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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/samtools">Debian Med / samtools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/samtools/-/commit/ee4c97ec5b30706383eaa84182e49617125237a3">ee4c97ec</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-24T19:24:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/rules: fix several issues in manual pages
Most of these were reported by lintian as bad-whatis-entry or
groff-message. Some are still under the radar though.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/samtools/-/commit/488881b3a4b634343d9626646d0f00b469834a91">488881b3</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-24T19:29:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add fix-ftbfs-mvprintw.patch
Closes: #997180
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/samtools/-/commit/d9a875185ab0b58becc2c6b820b141fd95fe8a19">d9a87518</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-24T19:35:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/rules: prudent pattern to fix whatis entries
Gbp-Dcp: ignore
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/samtools/-/commit/da4dc4aeb3be219b7bfb7b30b186eccb3f828872">da4dc4ae</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-24T19:50:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/rules: disable executable bit on ac_test.bed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/samtools/-/commit/fbfd6c99cd3c8e09282a4e9eede187fd014a27f7">fbfd6c99</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-24T19:52:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add samtools-fasta-q-whatis.patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/samtools/-/commit/06566462302cef1fe60d4512228bca03a7941ccd">06566462</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-24T19:56:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/samtools/-/commit/4cfbf2b48c40ee7aadc39fbdcd9fa8392bf3354b">4cfbf2b4</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-24T20:00:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/samtools.lintian-overrides removed *.py pattern
Apparently, the samtools do not ship python scripts anymore.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/samtools/-/commit/015d416236770203581849a59c3a8f4f792ab5f4">015d4162</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-24T20:28:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adjust fix-ftbfs-mvprintw.patch metainformations
Thanks: John Marshall
This is done in the light of information forwarded upstream and
existing patch with minimum change.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/samtools/-/commit/a35323b79a488fda60725883670bf9fe132dec9b">a35323b7</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-24T20:31:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ready to upload to unstable
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#78ec04987d209875b1b7b5e6b9ec88f210b1e4f7">
<span class="new-file">
+
debian/patches/fix-ftbfs-mvprintw.patch
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<li class="file-stats">
<a href="#2ce6b3a501f5c8d5b36bcc4a0fc3ffdc981aef24">
<span class="new-file">
+
debian/patches/samtools-fasta-q-whatis.patch
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</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#f3cc17c7ee6389c4525d204f351c416f7835521b">
debian/samtools.lintian-overrides
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/samtools/-/compare/fc228655e35308a3cb76a0ba97ff167edc2a75df...a35323b79a488fda60725883670bf9fe132dec9b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">samtools (1.13-3) unstable; 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"> * [ee4c97e] d/rules: fix several issues in manual pages.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * [488881b] Add fix-ftbfs-mvprintw.patch (Closes: #997180)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * [da4dc4a] d/rules: disable executable bit on ac_test.bed.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * [fbfd6c9] Add samtools-fasta-q-whatis.patch.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * [4cfbf2b] d/samtools.lintian-overrides: remove *.py pattern.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * [015d416] Adjust fix-ftbfs-mvprintw.patch metainformations.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> Thanks to John Marshall for the forward upstream!</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Étienne Mollier <emollier@debian.org> Sun, 24 Oct 2021 20:25:10 +0200</span>
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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">samtools (1.13-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> [ Étienne Mollier ]</span>
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<li id="78ec04987d209875b1b7b5e6b9ec88f210b1e4f7">
<a href="https://salsa.debian.org/med-team/samtools/-/compare/fc228655e35308a3cb76a0ba97ff167edc2a75df...a35323b79a488fda60725883670bf9fe132dec9b#78ec04987d209875b1b7b5e6b9ec88f210b1e4f7"><strong>debian/patches/fix-ftbfs-mvprintw.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fix format not a string literal in mvprintw call</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> The idea is to use an equivalent function that does not do the format</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> parsing, since it does not seem to be the intent.</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"> Thanks John Marshall for the forward of the elegant solution!</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Author: Étienne Mollier <emollier@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=997180</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Forwarded: https://github.com/samtools/samtools/pull/1509</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">Applied-Upstream: 1.14</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">Last-Update: 2021-10-24</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- samtools.orig/bam_tview_curses.c</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ samtools/bam_tview_curses.c</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -85,7 +85,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> va_start(argptr, fmt);</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> vsnprintf(str,size, fmt, argptr);</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> va_end(argptr);</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mvprintw(y,x,str);</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mvprintw(y,x,"%s",str);</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> free(str);</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"> </span></pre>
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<li id="2ce6b3a501f5c8d5b36bcc4a0fc3ffdc981aef24">
<a href="https://salsa.debian.org/med-team/samtools/-/compare/fc228655e35308a3cb76a0ba97ff167edc2a75df...a35323b79a488fda60725883670bf9fe132dec9b#2ce6b3a501f5c8d5b36bcc4a0fc3ffdc981aef24"><strong>debian/patches/samtools-fasta-q-whatis.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fix bad whatis entry for samtools-fasta and samtools-fastq manual</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> The format is inspired from printf(3) to fit automatically several commands</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> with same purpose in one page, while keeping the whatis entries parse happy.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Author: Étienne Mollier <emollier@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Last-Update: 2021-10-24</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- samtools.orig/doc/samtools-fasta.1</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ samtools/doc/samtools-fasta.1</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -1,7 +1,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> '\" t</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> .TH samtools-fasta 1 "7 July 2021" "samtools-1.13" "Bioinformatics tools"</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> .SH NAME</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-samtools fasta / fastq \- converts a SAM/BAM/CRAM file to FASTA or FASTQ</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+samtools-fasta, samtools-fastq \- converts a SAM/BAM/CRAM file to FASTA or FASTQ</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> .\"</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> .\" Copyright (C) 2008-2011, 2013-2020 Genome Research Ltd.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> .\" Portions copyright (C) 2010, 2011 Broad Institute.</span></pre>
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<a href="https://salsa.debian.org/med-team/samtools/-/compare/fc228655e35308a3cb76a0ba97ff167edc2a75df...a35323b79a488fda60725883670bf9fe132dec9b#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">reproducible.patch</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">fix-ftbfs-mvprintw.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">samtools-fasta-q-whatis.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/samtools/-/compare/fc228655e35308a3cb76a0ba97ff167edc2a75df...a35323b79a488fda60725883670bf9fe132dec9b#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -28,6 +28,15 @@ override_dh_auto_build:</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> CPPFLAGS="\$$(DFLAGS) \$$(INCLUDES) $$(dpkg-buildflags --get CPPFLAGS)" \</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> LDFLAGS="$$(dpkg-buildflags --get LDFLAGS)"</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"># Fix several issues in the manual pages.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">execute_before_dh_installman:</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> # Fix whatis entries for subcommands; "samtools subcommand \- desc."</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> # will confuse the lexer, but "samtools-subcommand \- desc." will work.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> sed -i '/^\.SH NAME/{n;s/^\([^ ]\+\) \([^ ]\+\) \\- /\1-\2 \\- /}' \</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> debian/*/usr/share/man/man*/*.*</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> # .EX expects a indentation width.</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> sed -i 's/^.EX$$/.EX 8/' debian/*/usr/share/man/man*/*.*</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"></span>
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">ifeq (,$(filter $(DEB_HOST_ARCH),mipsel))</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -48,6 +57,8 @@ override_dh_install:</td>
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48
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"> for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \</span>
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49
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' $${pscript} ; \</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> done</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> # Disable the executable bit on a dataset.</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> chmod 0644 debian/samtools-test/usr/share/samtools/test/ampliconclip/ac_test.bed</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">override_dh_installchangelogs:</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"> dh_installchangelogs NEWS</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># Even if there is a conflict with Debian policy samtools internally</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"># relies on these extensions (see #799698)</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">samtools: script-with-language-extension usr/bin/*.pl</span></pre>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">samtools: script-with-language-extension usr/bin/*.py</span></pre>
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