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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/samtools-legacy">Debian Med / samtools-legacy</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/samtools-legacy/-/commit/66db4bab392863bfc650c6c4b1a6e46ccd28e159">66db4bab</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-07-25T20:47:02+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Re-add non-essential changes
This reverts commit 3518e10c1642a371ce2afebc7aa847a7ed146b72.
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<strong><a href="https://salsa.debian.org/med-team/samtools-legacy/-/commit/e0cc6be54d4471a8e63fe4d280a31b2a8e16f4e9">e0cc6be5</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-07-25T20:48:25+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Interim changelog entry
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#4d4a394ff4174f20019a8af4d8b6185efe92c21f">
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+
debian/patches/hardening.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/samtools-legacy/-/compare/52f7c6aa0fbfe7dfbb973b80b3ff5ea242f2fb9d...e0cc6be54d4471a8e63fe4d280a31b2a8e16f4e9#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">samtools-legacy (0.1.19+dfsg-3) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Re-add non-essential changes</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add patch to add in hardening options</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Sun, 25 Jul 2021 20:47:46 +0530</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">samtools-legacy (0.1.19+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Team Upload.</span>
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<a href="https://salsa.debian.org/med-team/samtools-legacy/-/compare/52f7c6aa0fbfe7dfbb973b80b3ff5ea242f2fb9d...e0cc6be54d4471a8e63fe4d280a31b2a8e16f4e9#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">@@ -6,7 +6,7 @@ Priority: optional</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> libncurses5-dev,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> zlib1g-dev</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/samtools-legacy</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/samtools-legacy.git</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Homepage: https://www.htslib.org/</span>
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<a href="https://salsa.debian.org/med-team/samtools-legacy/-/compare/52f7c6aa0fbfe7dfbb973b80b3ff5ea242f2fb9d...e0cc6be54d4471a8e63fe4d280a31b2a8e16f4e9#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">Description: Inject essential hardening options</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Nilesh Patra <nilesh@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2021-07-24</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;">--- a/examples/Makefile</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;">+++ b/examples/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -34,7 +34,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> (cd ..; make libbam.a)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> calDepth:../libbam.a calDepth.c</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gcc -g -Wall -O2 -I.. calDepth.c -o $@ -L.. -lbam -lm -lz -lpthread</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) $(CFLAGS) $(CPPFLAGS) -g -Wall -O2 -I.. calDepth.c -o $@ -L.. -lbam -lm -lz -lpthread $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> clean:</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> rm -fr *.bam *.bai *.glf* *.fai *.pileup* *~ calDepth *.dSYM ex1*.rg ex1.bcf</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">fix_example_makefile.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">fix_segfault_with_small_ref.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">fix_coverage_cap.patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">hardening.patch</span></pre>
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