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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/vg">Debian Med / vg</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/vg/-/commit/c7109a32d2ed6493a00b5cac2c2e7a4584af4c40">c7109a32</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-01-21T11:51:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added patch to fix include path for vgio's libhandlegraph copy
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vg/-/commit/ba581dae74fef580374ce8a64968e142ab036acb">ba581dae</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-01-21T11:51:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more cleaning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vg/-/commit/2c0905c2364639713f7b72fbbe3a7b4403546214">2c0905c2</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-01-21T11:52:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TODO: compilation error needs fixing: https://github.com/vgteam/vg/issues/3170
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#29172be4cd9230c10883c1ff07f12795a2a87389">
<span class="new-file">
+
debian/patches/fix-handlegraph
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/vg/-/compare/f181c5a15bf3e43dc199e137cd8a5a99844f1247...2c0905c2364639713f7b72fbbe3a7b4403546214#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,6 +4,9 @@ vg (1.30.0+ds-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">  * Re-enable tests on avx.</span>
</pre>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">  * New upstream version</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">  * Refresh patches. No longer uses rocksdb.</span>
</pre>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">  * Added patch to fix include path for vgio's libhandlegraph copy</span>
</pre>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">    TODO: compilation error needs fixing: https://github.com/vgteam/vg/issues/3170</span>
</pre>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org>  Wed, 20 Jan 2021 16:33:05 +0100</span>
</pre>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
</pre>
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</table>
<br>
</li>
<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/vg/-/compare/f181c5a15bf3e43dc199e137cd8a5a99844f1247...2c0905c2364639713f7b72fbbe3a7b4403546214#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
<hr>
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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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,6 +25,7 @@ Files-Excluded: deps/libdeflate</td>
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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="plaintext">                deps/libVCFH</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">                deps/vcflib</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">                deps/sublinear-Li-Stephens/deps/htslib</span>
</pre>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">                deps/sublinear-Li-Stephens/deps</span>
</pre>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">                deps/sparsehash</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">                deps/sdsl-lite/external</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">                deps/sonLib/C/impl/lz4hc.h</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">@@ -33,7 +34,9 @@ Files-Excluded: deps/libdeflate</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">                deps/sonLib/C/impl/lz4hc.c</span>
</pre>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">                deps/FlameGraph</span>
</pre>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">                deps/htslib</span>
</pre>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">                obj/*</span>
</pre>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">                obj/</span>
</pre>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">                bin/</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">                lib/</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">Files: *</span>
</pre>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">Copyright: © 2014, 2010, 2012, 2014-2015 Erik Garrison</span>
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<br>
</li>
<li id="29172be4cd9230c10883c1ff07f12795a2a87389">
<a href="https://salsa.debian.org/med-team/vg/-/compare/f181c5a15bf3e43dc199e137cd8a5a99844f1247...2c0905c2364639713f7b72fbbe3a7b4403546214#29172be4cd9230c10883c1ff07f12795a2a87389"><strong>debian/patches/fix-handlegraph</strong></a>
<hr>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <crusoe@debian.org></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: libvgio: fix include path for libhandlegraph</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">It is odd that this is needed...</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- vg.orig/deps/libvgio/CMakeLists.txt</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;">+++ vg/deps/libvgio/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -86,7 +86,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">   SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/libhandlegraph"</span>
</pre>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">   CMAKE_ARGS "${CMAKE_ARGS};-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>")</span>
</pre>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> ExternalProject_Get_property(handlegraph INSTALL_DIR)</span>
</pre>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set(handlegraph_INCLUDE "${INSTALL_DIR}/include")</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set(handlegraph_INCLUDE "${CMAKE_SOURCE_DIR}/deps/libhandlegraph/src/include")</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> set(handlegraph_LIB "${INSTALL_DIR}/lib")</span>
</pre>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> # Set link directories. We can't use target_link_directories to keep these</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/vg/-/compare/f181c5a15bf3e43dc199e137cd8a5a99844f1247...2c0905c2364639713f7b72fbbe3a7b4403546214#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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="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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,3 +27,4 @@ use_packaged_htslib</td>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">simde</span>
</pre>
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28
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">crossbuild</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">
29
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">python3</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="30" 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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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">fix-handlegraph</span></pre>
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