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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/staden-io-lib">Debian Med / staden-io-lib</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/staden-io-lib/commit/1f2868f0dcb185792746f3f7e596019dbee53152">1f2868f0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-04T18:34:47Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove bashism in test script
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/staden-io-lib/commit/dd8481532c4a66ab2870a5bf82057cc9af0980c6">dd848153</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-04T18:38:47Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#d938218a50fb9da3cc3674238ca55a7d5def5915">
debian/patches/pathmax.patch
</a>
</li>
<li class="file-stats">
<a href="#cd77fdc1d933b238eff364b68504c7191c5cc658">
<span class="new-file">
+
debian/patches/remove_bashism.patch
</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/staden-io-lib/compare/5c3fba39f428259e4f47cbab4ecacf3d8a244854...dd8481532c4a66ab2870a5bf82057cc9af0980c6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">staden</span><span class="p">-</span><span class="n" style="color: #333;">io</span><span class="p">-</span><span class="n" style="color: #333;">lib</span> <span class="p">(</span><span class="m" style="color: #099;">1.14.11</span><span class="p">-</span><span class="m" style="color: #099;">3</span><span class="p">)</span> <span class="n" style="color: #333;">unstable</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Remove</span> <span class="n" style="color: #333;">bashism</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">script</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="mosel"> <span class="n" style="color: #333;">Closes</span><span class="p">:</span> <span class="p">#</span><span class="m" style="color: #099;">915460</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"> <span class="p">--</span> <span class="n" style="color: #333;">Andreas</span> <span class="n" style="color: #333;">Tille</span> <span class="p"><</span><span class="n" style="color: #333;">tille</span><span class="p">@</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span> <span class="n" style="color: #333;">Tue</span><span class="p">,</span> <span class="m" style="color: #099;">04</span> <span class="n" style="color: #333;">Dec</span> <span class="m" style="color: #099;">2018</span> <span class="m" style="color: #099;">19</span><span class="p">:</span><span class="m" style="color: #099;">35</span><span class="p">:</span><span class="m" style="color: #099;">00</span> <span class="p">+</span><span class="m" style="color: #099;">0100</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="mosel"></span>
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<td class="diff-line-num new_line" data-linenumber="8" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="mosel"><span class="n" style="color: #333;">staden</span><span class="p">-</span><span class="n" style="color: #333;">io</span><span class="p">-</span><span class="n" style="color: #333;">lib</span> <span class="p">(</span><span class="m" style="color: #099;">1.14.11</span><span class="p">-</span><span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">unstable</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
</pre>
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2
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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="mosel"></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="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Fix</span> <span class="n" style="color: #333;">build</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">non</span><span class="p">-</span><span class="n" style="color: #333;">x86</span> <span class="n" style="color: #333;">architectures</span> <span class="p">(</span><span class="n" style="color: #333;">thanks</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">James</span> <span class="n" style="color: #333;">Bonfield</span></span>
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<li id="d938218a50fb9da3cc3674238ca55a7d5def5915">
<a href="https://salsa.debian.org/med-team/staden-io-lib/compare/5c3fba39f428259e4f47cbab4ecacf3d8a244854...dd8481532c4a66ab2870a5bf82057cc9af0980c6#d938218a50fb9da3cc3674238ca55a7d5def5915"><strong>debian/patches/pathmax.patch</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" 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="20" 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">@@ -20,7 +20,7 @@ Description: define PATH_MAX in case it is not available</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> int i, n;</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/io_lib/cram_io.c</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/io_lib/cram_io.c</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">94,6 +94</span>,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">107,6 +107</span>,14 @@</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> #include <stdio_ext.h></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> </span>
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<a href="https://salsa.debian.org/med-team/staden-io-lib/compare/5c3fba39f428259e4f47cbab4ecacf3d8a244854...dd8481532c4a66ab2870a5bf82057cc9af0980c6#cd77fdc1d933b238eff364b68504c7191c5cc658"><strong>debian/patches/remove_bashism.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: Remove bashism in test script</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/915460</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Last-Update: Tue, 04 Dec 2018 19:32:55 +0100</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></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;">--- a/tests/scram.test</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;">+++ b/tests/scram.test</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -24,7 +24,7 @@ do</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> # Create BAM from SAM or SAM from BAM</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if [ `echo $i | sed 's/\.bam//'` == $i ]</span></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;">+ if [ `echo $i | sed 's/\.bam//'` = $i ]</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> then</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> echo "$scramble $i $outdir/$root.bam"</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> $scramble $i $outdir/$root.bam || exit 1</span></pre>
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<a href="https://salsa.debian.org/med-team/staden-io-lib/compare/5c3fba39f428259e4f47cbab4ecacf3d8a244854...dd8481532c4a66ab2870a5bf82057cc9af0980c6#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">pathmax.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">fix_fseeko.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">fix_non_x86.patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">remove_bashism.patch</span></pre>
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