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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/b048884e3843f507c33840d5583d10f0e7532358">b048884e</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-06-25T16:49:55+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">forward patches upstream
</pre>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#c99edf3687f92ddaeb98b563e4f5489c663bf73c">
debian/patches/crossbuild
</a>
</li>
<li class="file-stats">
<a href="#905bf2aeef99918e81405a9b9d92b52dc1016a00">
debian/patches/hardening_flags
</a>
</li>
<li class="file-stats">
<a href="#c6945b23e3ee25ceb7c9e38c2c191d8329a3b719">
debian/patches/parallize_better
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</li>
<li class="file-stats">
<a href="#0a4e986b60a9240ca7d53abf5e2ed246987e8ffc">
debian/patches/python3
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<li class="file-stats">
<a href="#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
debian/patches/simde
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<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
debian/patches/spelling
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<h4>Changes:</h4>
<li id="c99edf3687f92ddaeb98b563e4f5489c663bf73c">
<a href="https://salsa.debian.org/med-team/vg/-/commit/b048884e3843f507c33840d5583d10f0e7532358#c99edf3687f92ddaeb98b563e4f5489c663bf73c"><strong>debian/patches/crossbuild</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Subject: Enable cross building</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/benedictpaten/sonLib/pull/41</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: https://github.com/yoheirosen/sublinear-Li-Stephens/pull/7</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Forwarded: https://github.com/benedictpaten/sonLib/pull/42</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Forwarded: https://github.com/vgteam/cpp_progress_bar/pull/2</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Forwarded: https://github.com/vgteam/libvgio/pull/24</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Forwarded: https://github.com/vgteam/gfakluge/pull/6</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">Forwarded: https://github.com/jltsiren/gbwtgraph/pull/8</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">Forwarded: https://github.com/vgteam/DYNAMIC/pull/3</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff">--- vg.orig/source_me.sh</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;">+++ vg/source_me.sh</span></span>
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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">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="p">@@ -9,8 +9,8 @@</span></span>
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<li id="905bf2aeef99918e81405a9b9d92b52dc1016a00">
<a href="https://salsa.debian.org/med-team/vg/-/commit/b048884e3843f507c33840d5583d10f0e7532358#905bf2aeef99918e81405a9b9d92b52dc1016a00"><strong>debian/patches/hardening_flags</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Subject: Make build system more flexible</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/vgteam/vg/pull/2864</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">So that Debian can pass hardening flags</span>
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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="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- vg.orig/deps/sdsl-lite/install.sh</span></span>
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<li id="c6945b23e3ee25ceb7c9e38c2c191d8329a3b719">
<a href="https://salsa.debian.org/med-team/vg/-/commit/b048884e3843f507c33840d5583d10f0e7532358#c6945b23e3ee25ceb7c9e38c2c191d8329a3b719"><strong>debian/patches/parallize_better</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Subject: improve build parallelization</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/vgteam/structures/pull/10</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: https://github.com/benedictpaten/sonLib/pull/40</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- vg.orig/deps/sonLib/externalTools/Makefile</span></span>
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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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ vg/deps/sonLib/externalTools/Makefile</span></span>
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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="diff"><span class="p">@@ -8,13 +8,13 @@</span></span>
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<li id="0a4e986b60a9240ca7d53abf5e2ed246987e8ffc">
<a href="https://salsa.debian.org/med-team/vg/-/commit/b048884e3843f507c33840d5583d10f0e7532358#0a4e986b60a9240ca7d53abf5e2ed246987e8ffc"><strong>debian/patches/python3</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Subject: convert all Python scripts to Python v3</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/vgteam/vg/pull/2865</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: https://github.com/vgteam/gfakluge/pull/7</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Forwarded: https://github.com/benedictpaten/sonLib/pull/43</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- vg.orig/Doxyfile</span></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;">+++ vg/Doxyfile</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="p">@@ -863,7 +863,7 @@</span></span>
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<li id="4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
<a href="https://salsa.debian.org/med-team/vg/-/commit/b048884e3843f507c33840d5583d10f0e7532358#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2"><strong>debian/patches/simde</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Description: Increase portability by using SIMD Everywhere library</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/vgteam/gssw/pull/27</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: https://github.com/ocxtal/dozeu/pull/2</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Forwarded: https://github.com/vgteam/libbdsg/pull/72</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Forwarded: https://github.com/vgteam/structures/pull/11</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Forwarded: https://github.com/vgteam/vg/pull/2867</span></span>
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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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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- vg.orig/deps/dozeu/dozeu.h</span></span>
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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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ vg/deps/dozeu/dozeu.h</span></span>
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<td class="diff-line-num new_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"><span class="p">@@ -44,7 +44,8 @@</span></span>
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<li id="e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
<a href="https://salsa.debian.org/med-team/vg/-/commit/b048884e3843f507c33840d5583d10f0e7532358#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Subject: fix spelling typos</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/vgteam/vg/pull/2863</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- vg.orig/src/unittest/aligner.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ vg/src/unittest/aligner.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -149,7 +149,7 @@</span></span>
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