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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/410f60ac8309ba7b323eb18e2cbcc31bbff12903">410f60ac</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-16T13:42:53Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">checkout submodules for code copy of DALIGNER and DAZZ_DB which are specific adaptations to pbdagcon
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/commit/81358cad72e69a9717dfe70da5f819dc61e230bb">81358cad</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-16T13:44:43Z</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/62b820cc23ec59e3cefb8658c00a0c491bc05403">62b820cc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-16T13:44:43Z</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 a85d18131f664b4e13635b99b42c9c537411ca52</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/commit/188a976be45a820b5a65b0cc316fcc07effa1fcb">188a976b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-16T13:48:13Z</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/b4d560f61c536cc2e9ce2e1d3ef906b5789d636c">b4d560f6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-16T13:49:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 11
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/commit/453a82f2d5addb63f4dbb1c4012d125544af9e15">453a82f2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-16T13:52:50Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/commit/a1051d52c69d370ba69b1855d38038098afd16f4">a1051d52</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-16T13:52:50Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.2.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/commit/7444cf1a66f4e8fc00a67295f87cac52c5656d56">7444cf1a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-16T14:08:55Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add new include
</pre>
</li>
</ul>
<h4>18 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">
debian/compat
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#fc932f0eaa389a4e2b93916f3995aae4019ea823">
debian/get-orig-source
</a>
</li>
<li class="file-stats">
<a href="#af645134b14b2b35e00b98ef1750433e86979d51">
debian/patches/compiler-flags.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</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/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
<hr>
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<td class="diff-line-num unfold js-unfold old_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="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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130
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<td class="diff-line-num 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">
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<td class="line_content noteable_line" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<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>
</pre>
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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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<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>
</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="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">
133
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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 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">
134
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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">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="markdown"><span class="gh" style="color: #999;">----------</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="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/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56#8ab4e94f59343a8b2d003b0b47d21fff1724bfd9"><strong>bamboo_build.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>
</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: navy;">-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: teal;">NEXUS_BASEURL</span><span class="o" style="font-weight: 600;">=</span>http://ossnexus.pacificbiosciences.com/repository</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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=$NEXUS_BASEURL/unsupported/gcc-4.9.2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: navy;">-e</span> .distfiles/gtest/release-1.7.0.tar.gz <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: navy;">-p</span> .distfiles/gtest</span>
</pre>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"> curl <span class="nt" style="color: navy;">-sL</span> <span class="nv" style="color: teal;">$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: navy;">-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: navy;">-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: navy;">-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: navy;">-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: navy;">-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: navy;">-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: navy;">-1</span> | xargs <span class="nt" style="color: navy;">-r</span> <span class="nt" style="color: navy;">-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: navy;">--strip-components</span> 3 <span class="nt" style="color: navy;">-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: navy;">-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: navy;">-1</span> | xargs <span class="nt" style="color: navy;">-r</span> <span class="nt" style="color: navy;">-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: navy;">--strip-components</span> 3 <span class="nt" style="color: navy;">-C</span> deployment</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">/bin/ls <span class="nt" style="color: navy;">-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: navy;">-1</span> | xargs <span class="nt" style="color: navy;">-r</span> <span class="nt" style="color: navy;">-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: navy;">--strip-components</span> 2 <span class="nt" style="color: navy;">-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: teal;">DEPLOYMENT</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$PWD</span>/deployment</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: teal;">PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$PWD</span>/deployment/bin:<span class="nv" style="color: teal;">$PATH</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: teal;">LD_LIBRARY_PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$PWD</span>/deployment/lib:<span class="nv" style="color: teal;">$LD_LIBRARY_PATH</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">type </span>module <span class="o" style="font-weight: 600;">></span>& /dev/null <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">.</span> /mnt/software/Modules/current/init/bash</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">module load git</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">module load gcc</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">module load ccache</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="nv" style="color: teal;">$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: teal;">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: teal;">$BOOST_ROOT</span> <span class="o" style="font-weight: 600;">=</span>~ /include <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">-x</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"> <span class="nv" style="color: teal;">BOOST_ROOT</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">dirname</span> <span class="nv" style="color: teal;">$BOOST_ROOT</span><span class="k" style="font-weight: 600;">)</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">set</span> +x</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell">module load htslib</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell">module load hdf5-tools</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell">module load zlib</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="nv" style="color: teal;">DAZZDB</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$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: teal;">DALIGNER</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$PWD</span>/repos/daligner</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>repos/pbdagcon</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: teal;">CCACHE_BASEDIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$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: navy;">-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: navy;">-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: navy;">-p</span> build</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"> <span class="nv" style="color: teal;">BOOST_INCLUDE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$BOOST_ROOT</span>/include <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="nv" style="color: teal;">LIBPBDATA_INCLUDE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$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: teal;">LIBPBDATA_LIB</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$DEPLOYMENT</span>/lib <span class="se" style="color: #d14;">\</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"> <span class="nv" style="color: teal;">LIBBLASR_INCLUDE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$DEPLOYMENT</span>/include/alignment <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"> <span class="nv" style="color: teal;">LIBBLASR_LIB</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$DEPLOYMENT</span>/lib <span class="se" style="color: #d14;">\</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="nv" style="color: teal;">LIBPBIHDF_INCLUDE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$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: teal;">LIBPBIHDF_LIB</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$DEPLOYMENT</span>/lib <span class="se" style="color: #d14;">\</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"> <span class="nv" style="color: teal;">PBBAM_INCLUDE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$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: teal;">PBBAM_LIB</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$DEPLOYMENT</span>/lib <span class="se" style="color: #d14;">\</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"> <span class="nv" style="color: teal;">HTSLIB_CFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span>pkg-config <span class="nt" style="color: navy;">--cflags</span> htslib<span class="k" style="font-weight: 600;">)</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: teal;">HTSLIB_LIBS</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span>pkg-config <span class="nt" style="color: navy;">--libs</span> htslib<span class="k" style="font-weight: 600;">)</span> <span class="se" style="color: #d14;">\</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"> <span class="nv" style="color: teal;">HDF5_INCLUDE</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span>pkg-config <span class="nt" style="color: navy;">--cflags-only-I</span> hdf5|awk <span class="s1" style="color: #d14;">'{print $1}'</span>|sed <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/^-I//'</span><span class="k" style="font-weight: 600;">)</span> <span class="se" style="color: #d14;">\</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"> <span class="nv" style="color: teal;">HDF5_LIB</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span>pkg-config <span class="nt" style="color: navy;">--libs-only-L</span> hdf5|awk <span class="s1" style="color: #d14;">'{print $1}'</span>|sed <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/^-L//'</span><span class="k" style="font-weight: 600;">)</span> <span class="se" style="color: #d14;">\</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"> <span class="nv" style="color: teal;">DALIGNER_SRC</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$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: teal;">DAZZ_DB_SRC</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$DAZZDB</span> <span class="se" style="color: #d14;">\</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"> <span class="nv" style="color: teal;">GTEST_SRC</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$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: teal;">GTEST_INCLUDE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$PWD</span>/../gtest/include <span class="se" style="color: #d14;">\</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"> <span class="nv" style="color: teal;">ZLIB_LIBFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">$(</span>pkg-config <span class="nt" style="color: navy;">--libs</span> zlib<span class="k" style="font-weight: 600;">)</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: navy;">--build-dir</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$PWD</span>/build</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-i</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/-lpbihdf/-llibcpp/;s/-lblasr//;s/-lpbdata//'</span> build/defines.mk</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell">make <span class="nt" style="color: navy;">-C</span> build</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: navy;">-a</span> build/src/cpp/pbdagcon <span class="nv" style="color: teal;">$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: navy;">-a</span> build/src/cpp/dazcon <span class="nv" style="color: teal;">$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: teal;">myVERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>pbdagcon <span class="nt" style="color: navy;">--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: teal;">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/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56#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: teal;">PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$PWD</span>/deployment/bin:<span class="nv" style="color: teal;">$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: teal;">LD_LIBRARY_PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$PWD</span>/deployment/lib:<span class="nv" style="color: teal;">$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: navy;">-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: navy;">-R</span> repos/pbdagcon</span></pre>
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<a href="https://salsa.debian.org/med-team/pbdagcon/compare/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56#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>
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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">@@ -152,8 +152,8 @@ def compose_defines_pacbio(envin):</td>
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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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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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<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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157
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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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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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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="diff-line-num unfold js-unfold old_line" data-linenumber="244" 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="244" 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">@@ -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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245
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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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246
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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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247
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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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248
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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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249
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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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250
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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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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/pbdagcon/compare/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,9 +6,12 @@ pbdagcon (0.3+git20180411.c14c422+ds-1) UNRELEASED; urgency=low</td>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Add README.source</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> * d/watch: use git mode</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> TODO: Clarify role of code copies pointing to outdated versions of</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> daligner and dazzdb packages</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * d/watch: use git mode to detect new upstream commit</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * d/get-orig-source: checkout submodules for code copy of DALIGNER and</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> DAZZ_DB which are specific adaptations to pbdagcon</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * debhelper 11</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Standards-Version: 4.2.0</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 19 Jul 2018 11:25:43 +0200</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/pbdagcon/compare/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">0</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">1</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pbdagcon/compare/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: pbdagcon</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Afif Elghraoui <afif@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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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">Uploaders:</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> Afif Elghraoui <afif@debian.org>,</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends:</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> debhelper (>= 10),</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> python,</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> zlib1g-dev,</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> libhdf5-dev,</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> libboost-dev,</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> libtclap-dev,</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> libpbseq-dev,</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> libpbbam-dev,</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> python,</span>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> zlib1g-dev,</span>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> libhdf5-dev,</span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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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 new old_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">
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> libtclap-dev,</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> libpbseq-dev,</span>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> libpbbam-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="16" 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">
16
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<td class="diff-line-num 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">
14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"># Test-Depends:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<td class="diff-line-num new_line old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> googletest,</span>
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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
18
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<td class="diff-line-num new_line old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Standards-Version: 3.9.8</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> googletest</span>
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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.2.0</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/pbdagcon</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/pbdagcon.git</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="19" 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">
19
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<td class="diff-line-num new_line" data-linenumber="19" 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">
19
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Homepage: https://github.com/PacificBiosciences/pbdagcon</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
20
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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">Vcs-Git: https://anonscm.debian.org/git/debian-med/pbdagcon.git</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pbdagcon.git</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
22
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
23
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<td class="diff-line-num new_line" data-linenumber="21" 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="LC21" class="line" lang="plaintext">Package: pbdagcon</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="24" 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">
24
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Architecture: any</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
25
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<td class="diff-line-num new_line old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">Depends:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
26
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<td class="diff-line-num new_line old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> ${shlibs:Depends},</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> libpbseq,</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> libpbbam,</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">Suggests:</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> blasr,</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> libpbseq,</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> libpbbam</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Suggests: blasr</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Description: sequence consensus using directed acyclic graphs</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus)</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> which is a sequence consensus algorithm based on using directed acyclic</span>
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<li id="fc932f0eaa389a4e2b93916f3995aae4019ea823">
<a href="https://salsa.debian.org/med-team/pbdagcon/compare/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56#fc932f0eaa389a4e2b93916f3995aae4019ea823"><strong>debian/get-orig-source</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,28 +8,50 @@ PKGDIR="$PWD"</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># using source package name $SPKG from debian/changelog</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># This makes it more robust for newer uupdate in future</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="nv" style="color: teal;">SPKG</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span>dpkg-parsechangelog <span class="nt" style="color: navy;">-SSource</span><span class="k" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="nv" style="color: teal;">NEW_VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span>dpkg-parsechangelog <span class="nt" style="color: navy;">-SVersion</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/\-[0-9]*$//'</span><span class="k" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#NEW_VERSION=$(dpkg-parsechangelog -SVersion | sed 's/\-[0-9]*$//')</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$@</span> | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-q</span> upstream-version <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">NEW_VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ { print $2 }'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/+ds[0-9]*//'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/\([0-9\.]\+\)-[0-9]\+$/\1/'</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"> uscan <span class="nt" style="color: navy;">--force-download</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">NEW_VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$@</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s2" style="color: #d14;">"s?^.*--upstream-version </span><span class="se" style="color: #d14;">\(</span><span class="s2" style="color: #d14;">[0-9.+gitabcdef]</span><span class="se" style="color: #d14;">\+\)</span><span class="s2" style="color: #d14;">+ds.*?</span><span class="se" style="color: #d14;">\1</span><span class="s2" style="color: #d14;">?"</span><span class="sb" style="color: #d14;">`</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-q</span> <span class="s2" style="color: #d14;">"upstream-version"</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Unable to parse version number"</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;">exit</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="k" style="font-weight: 600;">fi</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"></span>
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12
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"><span class="nv" style="color: teal;">new_package</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">SPKG</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">-</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">NEW_VERSION</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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13
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"></span>
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14
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell">clean <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> ../<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">new_package</span><span class="k" style="font-weight: 600;">}</span> ../<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">SPKG</span><span class="k" style="font-weight: 600;">}</span><span class="idiff left">-</span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: teal;"><span class="idiff">NEW_VERSION</span></span><span class="k" style="font-weight: 600;"><span class="idiff right">}</span></span>.tar.gz</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> ../<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">new_package</span><span class="k" style="font-weight: 600;">}</span> ../<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">SPKG</span><span class="k" style="font-weight: 600;">}</span><span class="idiff left right">.tmp</span>.tar.gz</span>
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16
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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17
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"></span>
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18
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">trap </span>clean EXIT</span>
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19
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"></span>
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20
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ..</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <span class="idiff left right">Now ${SPKG}_${NEW_VERSION}.orig.tar.xz is upstream tarball</span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-f</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">SPKG</span><span class="k" style="font-weight: 600;">}</span><span class="idiff left">_</span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: teal;"><span class="idiff">NEW_VERSION</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="idiff">.orig.tar.</span><span class="k" style="font-weight: 600;"><span class="idiff right">*</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># <span class="idiff left right">Remove original download since its lacking DALIGNER and DAZZ_DB</span></span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-f</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">SPKG</span><span class="k" style="font-weight: 600;">}</span><span class="idiff left">-</span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: teal;"><span class="idiff">NEW_VERSION</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="idiff right">.tar.[gx]z</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># since daligner und dazz_db are needed and are only provided</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># as submodules and this old code seems to be really needed</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># see https://lists.debian.org/debian-med/2018/07/msg00088.html</span></span>
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24
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Cloning </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">SPKG</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> version </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">NEW_VERSION</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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25
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell">git clone <span class="se" style="color: #d14;">\</span></span>
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26
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"> https://github.com/PacificBiosciences/pbdagcon.git <span class="nv" style="color: teal;">$new_package</span></span>
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27
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$new_package</span> <span class="se" style="color: #d14;">\</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell"> <span class="o" style="font-weight: 600;">&&</span> make update-submodule <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> blasr_libcpp <span class="se" style="color: #d14;">\</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell"> <span class="o" style="font-weight: 600;">&&</span> find <span class="nt" style="color: navy;">-name</span> <span class="s2" style="color: #d14;">".git*"</span> <span class="nt" style="color: navy;">-exec</span> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="o" style="font-weight: 600;">{}</span> + <span class="se" style="color: #d14;">\</span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$PKGDIR</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell"></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: navy;">-czf</span> ../<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">SPKG</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">NEW_VERSION</span><span class="k" style="font-weight: 600;">}</span>.tar.gz ../<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">new_package</span><span class="k" style="font-weight: 600;">}</span></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell">mk-origtargz <span class="nt" style="color: navy;">--compression</span> xz ../<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">SPKG</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">NEW_VERSION</span><span class="k" style="font-weight: 600;">}</span>.tar.gz</span></pre>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$new_package</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Add "|| true" since it returns:</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Fetched in submodule path 'blasr_libcpp', but it did not contain 9b4faa3efa2d59484af3c3562a3af6ce421e0294. Direct fetching of that commit failed.</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># makefile:22: recipe for target 'update-submodule' failed</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell">make update-submodule <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">true</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># debug</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># ls -l DALIGNER</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># ls -l DAZZ_DB</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> blasr_libcpp</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell">find <span class="nt" style="color: navy;">-name</span> <span class="s2" style="color: #d14;">".git*"</span> | xargs <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$PKGDIR</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: navy;">-czf</span> ../<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">SPKG</span><span class="k" style="font-weight: 600;">}</span>.tmp.tar.gz ../<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">new_package</span><span class="k" style="font-weight: 600;">}</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell">mk-origtargz <span class="nt" style="color: navy;">--compression</span> xz <span class="nt" style="color: navy;">--repack</span> <span class="nt" style="color: navy;">--version</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">NEW_VERSION</span><span class="k" style="font-weight: 600;">}</span>+ds ../<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">SPKG</span><span class="k" style="font-weight: 600;">}</span>.tmp.tar.gz</span></pre>
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<li id="af645134b14b2b35e00b98ef1750433e86979d51">
<a href="https://salsa.debian.org/med-team/pbdagcon/compare/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56#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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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff">Author: Afif Elghraoui <afif@debian.org></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff">Forwarded: no</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="diff">Last-Update: 2016-10-23</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">pbdagcon.orig</span>/src/cpp/makefile</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">pbdagcon</span>/src/cpp/makefile</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -8,8 +8,8 @@</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/src/cpp/makefile</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <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="gu" style="color: #800080; font-weight: 600;">@@ -8,8 +8,8 @@<span class="idiff left right"> PBDAGCON_OBJECTS := BlasrM5AlnProvider.o</span></span></span>
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8
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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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11
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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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<a href="https://salsa.debian.org/med-team/pbdagcon/compare/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,6 +11,7 @@ PBSEQ_BASE=/usr/include/pbseq</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">export LIBBLASR_INCLUDE = $(PBSEQ_BASE)/alignment</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">export LIBPBDATA_INCLUDE = $(PBSEQ_BASE)/pbdata</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">export LIBPBIHDF_INCLUDE = $(PBSEQ_BASE)/hdf</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">export PBBAM_INCLUDE = $(PBSEQ_BASE)</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">export HDF5_LIB = /usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">export DALIGNER_SRC = $(CURDIR)/DALIGNER</span>
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<a href="https://salsa.debian.org/med-team/pbdagcon/compare/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">opts="mode=git,gitmode=full,pretty=0.3+git%cd.%h,repacksuffix=+ds,dversionmangle=s/\+ds//g,repack,compression=xz" \</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> https://github.com/PacificBiosciences/pbdagcon.git HEAD</span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> https://github.com/PacificBiosciences/pbdagcon.git HEAD \</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> debian debian/get-orig-source</span></pre>
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<a href="https://salsa.debian.org/med-team/pbdagcon/compare/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56#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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<li id="f1ff314bb7b6f56e6132e1d24b52b6b4b47d76e7">
<a href="https://salsa.debian.org/med-team/pbdagcon/compare/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56#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="k" style="font-weight: 600;">public</span><span class="o" style="font-weight: 600;">:</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="k" style="font-weight: 600;">private</span><span class="o" style="font-weight: 600;">:</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/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56#87730016f20b7a818290092a15e077be866de047"><strong>src/cpp/makefile</strong></a>
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<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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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"><span class="nv" style="color: teal;">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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<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: teal;">CPPFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-MMD</span> <span class="nt" style="color: navy;">-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: teal;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: navy;">-O3</span> <span class="nt" style="color: navy;">-std</span><span class="o" style="font-weight: 600;">=</span>c++1<span class="idiff left right">1</span> <span class="nt" style="color: navy;">-Wall</span> <span class="nt" style="color: navy;">-Wuninitialized</span> <span class="nt" style="color: navy;">-pedantic</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="make"><span class="nv" style="color: teal;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: navy;">-O3</span> <span class="nt" style="color: navy;">-std</span><span class="o" style="font-weight: 600;">=</span>c++1<span class="idiff left right">4</span> <span class="nt" style="color: navy;">-Wall</span> <span class="nt" style="color: navy;">-Wuninitialized</span> <span class="nt" style="color: navy;">-pedantic</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"><span class="nv" style="color: teal;">CFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: navy;">-O3</span> <span class="nt" style="color: navy;">-Wall</span> <span class="nt" style="color: navy;">-Wextra</span> <span class="nt" style="color: navy;">-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: teal;">INCDIRS</span> <span class="o" style="font-weight: 600;">:=</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -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: teal;">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;">${</span><span class="nv" style="color: teal;">LIBPBIHDF_INCLUDE</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">PBBAM_INCLUDE</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">HDF5_INCLUDE</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">HDF5_INCLUDE</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="make"><span class="nv" style="color: teal;">SYS_INCDIRS</span> <span class="o" style="font-weight: 600;">:=</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">THISDIR</span><span class="k" style="font-weight: 600;">}</span>/third-party</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,7 +28,6 @@ LIBDIRS := \</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">PBBAM_LIB</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">HTSLIB_LIB</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">ZLIB_LIB</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="make"><span class="nv" style="color: teal;">LDLIBS</span><span class="o" style="font-weight: 600;">+=</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,11 +36,11 @@ LDLIBS+= \</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">PBBAM_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">HTSLIB_LIB<span class="idiff left right">FLAG</span>S</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">ZLIB_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">DL_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="make"><span class="nv" style="color: teal;">CPPFLAGS</span><span class="o" style="font-weight: 600;">+=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %,-I%,<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">INCDIRS</span><span class="k" style="font-weight: 600;">}</span><span class="o" style="font-weight: 600;">)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %,-isystem%,<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">SYS_INCDIRS</span><span class="k" style="font-weight: 600;">}</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="make"><span class="nv" style="color: teal;">CPPFLAGS</span><span class="o" style="font-weight: 600;">+=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %,-I%,<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">INCDIRS</span><span class="k" style="font-weight: 600;">}</span><span class="o" style="font-weight: 600;">)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %,-isystem%,<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">SYS_INCDIRS</span><span class="k" style="font-weight: 600;">}</span><span class="o" style="font-weight: 600;">)</span><span class="idiff left"> </span><span class="nv" style="color: teal;"><span class="idiff right">$(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: teal;">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: teal;">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: teal;">LDFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56#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="c" 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="c" 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/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56#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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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"></span>
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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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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/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56#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="c" 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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<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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<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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<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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<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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<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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<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/439fc65a84f142570223a477914d403ece9f2354...7444cf1a66f4e8fc00a67295f87cac52c5656d56#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: teal;">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;">${</span><span class="nv" style="color: teal;">PBBAM_INCLUDE</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">HTSLIB_INCLUDE</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">GTEST_INCLUDE</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="make"> third-party</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,7 +25,6 @@ LIBDIRS := \</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">PBBAM_LIB</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">HTSLIB_LIB</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">ZLIB_LIB</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,11 +35,11 @@ LDLIBS+= \</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">PBBAM_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">HTSLIB_LIB<span class="idiff left right">FLAG</span>S</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">ZLIB_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="make"> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">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;">${</span><span class="nv" style="color: teal;">DL_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="make"><span class="nv" style="color: teal;">CPPFLAGS</span><span class="o" style="font-weight: 600;">+=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %,-I%,<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">INCDIRS</span><span class="k" style="font-weight: 600;">}</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="make"><span class="nv" style="color: teal;">CPPFLAGS</span><span class="o" style="font-weight: 600;">+=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>patsubst %,-I%,<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">INCDIRS</span><span class="k" style="font-weight: 600;">}</span><span class="o" style="font-weight: 600;">)</span><span class="idiff left"> </span><span class="nv" style="color: teal;"><span class="idiff right">$(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: teal;">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: teal;">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>
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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">@@ -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: teal;">GTEST_CPPFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-isystem</span> <span class="nv" style="color: teal;">$(GTEST_INCLUDE)</span> <span class="nt" style="color: navy;">-isystem</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">GTEST_SRC</span><span class="k" style="font-weight: 600;">}</span>/..</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="make"><span class="nv" style="color: teal;">GTEST_CXXFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-g</span> <span class="nt" style="color: navy;">-Wall</span> <span class="nt" style="color: navy;">-Wextra</span> <span class="nt" style="color: navy;">-pthread</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="make"><span class="nv" style="color: teal;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nt" style="color: navy;">-O3</span> <span class="nt" style="color: navy;">-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: teal;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nt" style="color: navy;">-O3</span> <span class="nt" style="color: navy;">-std</span><span class="o" style="font-weight: 600;">=</span>c++1<span class="idiff left right">4</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="make"><span class="nv" style="color: teal;">GTEST_OBJECTS</span> <span class="o" style="font-weight: 600;">:=</span> gtest-all.o gtest_main.o</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="make"><span class="nv" style="color: teal;">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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