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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/blasr">Debian Med / blasr</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/blasr/-/commit/1e85b93604227e3fb3c13994936b52d8a0f13565">1e85b936</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-08T16:07:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix watchfile to detect new versions on github
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/blasr/-/commit/c2755bbb5fe03cf90b30a0097235de4fd634ef53">c2755bbb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-08T16:07:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.3.5+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/blasr/-/commit/c6fcc0835b981fd0c337269e2c5ad087d4ecd523">c6fcc083</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-08T16:07:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/blasr/-/commit/d3845c6c89d7da2680a603fe6e051e7664755490">d3845c6c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-08T16:07:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/5.3.5+dfsg'
Update to upstream version '5.3.5+dfsg'
with Debian dir 0bb0fd8478b790d82690ceb965da21feb3dd8055</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/blasr/-/commit/de6bcaf012572ae30feaf9c31b2cb14169ce3db4">de6bcaf0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-08T16:07:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/blasr/-/commit/7103381e2a04f4678f0819937b963f697ed53690">7103381e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-08T16:10:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/blasr/-/commit/6284305cde9672f7df076d27a6c4c8834aad811c">6284305c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-08T16:14:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TODO: Fix test
</pre>
</li>
</ul>
<h4>13 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
</a>
</li>
<li class="file-stats">
<a href="#3261916a932aec8d2cae478e6aac183e1e87ea1c">
Blasr.cpp
</a>
</li>
<li class="file-stats">
<a href="#8ab4e94f59343a8b2d003b0b47d21fff1724bfd9">
bamboo_build.sh
</a>
</li>
<li class="file-stats">
<a href="#490d9bbfafbadf3f3e9f14ae4eb510281bafe310">
ctest/meson.build
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#699a148889746a2dddf1a6e242a965a12b1f270d">
debian/patches/use_debian_packaged_pblibs.patch
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
<li class="file-stats">
<a href="#20a2e41b2b9a5242a547b6146a4ef789ea3846f2">
iblasr/BlasrUtilsImpl.hpp
</a>
</li>
<li class="file-stats">
<a href="#0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa">
meson.build
</a>
</li>
<li class="file-stats">
<a href="#cc433c731b25b0dbbaccf402481864ffaf3bf16d">
<span class="new-file">
+
subprojects/htslib.wrap
</span>
</a>
</li>
<li class="file-stats">
<a href="#1e765d81bd25b5e4761ffd8bdfabd36cfdff97ec">
<span class="new-file">
+
subprojects/pbcopper.wrap
</span>
</a>
</li>
<li class="file-stats">
<a href="#7b1d2778171cb29c29533faddd0eaf0a22df0568">
<span class="new-file">
+
subprojects/zlib.wrap
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/blasr/-/compare/2a8fa30ecc9a3629ee55b69e32edcd3b620cc536...6284305cde9672f7df076d27a6c4c8834aad811c#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,5 @@ build/</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">/utils/bax2bam/tests/src/TestData.h</span>
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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num" 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="plaintext"># Meson WrapDB stuff</span>
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<td class="old_line diff-line-num old" 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">
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<td class="new_line diff-line-num old" 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">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">subprojects/packagecache/</span>
</pre>
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<td class="old_line diff-line-num old" 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">
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<td class="new_line diff-line-num old" 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">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">subprojects/blasr_libcpp*</span>
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<td class="old_line diff-line-num old" 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="new_line diff-line-num old" 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">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">subprojects/pbbam*</span></pre>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">/subprojects/*</span>
</pre>
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<td class="new_line diff-line-num new" 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="plaintext">!/subprojects/*.wrap</span></pre>
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<br>
</li>
<li id="3261916a932aec8d2cae478e6aac183e1e87ea1c">
<a href="https://salsa.debian.org/med-team/blasr/-/compare/2a8fa30ecc9a3629ee55b69e32edcd3b620cc536...6284305cde9672f7df076d27a6c4c8834aad811c#3261916a932aec8d2cae478e6aac183e1e87ea1c"><strong>Blasr.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1459" 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="1459" 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">@@ -1459,7 +1459,7 @@ int main(int argc, char *argv[])</td>
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1459
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1459
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<pre style="margin: 0;"> <span id="LC1459" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1460" 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="new_line diff-line-num" data-linenumber="1460" 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="LC1460" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">bamWriterPtr</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1461" 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="new_line diff-line-num" data-linenumber="1461" 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="LC1461" class="line" lang="cpp"> <span class="n" style="color: #333;">bamWriterPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="new_line diff-line-num old" data-linenumber="1462" 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="LC1462" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exception</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1462" style="width: 35px; color: rgba(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="LC1462" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exception</span> <span class="o" style="font-weight: 600;"><span class="idiff right">&</span></span><span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1463" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Error, could not flush bam records to bam file."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1464" 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;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1465" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/blasr/-/compare/2a8fa30ecc9a3629ee55b69e32edcd3b620cc536...6284305cde9672f7df076d27a6c4c8834aad811c#8ab4e94f59343a8b2d003b0b47d21fff1724bfd9"><strong>bamboo_build.sh</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">@@ -64,7 +64,7 @@ export ENABLED_TESTS="true"</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># TODO(dseifert)</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># HDF5 doesn't have pkg-config files yet</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">CPPFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HDF5_CFLAGS</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LDFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-static-libstdc++ -static-libgcc </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HDF5_LIBS</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LDFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-static-libstdc++ -static-libgcc </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HDF5_LIBS</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"><span class="idiff left"> -Wl,-rpath-link,</span></span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">LD_LIBRARY_PATH</span></span><span class="k" style="font-weight: 600;"><span class="idiff right">}</span></span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="shell">bash scripts/ci/build.sh</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="shell">bash scripts/ci/test.sh</span>
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<a href="https://salsa.debian.org/med-team/blasr/-/compare/2a8fa30ecc9a3629ee55b69e32edcd3b620cc536...6284305cde9672f7df076d27a6c4c8834aad811c#490d9bbfafbadf3f3e9f14ae4eb510281bafe310"><strong>ctest/meson.build</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">@@ -41,7 +41,7 @@ blasr_test_outdir = join_paths(blasr_test_testdir, 'out')</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">foreach i : blasr_fast_test_list</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> test(</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> 'blasr <span class="idiff left">*' + i[1] + '* </span>cram test<span class="idiff">: "</span>' + i[0]<span class="idiff right"> + '"'</span>,</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> 'blasr cram test<span class="idiff left right"> - </span>' + i[0],</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> blasr_cram_script,</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> args : [</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> '--xunit-file=' + join_paths(meson.build_root(), 'blasr-cram-' + i[0] + '.xml'),</span>
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<a href="https://salsa.debian.org/med-team/blasr/-/compare/2a8fa30ecc9a3629ee55b69e32edcd3b620cc536...6284305cde9672f7df076d27a6c4c8834aad811c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">blasr (5.3.5+dfsg-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Fix watchfile to detect new versions on github</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> TODO:</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">md5sum: WARNING: 1 computed checksum did NOT match</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">output: OK</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">alignment.sam: FAILED</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">autopkgtest [14:12:49]: test run-unit-test: -----------------------]</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">autopkgtest [14:12:49]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - -</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">run-unit-test FAIL non-zero exit status 1</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">autopkgtest [14:12:49]: @@@@@@@@@@@@@@@@@@@@ summary</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">run-unit-test FAIL non-zero exit status 1</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 08 Oct 2021 16:07:31 +0200</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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1
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">blasr (5.3.3+dfsg-7) unstable; urgency=medium</span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> * Team Upload.</span>
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<a href="https://salsa.debian.org/med-team/blasr/-/compare/2a8fa30ecc9a3629ee55b69e32edcd3b620cc536...6284305cde9672f7df076d27a6c4c8834aad811c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,12 +12,12 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libhdf5-dev,</span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> zlib1g-dev,</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libpbseq-dev,</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> libpbbam-dev<span class="idiff left right"> (>= 0.18.0~)</span>,</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> libpbbam-dev,</span>
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16
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> libpbdata-dev,</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> libpbcopper-dev,</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> libgtest-dev,</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> libblasr-dev (>= 5.3.4+dfsg-3~)</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.1</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6.0</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/blasr</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/blasr.git</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Homepage: https://github.com/PacificBiosciences/blasr</span>
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<li id="699a148889746a2dddf1a6e242a965a12b1f270d">
<a href="https://salsa.debian.org/med-team/blasr/-/compare/2a8fa30ecc9a3629ee55b69e32edcd3b620cc536...6284305cde9672f7df076d27a6c4c8834aad811c#699a148889746a2dddf1a6e242a965a12b1f270d"><strong>debian/patches/use_debian_packaged_pblibs.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,12 +5,11 @@ Description: Add some missing libraries to linker</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- a/meson.build</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/meson.build</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -51,1<span class="idiff left">5</span> +51,1<span class="idiff right">9</span> @@</span> blasr_thread_dep = dependency('threads',</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> blasr_boost_dep = dependency('boost', required : true)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -51,1<span class="idiff left">0</span> +51,1<span class="idiff right">0</span> @@</span> blasr_thread_dep = dependency('threads',</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> blasr_boost_dep = dependency('boost', <span class="idiff left right">include_type : 'system', </span>required : true)</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> # pbbam</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;">-blasr_pbbam_dep = dependency('pbbam', fallback : ['pbbam', 'pbbam_dep'])</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# blasr_pbbam_dep = dependency('pbbam', fallback : ['pbbam', 'pbbam_dep'])</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+blasr_pbbam_dep = cpp.find_library('pbbam')</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> # libblasr</span>
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<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">@@ -18,17 +17,24 @@ Description: Add some missing libraries to linker</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+blasr_libblasr_dep = dependency('libblasr', required : true)</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> # zlib</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> blasr_zlib_dep = dependency('zlib', required : true)</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> blasr_zlib_dep = dependency('zlib', required : true, fallback : ['zlib', 'zlib_dep'])</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="p">@@ -62,11 +62,15 @@</span> blasr_zlib_dep = dependency('zlib', requ</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> # htslib</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> blasr_htslib_dep = dependency('htslib', required : true, version : '>=1.4', fallback : ['htslib', 'htslib_dep'])</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-blasr_deps = [blasr_thread_dep, blasr_boost_dep, blasr_pbbam_dep, blasr_libblasr_dep, blasr_zlib_dep]</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# missing libs for linker</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+blasr_pbcopper_deps = cpp.find_library('pbcopper')</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+blasr_deps = [blasr_thread_dep, blasr_boost_dep, blasr_pbbam_dep, blasr_libblasr_dep, blasr_pbcopper_deps, blasr_zlib_dep]</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> blasr_deps = [</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> blasr_thread_dep,</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> blasr_boost_dep,</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> blasr_pbbam_dep,</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> blasr_libblasr_dep,</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ blasr_pbcopper_deps,</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> blasr_zlib_dep,</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> blasr_htslib_dep]</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> ########################</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> # sources + executable #</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="p">@@ -101,7 +105,7 @@</span> blasr_static_impl = static_library(</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="p">@@ -110,7 +114,7 @@</span> blasr_static_impl = static_library(</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"> blasr_sources,</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> install : false,</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> dependencies : blasr_deps,</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,7 +43,7 @@ Description: Add some missing libraries to linker</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"> blasr_main = executable(</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> 'blasr', [</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">11</span>,7 +1<span class="idiff right">15</span>,7 @@</span> blasr_main = executable(</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">20</span>,7 +1<span class="idiff right">24</span>,7 @@</span> blasr_main = executable(</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> install : true,</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> dependencies : blasr_deps,</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"> link_with : blasr_static_impl,</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">@@ -46,7 +52,7 @@ Description: Add some missing libraries to linker</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="diff"> blasr_utils_sawriter = executable(</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> 'sawriter', files([</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">19</span>,7 +1<span class="idiff right">2</span>3,7 @@</span> blasr_utils_sawriter = executable(</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">28</span>,7 +13<span class="idiff right">2</span>,7 @@</span> blasr_utils_sawriter = executable(</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> install : true,</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> dependencies : blasr_deps,</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> link_with : blasr_static_impl,</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">@@ -55,7 +61,7 @@ Description: Add some missing libraries to linker</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> blasr_utils_toAfg = executable(</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"> 'toAfg', files([</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">27</span>,7 +1<span class="idiff right">31</span>,7 @@</span> blasr_utils_toAfg = executable(</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">36</span>,7 +1<span class="idiff right">40</span>,7 @@</span> blasr_utils_toAfg = executable(</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="diff"> install : false,</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"> dependencies : blasr_deps,</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"> link_with : blasr_static_impl,</span>
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<a href="https://salsa.debian.org/med-team/blasr/-/compare/2a8fa30ecc9a3629ee55b69e32edcd3b620cc536...6284305cde9672f7df076d27a6c4c8834aad811c#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> https://github.com/PacificBiosciences/blasr/releases .*/<span class="idiff left right">archive/</span>v?@ANY_VERSION@@ARCHIVE_EXT@</span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> https://github.com/PacificBiosciences/blasr/releases .*/v?@ANY_VERSION@@ARCHIVE_EXT@</span></pre>
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<a href="https://salsa.debian.org/med-team/blasr/-/compare/2a8fa30ecc9a3629ee55b69e32edcd3b620cc536...6284305cde9672f7df076d27a6c4c8834aad811c#20a2e41b2b9a5242a547b6146a4ef789ea3846f2"><strong>iblasr/BlasrUtilsImpl.hpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -973,7 +973,7 @@ void PrintAlignment(T_AlignmentCandidate &alignment, SMRTSequence &fullRead,</td>
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<pre style="margin: 0;"> <span id="LC973" class="line" lang="cpp"> <span class="n" style="color: #333;">SummaryOutput</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Print</span><span class="p">(</span><span class="n" style="color: #333;">alignment</span><span class="p">,</span> <span class="n" style="color: #333;">outFile</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC974" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC975" class="line" lang="cpp"> <span class="p">}</span></span>
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976
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<pre style="margin: 0;">-<span id="LC976" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">failure</span> <span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">failure</span> <span class="o" style="font-weight: 600;"><span class="idiff right">&</span></span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC977" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"ERROR writing to output file. The output drive may be full, or you "</span></span>
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978
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978
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<pre style="margin: 0;"> <span id="LC978" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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979
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979
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<pre style="margin: 0;"> <span id="LC979" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"may not have proper write permissions."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">project(</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> 'blasr',</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> 'cpp',</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> version : '5.3.<span class="idiff left right">3</span>',</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> version : '5.3.<span class="idiff left right">5</span>',</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> default_options : [</span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> 'buildtype=release',</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> 'warning_level=3',</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> 'cpp_std=c++1<span class="idiff left right">1</span>',</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> 'cpp_std=c++1<span class="idiff left right">7</span>',</span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> 'b_ndebug=false'],</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> license : 'BSD-3',</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> meson_version : '>= 0.<span class="idiff left right">46</span>.0')</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> meson_version : '>= 0.<span class="idiff left right">52</span>.0')</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"># TODO:</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"># try to reenable 'b_ndebug=true'</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="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -48,7 +48,7 @@ endif</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">blasr_thread_dep = dependency('threads', required : true)</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"># boost</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">blasr_boost_dep = dependency('boost', required : true)</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">blasr_boost_dep = dependency('boost', <span class="idiff left right">include_type : 'system', </span>required : true)</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"># pbbam</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">blasr_pbbam_dep = dependency('pbbam', fallback : ['pbbam', 'pbbam_dep'])</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" 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="57" 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">@@ -57,9 +57,18 @@ blasr_pbbam_dep = dependency('pbbam', fallback : ['pbbam', 'pbbam_dep'])</td>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">blasr_libblasr_dep = dependency('libblasr', fallback : ['blasr_libcpp', 'libblasr_dep'])</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"># zlib</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">blasr_zlib_dep = dependency('zlib', required : true)</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">blasr_deps = [blasr_thread_dep, blasr_boost_dep, blasr_pbbam_dep, blasr_libblasr_dep, blasr_zlib_dep]</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">blasr_zlib_dep = dependency('zlib', required : true, fallback : ['zlib', 'zlib_dep'])</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"># htslib</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">blasr_htslib_dep = dependency('htslib', required : true, version : '>=1.4', fallback : ['htslib', 'htslib_dep'])</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">blasr_deps = [</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> blasr_thread_dep,</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> blasr_boost_dep,</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> blasr_pbbam_dep,</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> blasr_libblasr_dep,</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> blasr_zlib_dep,</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> blasr_htslib_dep]</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext">########################</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"># sources + executable #</span>
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<a href="https://salsa.debian.org/med-team/blasr/-/compare/2a8fa30ecc9a3629ee55b69e32edcd3b620cc536...6284305cde9672f7df076d27a6c4c8834aad811c#cc433c731b25b0dbbaccf402481864ffaf3bf16d"><strong>subprojects/htslib.wrap</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">[wrap-file]</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">directory = htslib-1.10.2</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">source_url = https://github.com/samtools/htslib/archive/1.10.2.zip</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">source_filename = htslib-1.10.2.zip</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">source_hash = f7994e9636f8a4032dea477a8613f5f73b330c23b5538e45666ce7306240ac14</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">patch_url = https://wrapdb.mesonbuild.com/v1/projects/htslib/1.10.2/1/get_zip</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">patch_filename = htslib-1.10.2-1-wrap.zip</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">patch_hash = 7e8a0bfef2fb17e78ba1a8fd78e152bfbcfcb941b555d88c75b6d818a07d49d1</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">[provide]</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">htslib = htslib_dep</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span></pre>
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<li id="1e765d81bd25b5e4761ffd8bdfabd36cfdff97ec">
<a href="https://salsa.debian.org/med-team/blasr/-/compare/2a8fa30ecc9a3629ee55b69e32edcd3b620cc536...6284305cde9672f7df076d27a6c4c8834aad811c#1e765d81bd25b5e4761ffd8bdfabd36cfdff97ec"><strong>subprojects/pbcopper.wrap</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">[wrap-git]</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">directory=pbcopper</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">url=https://github.com/PacificBiosciences/pbcopper.git</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">revision=develop</span></pre>
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<a href="https://salsa.debian.org/med-team/blasr/-/compare/2a8fa30ecc9a3629ee55b69e32edcd3b620cc536...6284305cde9672f7df076d27a6c4c8834aad811c#7b1d2778171cb29c29533faddd0eaf0a22df0568"><strong>subprojects/zlib.wrap</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">[wrap-file]</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">directory = zlib-1.2.11</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">source_url = http://zlib.net/fossils/zlib-1.2.11.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">source_filename = zlib-1.2.11.tar.gz</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">source_hash = c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">patch_url = https://wrapdb.mesonbuild.com/v1/projects/zlib/1.2.11/5/get_zip</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">patch_filename = zlib-1.2.11-5-wrap.zip</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">patch_hash = 728c8e24acbc2e6682fbd950fec39e2fc77528af361adb87259f8a8511434004</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">[provide]</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">zlib = zlib_dep</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span></pre>
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