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GitLab

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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/578071e0934f74f9a8fce1f559e3cc542d0a7fc1">578071e0</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-02-04T14:33:28Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.3+git20161121.0000000+ds</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pbdagcon/commit/76b61a9fb1896778f6e9358b5e3a75b3f9113f3b">76b61a9f</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-02-04T14:33:31Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.3+git20161121.0000000+ds'

Update to upstream version '0.3+git20161121.0000000+ds'

with Debian dir 1883d69ccbea71bd3e52b1cc40308b413e2f468c</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pbdagcon/commit/13468ef61491da6e1f18000834ae1a24fd6e8c03">13468ef6</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-02-04T14:34:16Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reimport old source with version number fitting git mode

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pbdagcon/commit/dfe9122fee18931eee8336d38730f7fac62a8c30">dfe9122f</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-02-04T14:34:48Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Re-adapt patch to old source

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pbdagcon/commit/3f2870b12f3648c3fd3b5d0e6f40c666ff2afef6">3f2870b1</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-02-04T14:39:14Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable

</pre>

</li>

</ul>

<h4>13 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#8ab4e94f59343a8b2d003b0b47d21fff1724bfd9">

<span class="deleted-file">

−

bamboo_build.sh

</span>

</a>

</li>

<li class="file-stats">

<a href="#657ba97c256772c813a44e0cf140908da4dfb60e">

<span class="deleted-file">

−

bamboo_test.sh

</span>

</a>

</li>

<li class="file-stats">

<a href="#8d9366bd88df2f74d12bfee71e917c42e0691bcc">

configure.py

</a>

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<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

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<li class="file-stats">

<a href="#af645134b14b2b35e00b98ef1750433e86979d51">

debian/patches/compiler-flags.patch

</a>

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<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>

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<li class="file-stats">

<a href="#87730016f20b7a818290092a15e077be866de047">

src/cpp/makefile

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<a href="#52d7c8311209fdc77c02878ea62709c921b6344b">

src/filterm4.py

</a>

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<li class="file-stats">

<a href="#040850ef33183469415e5992c39d5869b0d8e0a9">

src/m4topre.py

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<li class="file-stats">

<a href="#dcf1ae944f03fae6488243d0b2cca342eb19cd63">

src/q-sense.py

</a>

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<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/d1ce9f84b55a7e5be91a8880232828ffa9838156...3f2870b12f3648c3fd3b5d0e6f40c666ff2afef6#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -130,7 +130,3 @@ ga('send', 'pageview');</td>

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<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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<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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<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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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 old old_line" data-linenumber="134" 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">

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>

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<td class="diff-line-num old old_line" data-linenumber="135" 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="LC135" class="line" lang="markdown"><span class="gh" style="color: #999;">----------</span></span>

</pre>

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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/d1ce9f84b55a7e5be91a8880232828ffa9838156...3f2870b12f3648c3fd3b5d0e6f40c666ff2afef6#8ab4e94f59343a8b2d003b0b47d21fff1724bfd9"><strong>bamboo_build.sh</strong>

deleted

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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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<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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<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>

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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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<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 old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="10" 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">

10

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="13" 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">

13

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="14" 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">

14

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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">

15

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="16" 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">

16

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<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

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<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

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="19" 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">

19

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<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

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<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

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<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

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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">

23

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" 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">

24

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell">module load git</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="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell">module load gcc</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="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell">module load ccache</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">

27

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" 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">

28

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="29" 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">

29

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="30" 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">

30

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell">module load boost</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="31" 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">

31

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="32" 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">

32

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" 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">

33

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="34" 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">

34

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell">  <span class="nb" style="color: #0086b3;">set</span> +x</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="35" 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">

35

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="36" 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">

36

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC36" class="line" lang="shell">module load htslib</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="37" 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">

37

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="shell">module load hdf5-tools</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="38" 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">

38

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="shell">module load zlib</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="39" 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">

39

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="shell"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="40" 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">

40

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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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>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="41" 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">

41

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="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>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="42" 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">

42

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC42" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>repos/pbdagcon</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="43" 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="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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> build</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="45" 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">

45

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="46" 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">

46

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="47" 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">

47

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="48" 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">

48

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" 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">

49

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="50" 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">

50

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="51" 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">

51

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="52" 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">

52

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="53" 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">

53

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="55" 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">

55

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="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>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="58" 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">

58

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="59" 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">

59

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<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>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="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>

</pre>

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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>

</pre>

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="63" 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="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>

</pre>

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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>

</pre>

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="66" 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="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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="67" 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="LC67" class="line" lang="shell">make <span class="nt" style="color: navy;">-C</span> build</span>

</pre>

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="69" 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="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>

</pre>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ../..</span>

</pre>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="shell"></span>

</pre>

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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>

</pre>

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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>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>deployment</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="75" 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="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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<br>

</li>

<li id="657ba97c256772c813a44e0cf140908da4dfb60e">

<a href="https://salsa.debian.org/med-team/pbdagcon/compare/d1ce9f84b55a7e5be91a8880232828ffa9838156...3f2870b12f3648c3fd3b5d0e6f40c666ff2afef6#657ba97c256772c813a44e0cf140908da4dfb60e"><strong>bamboo_test.sh</strong>

deleted

</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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<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>

</pre>

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">.</span> /mnt/software/Modules/current/init/bash</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell">module load gcc</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell">module load htslib</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell">module load hdf5-tools</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell">module load zlib</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" 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">

10

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell">make <span class="nt" style="color: navy;">-C</span> repos/pbdagcon/build check</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="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>

</td>

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<br>

</li>

<li id="8d9366bd88df2f74d12bfee71e917c42e0691bcc">

<a href="https://salsa.debian.org/med-team/pbdagcon/compare/d1ce9f84b55a7e5be91a8880232828ffa9838156...3f2870b12f3648c3fd3b5d0e6f40c666ff2afef6#8d9366bd88df2f74d12bfee71e917c42e0691bcc"><strong>configure.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -152,8 +152,8 @@ def compose_defines_pacbio(envin):</td>

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<td class="diff-line-num 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">

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="153" 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="153" 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">

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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="154" 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="154" 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="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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="155" 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">

155

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<td class="diff-line-num new_line old" data-linenumber="155" 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="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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="155" 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="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>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="157" 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="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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<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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<td class="diff-line-num old_line" data-linenumber="159" 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="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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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python">    <span class="n" style="color: #333;">pbbam_defaults</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python">        <span class="s" style="color: #d14;">'LIBPBIHDF_LIBFLAGS'</span><span class="p">:</span> <span class="s" style="color: #d14;">'-lpbihdf'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python">        <span class="s" style="color: #d14;">'PBBAM_LIBFLAGS'</span><span class="p">:</span> <span class="s" style="color: #d14;">'-lpbbam'</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python">        <span class="s" style="color: #d14;">'HTSLIB_LIBS'</span><span class="p">:</span> <span class="s" style="color: #d14;">'-lhts'</span><span class="p">,</span></span>

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<td class="diff-line-num new old_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="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>

</pre>

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="249" 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="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>

</pre>

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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>

</pre>

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<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/pbdagcon/compare/d1ce9f84b55a7e5be91a8880232828ffa9838156...3f2870b12f3648c3fd3b5d0e6f40c666ff2afef6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">pbdagcon (0.3+git201<span class="idiff left right">80411.c14c422+ds-1) UNRELEASED</span>; urgency=low</span>

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<td class="diff-line-num new old_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">

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">pbdagcon (0.3+git201<span class="idiff left right">61121.0000000+ds-1) unstable</span>; urgency=low</span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">  * Team upload</span>

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<td class="diff-line-num old_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" 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="7" 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">@@ -7,6 +7,7 @@ pbdagcon (0.3+git20180411.c14c422+ds-1) UNRELEASED; urgency=low</td>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">  [ Andreas Tille ]</span>

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9

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<td class="diff-line-num new_line" data-linenumber="9" 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">

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>

</pre>

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<td class="diff-line-num new old_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">

</td>

<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">  * Reimport old source with version number fitting git mode</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">  * d/get-orig-source: checkout submodules for code copy of DALIGNER and</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext">    DAZZ_DB which are specific adaptations to pbdagcon</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" 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">

12

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">  * debhelper 12</span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" 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">@@ -16,7 +17,7 @@ pbdagcon (0.3+git20180411.c14c422+ds-1) UNRELEASED; urgency=low</td>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">    Closes: #916576</span>

</pre>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">  * Secure URI in copyright format</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="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="LC19" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  <span class="idiff left right">Thu, 19 Jul 2018 11:25:43 +02</span>00</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  <span class="idiff left right">Mon, 04 Feb 2019 15:36:14 +01</span>00</span>

</pre>

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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"></span>

</pre>

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<td class="diff-line-num old_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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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">pbdagcon (0.3+20161121+ds-1) unstable; urgency=medium</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>

</pre>

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<br>

</li>

<li id="af645134b14b2b35e00b98ef1750433e86979d51">

<a href="https://salsa.debian.org/med-team/pbdagcon/compare/d1ce9f84b55a7e5be91a8880232828ffa9838156...3f2870b12f3648c3fd3b5d0e6f40c666ff2afef6#af645134b14b2b35e00b98ef1750433e86979d51"><strong>debian/patches/compiler-flags.patch</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2" 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="2" 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">@@ -2,15 +2,15 @@ Description: Prevent override of dpkg-buildflags</td>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff">Author: Afif Elghraoui <afif@debian.org></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff">Forwarded: no</span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff">Last-Update: 2016-10-23</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/src/cpp/makefile</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/src/cpp/makefile</span></span>

</pre>

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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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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="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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<td class="diff-line-num new old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -8,8 +8,8 @@</span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> DAZCON_OBJECTS := DB.o QV.o align.o DazAlnProvider.o dazcon.o</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" 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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9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> </span>

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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> CPPFLAGS += -MMD -MP</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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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<td class="diff-line-num new old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS = -O3 -Wall -Wextra -fno-strict-aliasing</span></span>

</pre>

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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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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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>

</pre>

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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>

</pre>

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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">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> INCDIRS := \</span>

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<br>

</li>

<li id="043cfe66d8ab296344c0190710d4ff02fc647c21">

<a href="https://salsa.debian.org/med-team/pbdagcon/compare/d1ce9f84b55a7e5be91a8880232828ffa9838156...3f2870b12f3648c3fd3b5d0e6f40c666ff2afef6#043cfe66d8ab296344c0190710d4ff02fc647c21"><strong>src/cpp/DazAlnProvider.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="222" 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="222" 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">@@ -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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="223" 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="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>

</pre>

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"></span>

</pre>

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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="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="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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<br>

</li>

<li id="f1ff314bb7b6f56e6132e1d24b52b6b4b47d76e7">

<a href="https://salsa.debian.org/med-team/pbdagcon/compare/d1ce9f84b55a7e5be91a8880232828ffa9838156...3f2870b12f3648c3fd3b5d0e6f40c666ff2afef6#f1ff314bb7b6f56e6132e1d24b52b6b4b47d76e7"><strong>src/cpp/DazAlnProvider.hpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="94" 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="94" 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">@@ -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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<td class="diff-line-num old_line" data-linenumber="95" 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="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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<td class="diff-line-num old_line" data-linenumber="96" 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="LC96" class="line" lang="cpp">    <span class="n" style="color: #333;">Target</span><span class="p">();</span></span>

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<td class="diff-line-num old old_line" data-linenumber="97" 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="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="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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<td class="diff-line-num old_line" data-linenumber="98" 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="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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<td class="diff-line-num old_line" data-linenumber="99" 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="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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<td class="diff-line-num old_line" data-linenumber="120" 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="LC120" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="121" 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="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">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="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="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="diff-line-num unfold js-unfold old_line" data-linenumber="158" 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="158" 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">@@ -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">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="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>

</pre>

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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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<br>

</li>

<li id="87730016f20b7a818290092a15e077be866de047">

<a href="https://salsa.debian.org/med-team/pbdagcon/compare/d1ce9f84b55a7e5be91a8880232828ffa9838156...3f2870b12f3648c3fd3b5d0e6f40c666ff2afef6#87730016f20b7a818290092a15e077be866de047"><strong>src/cpp/makefile</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ PBDAGCON_OBJECTS := BlasrM5AlnProvider.o main.o SimpleAligner.o</td>

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<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>

</pre>

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<td class="diff-line-num new_line" data-linenumber="9" 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="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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<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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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">

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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="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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" 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="12" 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="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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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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="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>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +18,8 @@ INCDIRS := \</td>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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>

</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">

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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">

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" 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="20" 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="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>

</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">

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<td class="diff-line-num new_line old" 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">

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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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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>

</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">

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" 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>

</pre>

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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">

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<td class="diff-line-num new_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">

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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="LC24" 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>

</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">

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<td class="diff-line-num new_line" data-linenumber="25" 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="LC25" 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>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" 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="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>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,6 +29,7 @@ LIBDIRS := \</td>

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<td class="diff-line-num old_line" data-linenumber="28" 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="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">

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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;">LIBPBIHDF_LIB</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="30" 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="LC30" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" 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="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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;">HDF5_LIB</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="33" 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="LC33" 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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<td class="diff-line-num old_line" data-linenumber="32" 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="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" 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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<td class="diff-line-num new_line" data-linenumber="35" 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="LC35" 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>

</pre>

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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,11 +38,11 @@ LDLIBS+= \</td>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_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">

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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;">LIBPBIHDF_LIBFLAGS</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>

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<td class="diff-line-num old_line" data-linenumber="37" 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="LC39" 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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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="40" 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="LC40" 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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<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="41" 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="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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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(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="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="40" 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="42" 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="LC42" 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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<td class="diff-line-num old_line" data-linenumber="41" 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="43" 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="LC43" 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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<td class="diff-line-num old_line" data-linenumber="42" 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="44" 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="LC44" 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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<td class="diff-line-num old old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="45" 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="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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="44" style="width: 35px; color: rgba(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="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="44" 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="46" 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="LC46" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="45" 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="47" 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="LC47" 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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<td class="diff-line-num new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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="LC48" class="line" lang="make"></span>

</pre>

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<br>

</li>

<li id="52d7c8311209fdc77c02878ea62709c921b6344b">

<a href="https://salsa.debian.org/med-team/pbdagcon/compare/d1ce9f84b55a7e5be91a8880232828ffa9838156...3f2870b12f3648c3fd3b5d0e6f40c666ff2afef6#52d7c8311209fdc77c02878ea62709c921b6344b"><strong>src/filterm4.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,6 @@</td>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Filters for unique, highest scoring subread query/target pairs from an m4</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" 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="4" 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="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># file. Helps get rid of chimeras, at the cost of some yield.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" 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="5" 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="LC5" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" 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="6" 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="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="7" 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="LC7" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" 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="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">

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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="LC8" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" 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">@@ -37,7 +36,7 @@ def printUniq(qgroup, count):</td>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC37" 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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<td class="diff-line-num old_line" data-linenumber="39" 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="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">

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<pre style="margin: 0;"> <span id="LC38" 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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="39" 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="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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(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="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="41" 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="40" 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="LC40" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="42" 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="41" 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="LC41" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="43" 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="42" 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="LC42" class="line" lang="python"></span>

</pre>

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<br>

</li>

<li id="040850ef33183469415e5992c39d5869b0d8e0a9">

<a href="https://salsa.debian.org/med-team/pbdagcon/compare/d1ce9f84b55a7e5be91a8880232828ffa9838156...3f2870b12f3648c3fd3b5d0e6f40c666ff2afef6#040850ef33183469415e5992c39d5869b0d8e0a9"><strong>src/m4topre.py</strong></a>

<hr>

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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">@@ -2,7 +2,6 @@</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="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;">import</span> <span class="nn" style="color: #555;">sys</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;">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">@@ -202,8 +201,8 @@ def main(): # pylint: disable=R0914</td>

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<pre style="margin: 0;"> <span id="LC201" 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="LC202" 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="LC203" class="line" lang="python"></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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<td class="diff-line-num new_line old" data-linenumber="204" 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="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="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>

</pre>

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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>

</pre>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC207" 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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<pre style="margin: 0;"> <span id="LC208" 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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<br>

</li>

<li id="dcf1ae944f03fae6488243d0b2cca342eb19cd63">

<a href="https://salsa.debian.org/med-team/pbdagcon/compare/d1ce9f84b55a7e5be91a8880232828ffa9838156...3f2870b12f3648c3fd3b5d0e6f40c666ff2afef6#dcf1ae944f03fae6488243d0b2cca342eb19cd63"><strong>src/q-sense.py</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>

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<pre style="margin: 0;"> <span id="LC2" 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="LC3" 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="LC4" 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">@@ -86,8 +85,8 @@ class Consensus(PBMultiToolRunner):</td>

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<pre style="margin: 0;"> <span id="LC85" 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="LC86" 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="LC87" 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="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="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="LC90" 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="LC91" 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="LC92" 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>

</pre>

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<br>

</li>

<li id="e5b616885873858305226a78e6cc27143386e5a6">

<a href="https://salsa.debian.org/med-team/pbdagcon/compare/d1ce9f84b55a7e5be91a8880232828ffa9838156...3f2870b12f3648c3fd3b5d0e6f40c666ff2afef6#e5b616885873858305226a78e6cc27143386e5a6"><strong>test/cpp/makefile</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,6 +15,7 @@ INCDIRS := . \</td>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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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<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">

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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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<td class="diff-line-num old_line" data-linenumber="17" 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="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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<td class="diff-line-num new old_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">

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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="LC19" 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="LC20" 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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<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="make">  third-party</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" 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="26" 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">@@ -25,6 +26,7 @@ LIBDIRS := \</td>

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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;">LIBPBIHDF_LIB</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\</span></span>

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<td class="diff-line-num old_line" data-linenumber="26" 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="27" 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="LC27" 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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<td class="diff-line-num old_line" data-linenumber="27" 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="LC28" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" 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="30" 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="LC30" 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>

</pre>

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<td class="diff-line-num 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">

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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;">ZLIB_LIB</span><span class="k" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC32" 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">@@ -35,11 +37,11 @@ LDLIBS+= \</td>

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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;">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="LC38" 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="LC39" 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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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="40" 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="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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<td class="diff-line-num new old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="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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<td class="diff-line-num old_line" data-linenumber="39" 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="41" 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="LC41" 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="LC42" 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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<td class="diff-line-num old_line" data-linenumber="41" 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="43" 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="LC43" 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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<td class="diff-line-num old old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="44" 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="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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<td class="diff-line-num new old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="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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<td class="diff-line-num old_line" data-linenumber="43" 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="45" 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="LC45" 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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<td class="diff-line-num new_line" data-linenumber="46" 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="LC46" class="line" lang="make"></span>

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<pre style="margin: 0;"> <span id="LC47" 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="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -48,7 +50,7 @@ LDFLAGS+=$(patsubst %,-L %,${LIBDIRS})</td>

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<pre style="margin: 0;"> <span id="LC50" 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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<td class="diff-line-num new_line" data-linenumber="51" 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="LC51" 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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<td class="diff-line-num new_line" data-linenumber="52" 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="LC52" class="line" lang="make"></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>

</pre>

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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>

</pre>

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<td class="diff-line-num new_line" data-linenumber="54" 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="LC54" class="line" lang="make"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC55" 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>

</pre>

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<pre style="margin: 0;"> <span id="LC56" 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>

</pre>

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