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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/iva">Debian Med / iva</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/iva/commit/e2bf816db6cf839d9bb202768de397221ceeda62">e2bf816d</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2019-12-25T11:36:28Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix the samtools version logic
</pre>
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<strong><a href="https://salsa.debian.org/med-team/iva/commit/076bf419516898f671d1650806ad16f05db74d26">076bf419</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2019-12-25T11:37:11Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 12
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<strong><a href="https://salsa.debian.org/med-team/iva/commit/939480c456445d7a8ac871d9bb3c9ecdf48694ce">939480c4</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2019-12-25T11:41:31Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.1
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<h4>5 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
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−
debian/compat
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#0e7dcd3ba66c586c8c88678c775f0e9b2ee4f8ae">
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+
debian/patches/samtools1.10
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/iva/compare/7a61fefba06c49722109ae0dcaad2a4384b181b0...939480c456445d7a8ac871d9bb3c9ecdf48694ce#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">iva (1.0.9+ds-7) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * debian/patches/samtools1.10: fix the samtools version logic</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Wed, 25 Dec 2019 12:37:15 +0100</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">iva (1.0.9+ds-6) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Use correct Vcs-Git URL.</span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/iva/compare/7a61fefba06c49722109ae0dcaad2a4384b181b0...939480c456445d7a8ac871d9bb3c9ecdf48694ce#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/iva/compare/7a61fefba06c49722109ae0dcaad2a4384b181b0...939480c456445d7a8ac871d9bb3c9ecdf48694ce#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,7 @@ Uploaders: Andreas Tille <tille@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Sascha Steinbiss <satta@debian.org></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>),</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libssl-dev,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> bioperl,</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,6 +15,7 @@ Build-Depends: debhelper (>= 11~),</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> mummer,</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> python3-packaging,</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> python3-numpy,</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> python3-nose,</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> python3-networkx,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,7 +23,7 @@ Build-Depends: debhelper (>= 11~),</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> samtools,</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> smalt,</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> default-jdk-headless</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.4</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.1</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/iva</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/iva.git</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Homepage: https://github.com/sanger-pathogens/iva</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,6 +32,7 @@ Package: iva</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> ${perl:Depends},</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> fastaq (>= 1.6),</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> kmc,</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> mummer,</span>
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<a href="https://salsa.debian.org/med-team/iva/compare/7a61fefba06c49722109ae0dcaad2a4384b181b0...939480c456445d7a8ac871d9bb3c9ecdf48694ce#0e7dcd3ba66c586c8c88678c775f0e9b2ee4f8ae"><strong>debian/patches/samtools1.10</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Fix samtools version parsing so that 1.10 > 1.2</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- iva.orig/iva/mapping.py</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ iva/iva/mapping.py</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -21,6 +21,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> from iva import common</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> from iva import external_progs</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </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;">+from packaging import version</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> class Error (Exception): pass</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -93,7 +95,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> if sort:</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> threads = min(4, threads)</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> thread_mem = int(500 / threads)</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if str(external_progs.get_version('samtools')) >= '1.2':</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if version.parse(external_progs.get_version('samtools')) >= version.parse("1.2"):</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> sort_cmd = 'samtools sort -@' + str(threads) + ' -m ' + str(thread_mem) + 'M -o ' + final_bam + ' ' + intermediate_bam</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> sort_cmd = 'samtools sort -@' + str(threads) + ' -m ' + str(thread_mem) + 'M ' + intermediate_bam + ' ' + out_prefix</span></pre>
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<a href="https://salsa.debian.org/med-team/iva/compare/7a61fefba06c49722109ae0dcaad2a4384b181b0...939480c456445d7a8ac871d9bb3c9ecdf48694ce#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">disable-multithreaded-test.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">perl-shebang.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">samtools1.10</span></pre>
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