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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pbdagcon">Debian Med / pbdagcon</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/commit/f1293f7d77a30651b1baff77ed21729c941a9389">f1293f7d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-05T08:05:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Run 2to3 on Python2 files to try a Python3 port
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/commit/24e5ff6a71f667fceca02e43398958ee60b4c7e5">24e5ff6a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-05T08:29:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.3+git20180411.c14c422+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/commit/299cc7169363240685446ec3f3a375c55af07ae0">299cc716</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-05T08:29:37Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.3+git20180411.c14c422+ds'
Update to upstream version '0.3+git20180411.c14c422+ds'
with Debian dir c49b142db0e8aa891047acd5af464836ba587e34</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/commit/77a848a5e9d677a2a1e7b8391b94487a76bbd7af">77a848a5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-05T08:29:37Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/commit/8ced7a4ddf4066813af77b0c4d1773c23c1f4f3f">8ced7a4d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-05T08:29:37Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/commit/937e3bca656173c54b25d96ee6070ebcf0bfd6d2">937e3bca</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-05T08:29:45Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/commit/f7388d5312e0fdef873583b9b939f694f3455e5c">f7388d53</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-05T09:00:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapt patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/commit/eda89ff7df0d0243f9f010e5e6f4e6955e2a6f51">eda89ff7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-05T09:14:08Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build-Depends: s/python/python3/
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/commit/21b29a28aa525fdeb46918c40817e4190ca9cbbd">21b29a28</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-05T09:19:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set Python3 interpreter
</pre>
</li>
</ul>
<h4>17 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#8ab4e94f59343a8b2d003b0b47d21fff1724bfd9">
<span class="new-file">
+
bamboo_build.sh
</span>
</a>
</li>
<li class="file-stats">
<a href="#657ba97c256772c813a44e0cf140908da4dfb60e">
<span class="new-file">
+
bamboo_test.sh
</span>
</a>
</li>
<li class="file-stats">
<a href="#8d9366bd88df2f74d12bfee71e917c42e0691bcc">
configure.py
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
<span class="new-file">
+
debian/patches/2to3.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#af645134b14b2b35e00b98ef1750433e86979d51">
debian/patches/compiler-flags.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#043cfe66d8ab296344c0190710d4ff02fc647c21">
src/cpp/DazAlnProvider.cpp
</a>
</li>
<li class="file-stats">
<a href="#f1ff314bb7b6f56e6132e1d24b52b6b4b47d76e7">
src/cpp/DazAlnProvider.hpp
</a>
</li>
<li class="file-stats">
<a href="#87730016f20b7a818290092a15e077be866de047">
src/cpp/makefile
</a>
</li>
<li class="file-stats">
<a href="#52d7c8311209fdc77c02878ea62709c921b6344b">
src/filterm4.py
</a>
</li>
<li class="file-stats">
<a href="#040850ef33183469415e5992c39d5869b0d8e0a9">
src/m4topre.py
</a>
</li>
<li class="file-stats">
<a href="#dcf1ae944f03fae6488243d0b2cca342eb19cd63">
src/q-sense.py
</a>
</li>
<li class="file-stats">
<a href="#e5b616885873858305226a78e6cc27143386e5a6">
test/cpp/makefile
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/pbdagcon/compare/83dbb7eea91693f73f0432b5052919075bff6a3e...21b29a28aa525fdeb46918c40817e4190ca9cbbd#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="130" 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">@@ -130,3 +130,7 @@ ga('send', 'pageview');</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC130" class="line" lang="markdown"> <span class="sx" style="color: #d14;">src/filterm4.py</span> <span class="nn" style="color: #555;">'code'</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="131" 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">
131
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<td class="diff-line-num new_line" data-linenumber="131" 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="LC131" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">pbdagcon_wf.sh</span><span class="p">]:</span></span>
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<td class="diff-line-num old_line" data-linenumber="132" 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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<td class="diff-line-num new_line" data-linenumber="132" 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="LC132" class="line" lang="markdown"> <span class="sx" style="color: #d14;">src/cpp/pbdagcon_wf.sh</span> <span class="nn" style="color: #555;">'code'</span></span>
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<td class="diff-line-num new old_line" data-linenumber="133" style="width: 35px; color: rgba(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="133" style="width: 35px; color: rgba(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="LC133" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="133" style="width: 35px; color: rgba(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="134" style="width: 35px; color: rgba(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="LC134" class="line" lang="markdown"><span class="gh" style="color: #999;">DISCLAIMER</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="133" style="width: 35px; color: rgba(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="135" style="width: 35px; color: rgba(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="LC135" class="line" lang="markdown"><span class="gh" style="color: #999;">----------</span></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">
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="markdown">THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.</span></pre>
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<br>
</li>
<li id="8ab4e94f59343a8b2d003b0b47d21fff1724bfd9">
<a href="https://salsa.debian.org/med-team/pbdagcon/compare/83dbb7eea91693f73f0432b5052919075bff6a3e...21b29a28aa525fdeb46918c40817e4190ca9cbbd#8ab4e94f59343a8b2d003b0b47d21fff1724bfd9"><strong>bamboo_build.sh</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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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</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="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">NEXUS_BASEURL</span><span class="o" style="font-weight: 600;">=</span>http://ossnexus.pacificbiosciences.com/repository</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 class="c" style="color: #998; font-style: italic;">#NEXUS_URL=$NEXUS_BASEURL/unsupported/gcc-4.9.2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-e</span> .distfiles/gtest/release-1.7.0.tar.gz <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> .distfiles/gtest</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"> curl <span class="nt" style="color: #000080;">-sL</span> <span class="nv" style="color: #008080;">$NEXUS_BASEURL</span>/unsupported/distfiles/googletest/release-1.7.0.tar.gz <span class="se" style="color: #d14;">\</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="nt" style="color: #000080;">-o</span> .distfiles/gtest/release-1.7.0.tar.gz</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar </span>zxf .distfiles/gtest/release-1.7.0.tar.gz <span class="nt" style="color: #000080;">-C</span> repos/</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-sfn</span> googletest-release-1.7.0 repos/gtest</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> deployment</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> deployment</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">/bin/ls <span class="nt" style="color: #000080;">-t</span> tarballs/pbbam-<span class="k" style="font-weight: 600;">*</span>.tgz | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-1</span> | xargs <span class="nt" style="color: #000080;">-r</span> <span class="nt" style="color: #000080;">-n</span> 1 <span class="nb" style="color: #0086b3;">cat</span> | <span class="nb" style="color: #0086b3;">tar </span>zxv <span class="nt" style="color: #000080;">--strip-components</span> 3 <span class="nt" style="color: #000080;">-C</span> deployment</span>
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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="shell">/bin/ls <span class="nt" style="color: #000080;">-t</span> tarballs/blasr_libcpp-<span class="k" style="font-weight: 600;">*</span>.tgz | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-1</span> | xargs <span class="nt" style="color: #000080;">-r</span> <span class="nt" style="color: #000080;">-n</span> 1 <span class="nb" style="color: #0086b3;">cat</span> | <span class="nb" style="color: #0086b3;">tar </span>zxv <span class="nt" style="color: #000080;">--strip-components</span> 3 <span class="nt" style="color: #000080;">-C</span> deployment</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="shell">/bin/ls <span class="nt" style="color: #000080;">-t</span> tarballs/blasr-<span class="k" style="font-weight: 600;">*</span>.tgz | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-1</span> | xargs <span class="nt" style="color: #000080;">-r</span> <span class="nt" style="color: #000080;">-n</span> 1 <span class="nb" style="color: #0086b3;">cat</span> | <span class="nb" style="color: #0086b3;">tar </span>zxv <span class="nt" style="color: #000080;">--strip-components</span> 2 <span class="nt" style="color: #000080;">-C</span> deployment</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nv" style="color: #008080;">DEPLOYMENT</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PWD</span>/deployment</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PWD</span>/deployment/bin:<span class="nv" style="color: #008080;">$PATH</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LD_LIBRARY_PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PWD</span>/deployment/lib:<span class="nv" style="color: #008080;">$LD_LIBRARY_PATH</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">type </span>module <span class="o" style="font-weight: 600;">></span>& /dev/null <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">.</span> /mnt/software/Modules/current/init/bash</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">module load git</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">module load gcc</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">module load ccache</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="nv" style="color: #008080;">$USER</span> <span class="o" style="font-weight: 600;">==</span> bamboo <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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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">CCACHE_DIR</span><span class="o" style="font-weight: 600;">=</span>/mnt/secondary/Share/tmp/bamboo.mobs.ccachedir</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell">module load boost</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="nv" style="color: #008080;">$BOOST_ROOT</span> <span class="o" style="font-weight: 600;">=</span>~ /include <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"> <span class="nv" style="color: #008080;">BOOST_ROOT</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">dirname</span> <span class="nv" style="color: #008080;">$BOOST_ROOT</span><span class="si" style="color: #d14;">)</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">set</span> +x</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell">module load htslib</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell">module load hdf5-tools</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell">module load zlib</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="nv" style="color: #008080;">DAZZDB</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PWD</span>/repos/dazzdb</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="nv" style="color: #008080;">DALIGNER</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PWD</span>/repos/daligner</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>repos/pbdagcon</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">CCACHE_BASEDIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PWD</span></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;">rm</span> <span class="nt" style="color: #000080;">-rf</span> build</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> build</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"> <span class="nv" style="color: #008080;">BOOST_INCLUDE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$BOOST_ROOT</span>/include <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="nv" style="color: #008080;">LIBPBDATA_INCLUDE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$DEPLOYMENT</span>/include/pbdata <span class="se" style="color: #d14;">\</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"> <span class="nv" style="color: #008080;">LIBPBDATA_LIB</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$DEPLOYMENT</span>/lib <span class="se" style="color: #d14;">\</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"> <span class="nv" style="color: #008080;">LIBBLASR_INCLUDE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$DEPLOYMENT</span>/include/alignment <span class="se" style="color: #d14;">\</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"> <span class="nv" style="color: #008080;">LIBBLASR_LIB</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$DEPLOYMENT</span>/lib <span class="se" style="color: #d14;">\</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="nv" style="color: #008080;">LIBPBIHDF_INCLUDE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$DEPLOYMENT</span>/include/hdf <span class="se" style="color: #d14;">\</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"> <span class="nv" style="color: #008080;">LIBPBIHDF_LIB</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$DEPLOYMENT</span>/lib <span class="se" style="color: #d14;">\</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"> <span class="nv" style="color: #008080;">PBBAM_INCLUDE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$DEPLOYMENT</span>/include <span class="se" style="color: #d14;">\</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"> <span class="nv" style="color: #008080;">PBBAM_LIB</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$DEPLOYMENT</span>/lib <span class="se" style="color: #d14;">\</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"> <span class="nv" style="color: #008080;">HTSLIB_CFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>pkg-config <span class="nt" style="color: #000080;">--cflags</span> htslib<span class="si" style="color: #d14;">)</span> <span class="se" style="color: #d14;">\</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"> <span class="nv" style="color: #008080;">HTSLIB_LIBS</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>pkg-config <span class="nt" style="color: #000080;">--libs</span> htslib<span class="si" style="color: #d14;">)</span> <span class="se" style="color: #d14;">\</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"> <span class="nv" style="color: #008080;">HDF5_INCLUDE</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>pkg-config <span class="nt" style="color: #000080;">--cflags-only-I</span> hdf5|awk <span class="s1" style="color: #d14;">'{print $1}'</span>|sed <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^-I//'</span><span class="si" style="color: #d14;">)</span> <span class="se" style="color: #d14;">\</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"> <span class="nv" style="color: #008080;">HDF5_LIB</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>pkg-config <span class="nt" style="color: #000080;">--libs-only-L</span> hdf5|awk <span class="s1" style="color: #d14;">'{print $1}'</span>|sed <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^-L//'</span><span class="si" style="color: #d14;">)</span> <span class="se" style="color: #d14;">\</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"> <span class="nv" style="color: #008080;">DALIGNER_SRC</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$DALIGNER</span> <span class="se" style="color: #d14;">\</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"> <span class="nv" style="color: #008080;">DAZZ_DB_SRC</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$DAZZDB</span> <span class="se" style="color: #d14;">\</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"> <span class="nv" style="color: #008080;">GTEST_SRC</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PWD</span>/../gtest/src <span class="se" style="color: #d14;">\</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"> <span class="nv" style="color: #008080;">GTEST_INCLUDE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PWD</span>/../gtest/include <span class="se" style="color: #d14;">\</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"> <span class="nv" style="color: #008080;">ZLIB_LIBFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>pkg-config <span class="nt" style="color: #000080;">--libs</span> zlib<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell">./configure.py <span class="nt" style="color: #000080;">--build-dir</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PWD</span>/build</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-i</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/-lpbihdf/-llibcpp/;s/-lblasr//;s/-lpbdata//'</span> build/defines.mk</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell">make <span class="nt" style="color: #000080;">-C</span> build</span>
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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> build/src/cpp/pbdagcon <span class="nv" style="color: #008080;">$DEPLOYMENT</span>/bin/</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> build/src/cpp/dazcon <span class="nv" style="color: #008080;">$DEPLOYMENT</span>/bin/</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ../..</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"><span class="nv" style="color: #008080;">myVERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>pbdagcon <span class="nt" style="color: #000080;">--version</span>|awk <span class="s1" style="color: #d14;">'/version/{print $3}'</span><span class="sb" style="color: #d14;">`</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#rm -rf tarballs && mkdir -p tarballs</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>deployment</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar </span>zcf ../tarballs/pbdagcon-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">myVERSION</span><span class="k" style="font-weight: 600;">}</span>.tgz bin/pbdagcon bin/dazcon</span></pre>
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<a href="https://salsa.debian.org/med-team/pbdagcon/compare/83dbb7eea91693f73f0432b5052919075bff6a3e...21b29a28aa525fdeb46918c40817e4190ca9cbbd#657ba97c256772c813a44e0cf140908da4dfb60e"><strong>bamboo_test.sh</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PWD</span>/deployment/bin:<span class="nv" style="color: #008080;">$PATH</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LD_LIBRARY_PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PWD</span>/deployment/lib:<span class="nv" style="color: #008080;">$LD_LIBRARY_PATH</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">type </span>module <span class="o" style="font-weight: 600;">></span>& /dev/null <span class="se" style="color: #d14;">\</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">.</span> /mnt/software/Modules/current/init/bash</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell">module load gcc</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell">module load htslib</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell">module load hdf5-tools</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell">module load zlib</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell">make <span class="nt" style="color: #000080;">-C</span> repos/pbdagcon/build check</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;">chmod</span> +w <span class="nt" style="color: #000080;">-R</span> repos/pbdagcon</span></pre>
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<a href="https://salsa.debian.org/med-team/pbdagcon/compare/83dbb7eea91693f73f0432b5052919075bff6a3e...21b29a28aa525fdeb46918c40817e4190ca9cbbd#8d9366bd88df2f74d12bfee71e917c42e0691bcc"><strong>configure.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="152" 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="152" 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">@@ -152,8 +152,8 @@ def compose_defines_pacbio(envin):</td>
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"> <span class="s" style="color: #d14;">'LIBPBIHDF_INCLUDE'</span><span class="p">,</span> <span class="s" style="color: #d14;">'LIBPBIHDF_LIB'</span><span class="p">,</span> <span class="s" style="color: #d14;">'LIBPBIHDF_LIBFLAGS'</span><span class="p">,</span></span>
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153
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="s" style="color: #d14;">'HDF5_INCLUDE'</span><span class="p">,</span> <span class="s" style="color: #d14;">'HDF5_LIB'</span><span class="p">,</span> <span class="s" style="color: #d14;">'HDF5_LIBFLAGS'</span><span class="p">,</span></span>
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="s" style="color: #d14;">'PBBAM_INCLUDE'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PBBAM_LIB'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PBBAM_LIBFLAGS'</span><span class="p">,</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="s" style="color: #d14;">'HTSLIB_<span class="idiff left">INCLUDE'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'HTSLIB_LIB'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'HTSLIB_LIBFLAG</span>S'</span><span class="p">,</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"> <span class="s" style="color: #d14;">'BOOST_INCLUDE'</span><span class="p">,</span><span class="s" style="color: #d14;">'PTHREAD_LIBFLAGS'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="s" style="color: #d14;">'HTSLIB_<span class="idiff left">CFLAGS'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'HTSLIB_LIB</span>S'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="s" style="color: #d14;">'BOOST_INCLUDE'</span><span class="p">,</span><span class="idiff left right"> </span><span class="s" style="color: #d14;">'PTHREAD_LIBFLAGS'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <span class="s" style="color: #d14;">'ZLIB_LIB'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ZLIB_LIBFLAGS'</span><span class="p">,</span></span>
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="s" style="color: #d14;">'GCC_LIB'</span><span class="p">,</span></span>
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="s" style="color: #d14;">'DAZZ_DB_SRC'</span><span class="p">,</span> <span class="s" style="color: #d14;">'DAZZ_DB_INCLUDE'</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -244,7 +244,7 @@ def set_defs_defaults(env, nopbbam):</td>
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">pbbam_defaults</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"> <span class="s" style="color: #d14;">'LIBPBIHDF_LIBFLAGS'</span><span class="p">:</span> <span class="s" style="color: #d14;">'-lpbihdf'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"> <span class="s" style="color: #d14;">'PBBAM_LIBFLAGS'</span><span class="p">:</span> <span class="s" style="color: #d14;">'-lpbbam'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="s" style="color: #d14;">'HTSLIB_LIB<span class="idiff left right">FLAG</span>S'</span><span class="p">:</span> <span class="s" style="color: #d14;">'-lhts'</span><span class="p">,</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="s" style="color: #d14;">'HTSLIB_LIBS'</span><span class="p">:</span> <span class="s" style="color: #d14;">'-lhts'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"> <span class="s" style="color: #d14;">'HDF5_LIBFLAGS'</span><span class="p">:</span> <span class="s" style="color: #d14;">'-lhdf5_cpp -lhdf5'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python"> <span class="s" style="color: #d14;">'ZLIB_LIBFLAGS'</span><span class="p">:</span> <span class="s" style="color: #d14;">'-lz'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"> <span class="s" style="color: #d14;">'PTHREAD_LIBFLAGS'</span><span class="p">:</span> <span class="s" style="color: #d14;">'-lpthread'</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/pbdagcon/compare/83dbb7eea91693f73f0432b5052919075bff6a3e...21b29a28aa525fdeb46918c40817e4190ca9cbbd#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">pbdagcon (0.3+git201<span class="idiff left right">61121.0000000+ds-2</span>) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">pbdagcon (0.3+git201<span class="idiff left right">80411.c14c422+ds-1</span>) UNRELEASED; urgency=medium</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"></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Add myself to Uploaders to have at least one human uploader after</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Afif removed himself.</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Run 2to3 on Python2 files to try a Python3 port</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * New upstream version</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Standards-Version: 4.4.0</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Build-Depends: s/python/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="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Thu, 07 Feb 2019 08:22:25 +01</span>00</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Mon, 05 Aug 2019 10:29:37 +02</span>00</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">pbdagcon (0.3+git20161121.0000000+ds-1.1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/pbdagcon/compare/83dbb7eea91693f73f0432b5052919075bff6a3e...21b29a28aa525fdeb46918c40817e4190ca9cbbd#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">12</span></pre>
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<a href="https://salsa.debian.org/med-team/pbdagcon/compare/83dbb7eea91693f73f0432b5052919075bff6a3e...21b29a28aa525fdeb46918c40817e4190ca9cbbd#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" 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">@@ -3,8 +3,8 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 12~</span>),</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> python,</span>
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<pre style="margin: 0;">+<span id="LC6" 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="LC7" class="line" lang="plaintext"> python<span class="idiff left right">3</span>,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libhdf5-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libboost-dev,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" 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="14" 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">@@ -14,7 +14,7 @@ Build-Depends: debhelper (>= 12~),</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libpbdata-dev,</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"># Test-Depends:</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> googletest</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">3</span>.0</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4</span>.0</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/pbdagcon</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/pbdagcon.git</span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Homepage: https://github.com/PacificBiosciences/pbdagcon</span>
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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/pbdagcon/compare/83dbb7eea91693f73f0432b5052919075bff6a3e...21b29a28aa525fdeb46918c40817e4190ca9cbbd#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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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: Mon, 05 Aug 2019 10:03:14 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Run 2to3 on Python2 files to try a Python3 port</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/DALIGNER/py_utils/DAPipe.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/DALIGNER/py_utils/DAPipe.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -89,5 +89,5 @@</span> if __name__ == "__main__":</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> daligner_task = make_daligner_task ( run_daligner )</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> wf.addTask(daligner_task)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> job_id += 1</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print job_id</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(job_id)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> wf.refreshTargets(updateFreq = 45) #all</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/DALIGNER/py_utils/DBLA_to_falcon.py</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/DALIGNER/py_utils/DBLA_to_falcon.py</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -4,7 +4,7 @@</span> import LAPI</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-rcmap = dict(zip("ACGTacgtNn-","TGCATGCANN-"))</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+rcmap = dict(list(zip("ACGTacgtNn-","TGCATGCANN-")))</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> def rc(seq):</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> return "".join([rcmap[c] for c in seq[::-1]])</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -22,7 +22,7 @@</span> for aread in ovl_data:</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> LAPI.load_read(db, aread, aln.aseq, 2)</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> aseq = cast( aln.aseq, c_char_p)</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> aseq = aseq.value</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%08d" % aread, aseq</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%08d" % aread, aseq)</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> for aln_data in ovl_data[aread]:</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> aread, bread, acc, abpos, aepos, alen, comp, bbpos, bepos, blen = aln_data</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="p">@@ -34,9 +34,9 @@</span> for aread in ovl_data:</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> #load_read(db, ovl.bread, aln.bseq, 2)</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> if comp == 1:</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> bseq = rc(bseq)</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;">- print bread, bseq</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "+ +"</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(bread, bseq)</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("+ +")</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> count += 1</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print "- -"</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print("- -")</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> </span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> close_DB(db)</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/DALIGNER/py_utils/LAPI.py</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;">+++ b/DALIGNER/py_utils/LAPI.py</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="p">@@ -80,7 +80,7 @@</span> def get_ovl_data(fn):</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> ovl = Overlap()</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> ovl_data = {}</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for j in xrange(novl.value):</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for j in range(novl.value):</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> _read_overlap(in_f, ovl)</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> if ovl.path.tlen > tmax:</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/DALIGNER/py_utils/LAPipe.py</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/DALIGNER/py_utils/LAPipe.py</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="p">@@ -71,10 +71,10 @@</span> def run_consensus_task(self):</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> log_path = os.path.join( script_dir, "cp_%05d.log" % (job_id))</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> with open( os.path.join(cwd, "c_%05d.sh" % job_id), "w") as p_script:</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> p_script, ". /mnt/secondary/Share/HBAR_03202013/bin/activate"</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> p_script, "cd .."</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> p_script, """./LA4Falcon -o -f:%s las_files/%s.%d.las | """ % (prefix, prefix, job_id),</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> p_script, """ falcon_sense.py --trim --output_multi --min_idt 0.70 --min_cov 4 --local_match_count_threshold 3 --max_n_read 800 --n_core 8 > %s""" % fn(self.out_file)</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(". /mnt/secondary/Share/HBAR_03202013/bin/activate", file=p_script)</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("cd ..", file=p_script)</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("""./LA4Falcon -o -f:%s las_files/%s.%d.las | """ % (prefix, prefix, job_id), end=' ', file=p_script)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(""" falcon_sense.py --trim --output_multi --min_idt 0.70 --min_cov 4 --local_match_count_threshold 3 --max_n_read 800 --n_core 8 > %s""" % fn(self.out_file), file=p_script)</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> </span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> script = []</span>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> script.append( "cd %s" % cwd )</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="p">@@ -142,10 +142,10 @@</span> if __name__ == "__main__":</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> except OSError:</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> pass</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> with open("./p_%05d/p_%05d.sh" % (p_id, p_id), "w") as p_script:</span>
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> p_script, """for f in `find .. -wholename "*job*/%s.%d.%s.*.*.las"`; do ln -sf $f .; done""" % (prefix, p_id, prefix)</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("""for f in `find .. -wholename "*job*/%s.%d.%s.*.*.las"`; do ln -sf $f .; done""" % (prefix, p_id, prefix), file=p_script)</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> for l in s_data:</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> p_script, l</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> p_script, "mv %s.%d.las ../las_files" % (prefix, p_id)</span></span>
</pre>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(l, file=p_script)</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("mv %s.%d.las ../las_files" % (prefix, p_id), file=p_script)</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> </span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> p_file = os.path.abspath( "./p_%05d/p_%05d.sh" % (p_id, p_id) )</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> job_done = makePypeLocalFile(os.path.abspath( "./p_%05d/p_%05d_done" % (p_id,p_id) ))</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="p">@@ -173,5 +173,5 @@</span> if __name__ == "__main__":</span>
</pre>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> </span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> c_task = make_c_task( run_consensus_task )</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> wf.addTask(c_task)</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print p_id</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(p_id)</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> wf.refreshTargets(updateFreq = 15) #all</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/configure.py</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/configure.py</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="p">@@ -1,11 +1,11 @@</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> """Configure the build.</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> </span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> - Fetch boost/gtest.</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> - Create defines.mk</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> """</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> import argparse</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import commands</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import subprocess</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> import contextlib</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> import os</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> import sys</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="p">@@ -18,7 +18,7 @@</span> def log(msg):</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> def shell(cmd):</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> log(cmd)</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- status, output = commands.getstatusoutput(cmd)</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ status, output = subprocess.getstatusoutput(cmd)</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> if status:</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> raise Exception('%d <-| %r' %(status, cmd))</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> return output</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="p">@@ -178,7 +178,7 @@</span> def get_make_style_env(envin, args):</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> return envout</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> </span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> class OsType:</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Unknown, Linux, Darwin = range(3)</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Unknown, Linux, Darwin = list(range(3))</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> </span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> def getOsType():</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> uname = shell('uname -s')</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/filterm4.py</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/filterm4.py</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> </span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> # Filters for unique, highest scoring subread query/target pairs from an m4</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> # file. Helps get rid of chimeras, at the cost of some yield.</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="p">@@ -35,7 +35,7 @@</span> def printUniq(qgroup, count):</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> else:</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> top[k] = q</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> </span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for r in top.values():</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for r in list(top.values()):</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> count.filt += 1</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> print(r, end=' ')</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> </span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/m4topre.py</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/m4topre.py</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></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;">-#!/usr/bin/env python</span></span>
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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;">+#!/usr/bin/python3</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> """Super-simple converter from blasr m4 alignments to pbdagcon 'pre'</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> alignments. For use in the pre-assembler dagcon workflow.</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> """</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="p">@@ -7,7 +7,7 @@</span> from __future__ import print_function</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> import sys</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> import heapq</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> import string # pylint: disable=W0402</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from itertools import ifilter</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> from collections import namedtuple, defaultdict</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> import numpy as np</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> from pbcore.io.FastaIO import FastaReader</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="p">@@ -169,7 +169,7 @@</span> def main(): # pylint: disable=R0914</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> </span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> # take a max number of alignments for each target</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> limiter = AlnLimiter()</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- my_m4recs[:] = [x for x in ifilter(limiter, my_m4recs)]</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ my_m4recs[:] = [x for x in filter(limiter, my_m4recs)]</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> # load only related sequences</span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> seqs = {}</span></pre>
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<li id="af645134b14b2b35e00b98ef1750433e86979d51">
<a href="https://salsa.debian.org/med-team/pbdagcon/compare/83dbb7eea91693f73f0432b5052919075bff6a3e...21b29a28aa525fdeb46918c40817e4190ca9cbbd#af645134b14b2b35e00b98ef1750433e86979d51"><strong>debian/patches/compiler-flags.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,15 +2,15 @@ Description: Prevent override of dpkg-buildflags</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Author: Afif Elghraoui <afif@debian.org></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2016-10-23</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">pbdagcon.orig</span>/src/cpp/makefile</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">pbdagcon</span>/src/cpp/makefile</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -8,8 +8,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/src/cpp/makefile</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/src/cpp/makefile</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -8,8 +8,8 @@</span><span class="idiff left right"> PBDAGCON_OBJECTS := BlasrM5AlnProvider.o</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> DAZCON_OBJECTS := DB.o QV.o align.o DazAlnProvider.o dazcon.o</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> CPPFLAGS += -MMD -MP</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CXXFLAGS = -O3 -std=c++1<span class="idiff left right">1</span> -Wall -Wuninitialized -pedantic</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CXXFLAGS = -O3 -std=c++1<span class="idiff left right">4</span> -Wall -Wuninitialized -pedantic</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS = -O3 -Wall -Wextra -fno-strict-aliasing</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CXXFLAGS += -O3 -std=c++1<span class="idiff left right">1</span> -Wall -Wuninitialized -pedantic</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CXXFLAGS += -O3 -std=c++1<span class="idiff left right">4</span> -Wall -Wuninitialized -pedantic</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS += -O3 -Wall -Wextra -fno-strict-aliasing</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> INCDIRS := \</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">compiler-flags.patch</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">2to3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/pbdagcon/compare/83dbb7eea91693f73f0432b5052919075bff6a3e...21b29a28aa525fdeb46918c40817e4190ca9cbbd#043cfe66d8ab296344c0190710d4ff02fc647c21"><strong>src/cpp/DazAlnProvider.cpp</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">@@ -222,7 +222,7 @@ int TargetHit::aend() {</td>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// daligner structures.</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp"><span class="n" style="color: #333;">Target</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Target</span><span class="p">()</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">needsFree_</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="cpp"><span class="n" style="color: #333;">Target</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Target</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">HITS</span>_DB</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">db</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tspace</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">small</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"><span class="n" style="color: #333;">Target</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Target</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">DAZZ</span>_DB</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">db</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tspace</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">small</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp"> <span class="n" style="color: #333;">db_</span><span class="p">(</span><span class="n" style="color: #333;">db</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="cpp"> <span class="n" style="color: #333;">tspace_</span><span class="p">(</span><span class="n" style="color: #333;">tspace</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cpp"> <span class="n" style="color: #333;">small_</span><span class="p">(</span><span class="n" style="color: #333;">small</span><span class="p">),</span></span>
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<a href="https://salsa.debian.org/med-team/pbdagcon/compare/83dbb7eea91693f73f0432b5052919075bff6a3e...21b29a28aa525fdeb46918c40817e4190ca9cbbd#f1ff314bb7b6f56e6132e1d24b52b6b4b47d76e7"><strong>src/cpp/DazAlnProvider.hpp</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">@@ -94,7 +94,7 @@ std::ostream& operator<<(std::ostream& ostrm, TargetHit& hit);</td>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Target</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"><span class="nl">public:</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">Target</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">Target</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">HITS</span>_DB</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">db</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tspace</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">small</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">Target</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">DAZZ</span>_DB</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">db</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tspace</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">small</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">Target</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Initializes this target based on the given record, possibly scoring as</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" 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="119" 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">@@ -119,7 +119,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TargetHit</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">hits</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"><span class="nl">private:</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">HITS</span>_DB</span> <span class="n" style="color: #333;">db_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">DAZZ</span>_DB</span> <span class="n" style="color: #333;">db_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">abuffer_</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bbuffer_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">Work_Data</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">work_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tspace_</span><span class="p">,</span> <span class="n" style="color: #333;">small_</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -158,7 +158,7 @@ private:</td>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ProgramOpts</span> <span class="n" style="color: #333;">popts_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Dazzler-related data</span></span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">HITS</span>_DB</span> <span class="n" style="color: #333;">db_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">DAZZ</span>_DB</span> <span class="n" style="color: #333;">db_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">int64</span> <span class="n" style="color: #333;">novl_</span><span class="p">,</span> <span class="n" style="color: #333;">covl_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tbytes_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">input_</span><span class="p">;</span></span>
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<li id="87730016f20b7a818290092a15e077be866de047">
<a href="https://salsa.debian.org/med-team/pbdagcon/compare/83dbb7eea91693f73f0432b5052919075bff6a3e...21b29a28aa525fdeb46918c40817e4190ca9cbbd#87730016f20b7a818290092a15e077be866de047"><strong>src/cpp/makefile</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" 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="8" 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">@@ -8,7 +8,7 @@ PBDAGCON_OBJECTS := BlasrM5AlnProvider.o main.o SimpleAligner.o</td>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"><span class="nv" style="color: #008080;">DAZCON_OBJECTS</span> <span class="o" style="font-weight: 600;">:=</span> DB.o QV.o align.o DazAlnProvider.o dazcon.o</span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="nv" style="color: #008080;">CPPFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-MMD</span> <span class="nt" style="color: #000080;">-MP</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++1<span class="idiff left right">1</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wuninitialized</span> <span class="nt" style="color: #000080;">-pedantic</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++1<span class="idiff left right">4</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wuninitialized</span> <span class="nt" style="color: #000080;">-pedantic</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"><span class="nv" style="color: #008080;">CFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wextra</span> <span class="nt" style="color: #000080;">-fno-strict-aliasing</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="make"><span class="nv" style="color: #008080;">INCDIRS</span> <span class="o" style="font-weight: 600;">:=</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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="18" 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">@@ -18,8 +18,7 @@ INCDIRS := \</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LIBPBDATA_INCLUDE</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LIBPBIHDF_INCLUDE</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PBBAM_INCLUDE</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HDF5_INCLUDE</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HTSLIB_INCLUDE</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HDF5_INCLUDE</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="make"><span class="nv" style="color: #008080;">SYS_INCDIRS</span> <span class="o" style="font-weight: 600;">:=</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BOOST_INCLUDE</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">THISDIR</span><span class="k" style="font-weight: 600;">}</span>/third-party</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,7 +28,6 @@ LIBDIRS := \</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LIBPBIHDF_LIB</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PBBAM_LIB</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HDF5_LIB</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HTSLIB_LIB</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">GCC_LIB</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ZLIB_LIB</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="make"><span class="nv" style="color: #008080;">LDLIBS</span><span class="o" style="font-weight: 600;">+=</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,11 +36,11 @@ LDLIBS+= \</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LIBPBIHDF_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PBBAM_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HDF5_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HTSLIB_LIB<span class="idiff left right">FLAG</span>S</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HTSLIB_LIBS</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ZLIB_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PTHREAD_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">DL_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="make"><span class="nv" style="color: #008080;">CPPFLAGS</span><span class="o" style="font-weight: 600;">+=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %,-I%,<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">INCDIRS</span><span class="k" style="font-weight: 600;">}</span><span class="o" style="font-weight: 600;">)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %,-isystem%,<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SYS_INCDIRS</span><span class="k" style="font-weight: 600;">}</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="make"><span class="nv" style="color: #008080;">CPPFLAGS</span><span class="o" style="font-weight: 600;">+=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %,-I%,<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">INCDIRS</span><span class="k" style="font-weight: 600;">}</span><span class="o" style="font-weight: 600;">)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %,-isystem%,<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SYS_INCDIRS</span><span class="k" style="font-weight: 600;">}</span><span class="o" style="font-weight: 600;">)</span><span class="idiff left"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(HTSLIB_CFLAGS)</span></span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="make"><span class="nv" style="color: #008080;">LDFLAGS</span><span class="o" style="font-weight: 600;">+=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %,-L %,<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LIBDIRS</span><span class="k" style="font-weight: 600;">}</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="make"><span class="nv" style="color: #008080;">LDFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">EXTRA_LDFLAGS</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="make"></span>
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<a href="https://salsa.debian.org/med-team/pbdagcon/compare/83dbb7eea91693f73f0432b5052919075bff6a3e...21b29a28aa525fdeb46918c40817e4190ca9cbbd#52d7c8311209fdc77c02878ea62709c921b6344b"><strong>src/filterm4.py</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">@@ -3,6 +3,7 @@</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Filters for unique, highest scoring subread query/target pairs from an m4</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># file. Helps get rid of chimeras, at the cost of some yield.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">namedtuple</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,7 +37,7 @@ def printUniq(qgroup, count):</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">top</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">r</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">r</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">' '</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">qgroup</span><span class="p">[:]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/pbdagcon/compare/83dbb7eea91693f73f0432b5052919075bff6a3e...21b29a28aa525fdeb46918c40817e4190ca9cbbd#040850ef33183469415e5992c39d5869b0d8e0a9"><strong>src/m4topre.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,7 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">"""Super-simple converter from blasr m4 alignments to pbdagcon 'pre'</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">alignments. For use in the pre-assembler dagcon workflow.</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">heapq</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -201,8 +202,8 @@ def main(): # pylint: disable=R0914</td>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">tseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tname</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">translate</span><span class="p">(</span><span class="n" style="color: #333;">__rc__</span><span class="p">)[::</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">tst</span><span class="p">:</span><span class="n" style="color: #333;">tnd</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qname</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tname</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tseqlength</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tst</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tnd</span><span class="p">),</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">tseq</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">(</span></span><span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qname</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tname</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tseqlength</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tst</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tnd</span><span class="p">),</span> <span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">tseq</span><span class="p">])<span class="idiff left right">)</span></span></span>
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"></span>
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207
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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208
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="n" style="color: #333;">main</span><span class="p">())</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pbdagcon/compare/83dbb7eea91693f73f0432b5052919075bff6a3e...21b29a28aa525fdeb46918c40817e4190ca9cbbd#dcf1ae944f03fae6488243d0b2cca342eb19cd63"><strong>src/q-sense.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -85,8 +86,8 @@ class Consensus(PBMultiToolRunner):</td>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"."</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">)</span></span>
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86
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">full_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out_dir_name</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">)</span></span>
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87
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s_ref.fa"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">full_prefix</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="idiff"> </span><span class="p"><span class="idiff">,</span></span><span class="s" style="color: #d14;"><span class="idiff">"></span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s_ref"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">consensus_seq_name</span></span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>></span></span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">s</span></span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"></span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s_ref"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">consensus_seq_name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">s</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff right">)</span></span></span>
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90
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">hp_corr</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">enable_hp_corr</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">mark_lower_case</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mark_lower_case</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">generate_consensus</span><span class="p">(</span><span class="n" style="color: #333;">input_fasta_name</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s_ref.fa"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">full_prefix</span><span class="p">,</span> <span class="n" style="color: #333;">full_prefix</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">consensus_seq_name</span><span class="p">,</span> </span>
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<a href="https://salsa.debian.org/med-team/pbdagcon/compare/83dbb7eea91693f73f0432b5052919075bff6a3e...21b29a28aa525fdeb46918c40817e4190ca9cbbd#e5b616885873858305226a78e6cc27143386e5a6"><strong>test/cpp/makefile</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">@@ -15,7 +15,6 @@ INCDIRS := . \</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LIBPBIHDF_INCLUDE</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PBBAM_INCLUDE</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HDF5_INCLUDE</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HTSLIB_INCLUDE</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BOOST_INCLUDE</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">GTEST_INCLUDE</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="make"> third-party</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,7 +25,6 @@ LIBDIRS := \</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LIBPBIHDF_LIB</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PBBAM_LIB</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HDF5_LIB</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HTSLIB_LIB</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">GCC_LIB</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ZLIB_LIB</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,11 +35,11 @@ LDLIBS+= \</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LIBPBIHDF_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PBBAM_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HDF5_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HTSLIB_LIB<span class="idiff left right">FLAG</span>S</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HTSLIB_LIBS</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ZLIB_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PTHREAD_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">DL_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="make"><span class="nv" style="color: #008080;">CPPFLAGS</span><span class="o" style="font-weight: 600;">+=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %,-I%,<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">INCDIRS</span><span class="k" style="font-weight: 600;">}</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="make"><span class="nv" style="color: #008080;">CPPFLAGS</span><span class="o" style="font-weight: 600;">+=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %,-I%,<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">INCDIRS</span><span class="k" style="font-weight: 600;">}</span><span class="o" style="font-weight: 600;">)</span><span class="idiff left"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(HTSLIB_CFLAGS)</span></span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="make"><span class="nv" style="color: #008080;">LDFLAGS</span><span class="o" style="font-weight: 600;">+=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %,-L %,<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LIBDIRS</span><span class="k" style="font-weight: 600;">}</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># For fused-src, gtest-all.cc includes gtest/*.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="50" 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="48" 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">@@ -50,7 +48,7 @@ LDFLAGS+=$(patsubst %,-L %,${LIBDIRS})</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="make"><span class="nv" style="color: #008080;">GTEST_CPPFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-isystem</span> <span class="nv" style="color: #008080;">$(GTEST_INCLUDE)</span> <span class="nt" style="color: #000080;">-isystem</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">GTEST_SRC</span><span class="k" style="font-weight: 600;">}</span>/..</span>
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51
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="make"><span class="nv" style="color: #008080;">GTEST_CXXFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wextra</span> <span class="nt" style="color: #000080;">-pthread</span></span>
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52
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="make"></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++1<span class="idiff left right">1</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++1<span class="idiff left right">4</span></span>
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54
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="make"></span>
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55
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="make"><span class="nv" style="color: #008080;">GTEST_OBJECTS</span> <span class="o" style="font-weight: 600;">:=</span> gtest-all.o gtest_main.o</span>
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56
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="make"><span class="nv" style="color: #008080;">DAZCON_OBJECTS</span> <span class="o" style="font-weight: 600;">:=</span> DB.o QV.o align.o Alignment.o <span class="se" style="color: #d14;">\</span></span>
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