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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/allelecount">Debian Med / allelecount</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/allelecount/-/commit/31652ab412f16a60b96ccf96268c7a9491749d59">31652ab4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-12T11:31:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix typo
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/allelecount/-/commit/6c443d1b2eb7f76c518aeaa518af8d935fbeda87">6c443d1b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-12T11:34:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add ITP bug
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/allelecount/-/commit/871067d037e4c2f256fdf630ac9b0c82bb56455b">871067d0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-12T11:37:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use finally the correct package name
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/allelecount/-/commit/d728c8b593bb69cd62f85cf06aa4522cb99ea4cb">d728c8b5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-12T11:37:52+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Hardening
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#1c37626201ffec70e15c41643c0f96522b900c98">
debian/liballelecount-perl.lintian-overrides
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<li class="file-stats">
<a href="#4d4a394ff4174f20019a8af4d8b6185efe92c21f">
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+
debian/patches/hardening.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/allelecount/-/compare/e3f44a9c9627a27df84f7fde78f8889fe86f1e52...d728c8b593bb69cd62f85cf06aa4522cb99ea4cb#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">allelecount (4.1.0-1) 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"> * Initial release (Closes: #<span class="idiff left right"><bug></span>)</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<span class="idiff left right">960345</span>)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 11 May 2020 16:16:46 +0200</span></pre>
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<li id="1c37626201ffec70e15c41643c0f96522b900c98">
<a href="https://salsa.debian.org/med-team/allelecount/-/compare/e3f44a9c9627a27df84f7fde78f8889fe86f1e52...d728c8b593bb69cd62f85cf06aa4522cb99ea4cb#1c37626201ffec70e15c41643c0f96522b900c98"><strong>debian/liballelecount-perl.lintian-overrides</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># see https://lists.debian.org/debian-med/2018/06/msg00043.html</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">libal<span class="idiff left right">elecounter</span>-perl: script-with-language-extension usr/bin/*.*</span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">libal<span class="idiff left right">lelecount</span>-perl: script-with-language-extension usr/bin/*.*</span></pre>
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<li id="4d4a394ff4174f20019a8af4d8b6185efe92c21f">
<a href="https://salsa.debian.org/med-team/allelecount/-/compare/e3f44a9c9627a27df84f7fde78f8889fe86f1e52...d728c8b593bb69cd62f85cf06aa4522cb99ea4cb#4d4a394ff4174f20019a8af4d8b6185efe92c21f"><strong>debian/patches/hardening.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, 11 May 2020 16:16:46 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Propagate hardening flags</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">--- a/c/Makefile</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;">+++ b/c/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -6,7 +6,7 @@</span> CC = gcc -O3 -DALLELECOUNTER_VERSION='"$</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> #compiler flags</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> # -g adds debug info to the executable file</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> # -Wall turns on most warnings from compiler</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS = -g -Wall</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS += -g -Wall</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> #Location of samtools/htslib libraries</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> HTSLOC?=$(HTSLIB)</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -67,7 +67,7 @@</span> all: clean make_bin make_htslib_tmp $(CO</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> @echo Binaries have been compiled.</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"> $(COUNTER_TARGET): $(OBJS)</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(JOIN_INCLUDES) $(INCLUDES) $(CFLAGS) -o $(COUNTER_TARGET) $(OBJS) $(LFLAGS) $(CAT_LFLAGS) $(LIBS) ./src/alleleCounter.c</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) $(JOIN_INCLUDES) $(INCLUDES) $(CFLAGS) -o $(COUNTER_TARGET) $(OBJS) $(LFLAGS) $(CAT_LFLAGS) $(LIBS) ./src/alleleCounter.c $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> #Unit Tests</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> test: $(COUNTER_TARGET)</span></pre>
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<a href="https://salsa.debian.org/med-team/allelecount/-/compare/e3f44a9c9627a27df84f7fde78f8889fe86f1e52...d728c8b593bb69cd62f85cf06aa4522cb99ea4cb#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hardening.patch</span></pre>
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