proper (unmapped)'</span></span>
</pre>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('mismarked proper (unmapped)')</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> al.is_proper_pair = False</span>
</pre>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> </span>
</pre>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> elif al.reference_id != al.next_reference_id:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> if al.is_proper_pair:</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="104" 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">
104
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'mismarked proper (chrom)'</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="105" 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">
105
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('mismarked proper (chrom)')</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="106" 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">
106
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> al.is_proper_pair = False</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="107" 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">
107
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> </span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="108" 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">
108
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> elif (al.reference_start < al.next_reference_start</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="109" 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">
109
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> and (al.is_reverse or not al.mate_is_reverse)):</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="110" 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">
110
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> if al.is_proper_pair:</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="111" 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">
111
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'mismarked proper (orient +)'</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="112" 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">
112
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('mismarked proper (orient +)')</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="113" 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">
113
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> al.is_proper_pair = False</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="114" 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">
114
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> </span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="115" 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">
115
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> elif (al.reference_start > al.next_reference_start</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="116" 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">
116
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> and (not al.is_reverse or al.mate_is_reverse)):</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="117" 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">
117
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> if al.is_proper_pair:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="118" 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">
118
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'mismarked proper (orient -)'</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="119" 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">
119
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('mismarked proper (orient -)')</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="120" 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">
120
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> al.is_proper_pair = False</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="121" 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">
121
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> </span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="122" 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">
122
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> # if al.supp</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="123" 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">
123
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> elif (al.template_length >= proper[al.opt('RG')][0]</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="124" 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">
124
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> and al.template_length <= proper[al.opt('RG')][1]):</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="125" 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">
125
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> if not al.is_proper_pair:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="126" 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">
126
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'mismarked improper (insert size)'</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="127" 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">
127
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('mismarked improper (insert size)')</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="128" 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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> al.is_proper_pair = True</span>
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<td class="diff-line-num new new_line" data-linenumber="129" 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">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> else:</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> if al.is_proper_pair:</span>
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<td class="diff-line-num new new_line" data-linenumber="131" 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">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'mismarked proper (insert size)'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('mismarked proper (insert size)')</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> al.is_proper_pair = False</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> </span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> # out_bam.write(al)</span>
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<td class="diff-line-num new new_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print al</span></span>
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<td class="diff-line-num new new_line" data-linenumber="137" 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">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(al)</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> # print proper[al.opt('RG')], al.template_length</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> # print al</span>
</pre>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> # # must be in a user specified readgroup</span>
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<td class="diff-line-num new new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="p">@@ -301,7 +301,7 @@</span> def main():</span>
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<td class="diff-line-num new new_line" data-linenumber="142" 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">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> if __name__ == "__main__":</span>
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<td class="diff-line-num new new_line" data-linenumber="143" 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">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> try:</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> sys.exit(main())</span>
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<td class="diff-line-num new new_line" data-linenumber="145" 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">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except IOError, e:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="146" 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">
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;">+ except IOError as e:</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> if e.errno != 32: # ignore SIGPIPE</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> raise</span>
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<td class="diff-line-num new new_line" data-linenumber="149" 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">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> </span>
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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/bamgroupreads.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/bamgroupreads.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="152" 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">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="153" 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">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<td class="diff-line-num new new_line" data-linenumber="154" 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">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></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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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> # for tgi cluster:</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> #/gapp/x64linux/opt/pythonbrew/venvs/Python-2.7.6/gemini/bin/python</span>
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<td class="diff-line-num new new_line" data-linenumber="158" 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">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="p">@@ -169,7 +169,7 @@</span> def main():</span>
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<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> if __name__ == "__main__":</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> try:</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> sys.exit(main())</span>
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<td class="diff-line-num new new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except IOError, e:</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except IOError as e:</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> if e.errno != 32: # ignore SIGPIPE</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> raise</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> </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;">--- a/bamheadrg.py</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;">+++ b/bamheadrg.py</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> </span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> import argparse, sys</span>
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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"> from argparse import RawTextHelpFormatter</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"><span class="p">@@ -71,9 +71,9 @@</span> def bamheadrg(recipient, rg_out):</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> if in_header:</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> if line[0] != '@':</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> for readgroup in rg_out:</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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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print '@RG\t' + '\t'.join([':'.join((t,readgroup[t])) for t in readgroup])</span></span>
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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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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('@RG\t' + '\t'.join([':'.join((t,readgroup[t])) for t in readgroup]))</span></span>
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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"> in_header = False</span>
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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"><span class="gd" style="color: #000; background-color: #fdd;">- print line.rstrip()</span></span>
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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 class="gi" style="color: #000; background-color: #dfd;">+ print(line.rstrip())</span></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"> return</span>
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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>
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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>
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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"><span class="p">@@ -101,6 +101,6 @@</span> def main():</span>
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<td class="diff-line-num new new_line" data-linenumber="188" 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">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> if __name__ == '__main__':</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"> try:</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"> sys.exit(main())</span>
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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="gd" style="color: #000; background-color: #fdd;">- except IOError, e:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="192" 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">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except IOError as e:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="193" 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">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> if e.errno != 32: # ignore SIGPIPE</span>
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<td class="diff-line-num new new_line" data-linenumber="194" 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">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> raise</span>
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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/bamlibs.py</span></span>
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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/bamlibs.py</span></span>
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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="p">@@ -1,4 +1,4 @@</span></span>
</pre>
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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"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></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"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<td class="diff-line-num new new_line" data-linenumber="200" 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">
200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="201" 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">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> import argparse, sys</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="202" 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">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"> from argparse import RawTextHelpFormatter</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="203" 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">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="p">@@ -58,7 +58,7 @@</span> def get_libs(bam, is_sam, header_only):</span>
</pre>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> </span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> # print</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> for lib in lib_rg:</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ','.join(lib_rg[lib])</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(','.join(lib_rg[lib]))</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> in_bam.close()</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> </span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> return</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="p">@@ -77,6 +77,6 @@</span> def main():</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> if __name__ == '__main__':</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> sys.exit(main())</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except IOError, e:</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except IOError as e:</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> if e.errno != 32: # ignore SIGPIPE</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> raise</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bamtofastq.py</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bamtofastq.py</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> # for tgi cluster:</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> #/gapp/x64linux/opt/pythonbrew/venvs/Python-2.7.6/gemini/bin/python</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="p">@@ -131,15 +131,15 @@</span> description: Convert a coordinate sorted</span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="230" 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">
230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> def printfastq(al,read):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="231" 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">
231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> if(al.is_reverse):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="232" 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">
232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "@" + str(al.qname) + "/" + str(read) + "\n" + str(revcomp(al.seq)) + "\n" + "+" + "\n" + str(al.qual[::-1])</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="233" 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">
233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("@" + str(al.qname) + "/" + str(read) + "\n" + str(revcomp(al.seq)) + "\n" + "+" + "\n" + str(al.qual[::-1]))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="234" 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">
234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> else: </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="235" 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">
235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "@" + str(al.qname) + "/" + str(read) + "\n" + str(al.seq) + "\n" + "+" + "\n" + str(al.qual)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="236" 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">
236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("@" + str(al.qname) + "/" + str(read) + "\n" + str(al.seq) + "\n" + "+" + "\n" + str(al.qual))</span></span>
</pre>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> </span>
</pre>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> def printfastq_rg(al,read, rg):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="239" 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">
239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> if(al.is_reverse):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="240" 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">
240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "@" + str(al.qname) + "/" + str(read) + " " + "RG:Z:" + str(rg) + "\n" + str(revcomp(al.seq)) + "\n" + "+" + "\n" + str(al.qual[::-1])</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="241" 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">
241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("@" + str(al.qname) + "/" + str(read) + " " + "RG:Z:" + str(rg) + "\n" + str(revcomp(al.seq)) + "\n" + "+" + "\n" + str(al.qual[::-1]))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="242" 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">
242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> else: </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="243" 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">
243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "@" + str(al.qname) + "/" + str(read) + " " + "RG:Z:" + str(rg) + "\n" + str(al.seq) + "\n" + "+" + "\n" + str(al.qual)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="244" 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">
244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("@" + str(al.qname) + "/" + str(read) + " " + "RG:Z:" + str(rg) + "\n" + str(al.seq) + "\n" + "+" + "\n" + str(al.qual))</span></span>
</pre>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> </span>
</pre>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> def revcomp(seq):</span>
</pre>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> seq1 = seq.translate(maketrans("AGCTagct", "TCGAtcga"))</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="248" 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">
248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"><span class="p">@@ -166,7 +166,7 @@</span> def main():</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="249" 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">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> if __name__ == "__main__":</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="250" 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">
250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="251" 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">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"> sys.exit(main())</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="252" 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">
252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except IOError, e:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="253" 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="LC253" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except IOError as e:</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> if e.errno != 32: # ignore SIGPIPE</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"> raise</span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2to3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154#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">@@ -8,6 +8,15 @@ include /usr/share/dpkg/default.mk</td>
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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"> dh $@ --with python3</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">override_dh_link:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> dh_link</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> for py in debian/$(DEB_SOURCE)/usr/share/$(DEB_SOURCE)/*.py ; do \</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> dh_link `echo $${py} | sed 's:^debian/$(DEB_SOURCE)::'` usr/bin/`basename $${py}` ; \</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> done</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">override_dh_installman:</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> dh_installman --language=C</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">#override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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2
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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/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong>
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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: #000080;">-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: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="c" style="color: #998; font-style: italic;">#PACKAGENAME#</span></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="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</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;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"></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;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></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"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e92c0a3e1f1591a597cfd69a51f9d0fa916e1014...fbe2497195abd1060c69dcf00fe56558cd93d154#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Reference:</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Author: </span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> Title: </span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Journal: </span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> Year: </span>
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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> Volume: </span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Number: </span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> Pages: </span>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> DOI: </span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> PMID:</span>
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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> URL: </span>
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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> eprint: </span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Registry:</span>
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14
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> Entry:</span></pre>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Entry:<span class="idiff left right"> NA</span></span></pre>
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