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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/htslib">Debian Med / htslib</a>
</h3>
<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/htslib/commit/75fe8867618c3f8f9d1a7ad89dab7b3fbdc5e5de">75fe8867</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2019-12-09T18:06:06Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">i386 works!
</pre>
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<h4>3 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="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/htslib/commit/75fe8867618c3f8f9d1a7ad89dab7b3fbdc5e5de#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;">htslib</span> <span class="p">(</span><span class="m" style="color: #099;">1.9</span><span class="p">-</span><span class="m" style="color: #099;">12</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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2
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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;">Fix</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">autopkgtest</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">i386</span> <span class="n" style="color: #333;">means</span> <span class="n" style="color: #333;">we</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">re</span><span class="p">-</span><span class="n" style="color: #333;">enable</span> <span class="n" style="color: #333;">it</span><span class="c1" style="color: #998; font-style: italic;">! (Closes: #942580)</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"> <span class="p">--</span> <span class="n" style="color: #333;">Michael</span> <span class="n" style="color: #333;">R</span><span class="p">.</span> <span class="n" style="color: #333;">Crusoe</span> <span class="p"><</span><span class="n" style="color: #333;">michael</span><span class="p">.</span><span class="n" style="color: #333;">crusoe</span><span class="p">@</span><span class="n" style="color: #333;">gmail</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">></span> <span class="n" style="color: #333;">Mon</span><span class="p">,</span> <span class="m" style="color: #099;">09</span> <span class="n" style="color: #333;">Dec</span> <span class="m" style="color: #099;">2019</span> <span class="m" style="color: #099;">19</span><span class="p">:</span><span class="m" style="color: #099;">06</span><span class="p">:</span><span class="m" style="color: #099;">02</span> <span class="p">+</span><span class="m" style="color: #099;">0100</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"></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="mosel"><span class="n" style="color: #333;">htslib</span> <span class="p">(</span><span class="m" style="color: #099;">1.9</span><span class="p">-</span><span class="m" style="color: #099;">11</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="LC8" class="line" lang="mosel"></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="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Install</span> <span class="n" style="color: #333;">README</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">request</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">upstream</span></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/htslib/commit/75fe8867618c3f8f9d1a7ad89dab7b3fbdc5e5de#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" 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="19" 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">@@ -19,7 +19,7 @@ Vcs-Git: https://salsa.debian.org/med-team/htslib.git</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Homepage: https://github.com/samtools/htslib</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Package: libhts2</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">Architecture: any<span class="idiff left right">-amd64 arm64 armel armhf mips mips64el mipsel ppc64el s390x alpha hppa ia64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 x32</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Multi-Arch: same</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Section: libs</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="39" 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="39" 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">@@ -39,7 +39,7 @@ Description: C library for high-throughput sequencing data formats</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> new index and then for the old if the new index is absent.</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">Package: libhts-dev</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">Architecture: any<span class="idiff left right">-amd64 arm64 armel armhf mips mips64el mipsel ppc64el s390x alpha hppa ia64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 x32</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">Multi-Arch: same</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">Section: libdevel</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">Depends: libhts2 (= ${binary:Version}),</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="99" 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="99" 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">@@ -99,7 +99,7 @@ Description: Test data for HTSlib</td>
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext"> This package contains test files and scripts for the HTSlib.</span>
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext"></span>
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101
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext">Package: tabix</span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext">Architecture: any<span class="idiff left right">-amd64 arm64 armel armhf mips mips64el mipsel ppc64el s390x alpha hppa ia64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 x32</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">Architecture: any</span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext"> ${shlibs:Depends}</span>
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105
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext">Description: generic indexer for TAB-delimited genome position files</span>
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<br>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/htslib/commit/75fe8867618c3f8f9d1a7ad89dab7b3fbdc5e5de#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,16 +4,23 @@ set -e</td>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"htslib"</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"><span class="idiff left"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">AUTOPKGTEST_TMP</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="sb" style="color: #d14;"><span class="idiff">`</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">mktemp</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-d</span></span><span class="idiff"> /tmp/</span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">pkg</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="nt" style="color: #000080;"><span class="idiff">-test</span></span><span class="idiff">.XXXXXX</span><span class="sb" style="color: #d14;"><span class="idiff right">`</span></span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"><span class="idiff left"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">AUTOPKGTEST_TMP</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">mktemp</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-d</span></span><span class="idiff"> /tmp/</span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">pkg</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="nt" style="color: #000080;"><span class="idiff">-test</span></span><span class="idiff">.XXXXXX</span><span class="si" style="color: #d14;"><span class="idiff right">)</span></span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-aL</span> /usr/share/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;"><span class="idiff left right">$AUTOPKGTEST_TMP</span></span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-aL</span> /usr/share/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$AUTOPKGTEST_TMP</span></span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;"><span class="idiff left right">$AUTOPKGTEST_TMP</span></span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$AUTOPKGTEST_TMP</span></span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-i</span> <span class="s1" style="color: #d14;">'s#\$(HTSPREFIX)#/usr/include/#g'</span> htslib_vars.mk</span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-i</span> <span class="s1" style="color: #d14;">'s#\$(HTSLIB)#/usr/include/#g'</span> htslib.mk</span>
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16
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="nv" style="color: #008080;">CFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-O2 -fno-strict-aliasing -fno-code-hoisting"</span> make <span class="nt" style="color: #000080;">-e</span> check</span>
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<td class="diff-line-num new old_line" data-linenumber="18" 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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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nv" style="color: #008080;">CFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-O2 -fno-strict-aliasing -fno-code-hoisting"</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">grep </span>sse /proc/cpuinfo <span class="o" style="font-weight: 600;">></span> /dev/null<span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>CFLAGS+<span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -msse -mfpmath=sse"</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num new new_line" data-linenumber="22" 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">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span>CFLAGS</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="24" 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">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">make <span class="nt" style="color: #000080;">-e</span> check</span>
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<td class="diff-line-num old_line" data-linenumber="18" 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">
18
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"></span>
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19
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span></pre>
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