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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/htslib">Debian Med / htslib</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/commit/3ca6d381c6f4b5f37031d24f11f64d6a94c6c804">3ca6d381</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-03T11:40:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix symbols file.
Note: version 1.8 drops symbol cram_nop_decode_reset without bumping
soversion but this should be no issue according to upstream
(https://github.com/samtools/htslib/issues/695)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/commit/f2a8dc195033bb066d779d7a6b645e20e22e4763">f2a8dc19</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-03T11:55:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove deactivated patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/commit/3c62e7eb2a2e5d5feeec2f9e709364a1cb55ba5c">3c62e7eb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-03T11:55:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to experimental
</pre>
</li>
</ul>
<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#320e0a1f712271d8a80729a499fdcfd9c66d5fb3">
debian/libhts2.symbols
</a>
</li>
<li class="file-stats">
<a href="#d15f1d345f7f44c5504b59d09021db9079b73869">
<span class="deleted-file">
−
debian/patches/fix_pkg-config.patch
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/htslib/compare/8aaefae6089e0b5fd6ce0c73961a86e409b39550...3c62e7eb2a2e5d5feeec2f9e709364a1cb55ba5c#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;">1.8</span><span class="p">-</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;"><span class="idiff left right">UNRELEASED</span></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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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">htslib</span> <span class="p">(</span><span class="m" style="color: #099;">1.8</span><span class="p">-</span><span class="m" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;"><span class="idiff left right">experimental</span></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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<td class="diff-line-num new_line" data-linenumber="2" 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">
2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"></span>
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3
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<td class="diff-line-num new_line" data-linenumber="3" 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">
3
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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="LC3" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">New</span> <span class="n" style="color: #333;">upstream</span> <span class="k" style="font-weight: 600;">version</span></span>
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4
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<td class="diff-line-num new_line" data-linenumber="4" 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">
4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Point</span> <span class="n" style="color: #333;">Vcs</span> <span class="n" style="color: #333;">fields</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">salsa</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>
</pre>
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5
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<td class="diff-line-num new_line" data-linenumber="5" 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">
5
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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="LC5" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Standards</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">4.1.4</span></span>
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6
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6
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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;">debhelper</span> <span class="m" style="color: #099;">11</span></span>
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7
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<td class="diff-line-num new_line old" data-linenumber="7" 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">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="mosel"> <span class="n" style="color: #333;">TODO</span><span class="p">:</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">1.8</span> <span class="n" style="color: #333;">drops</span> <span class="n" style="color: #333;">symbol</span> <span class="n" style="color: #333;">cram_nop_decode_reset</span> <span class="n" style="color: #333;">without</span> <span class="n" style="color: #333;">bumping</span> <span class="n" style="color: #333;">soversion</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="mosel"> <span class="p">-></span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">samtools</span><span class="p">/</span><span class="n" style="color: #333;">htslib</span><span class="p">/</span><span class="n" style="color: #333;">issues</span><span class="p">/</span><span class="m" style="color: #099;">695</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 class="p">*</span> <span class="n" style="color: #333;">Fix</span> <span class="n" style="color: #333;">symbols</span> <span class="n" style="color: #333;">file</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="mosel"> <span class="n" style="color: #333;">Note</span><span class="p">:</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">1.8</span> <span class="n" style="color: #333;">drops</span> <span class="n" style="color: #333;">symbol</span> <span class="n" style="color: #333;">cram_nop_decode_reset</span> <span class="n" style="color: #333;">without</span> <span class="n" style="color: #333;">bumping</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"> <span class="n" style="color: #333;">soversion</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">should</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">issue</span> <span class="n" style="color: #333;">according</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">upstream</span></span>
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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;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">samtools</span><span class="p">/</span><span class="n" style="color: #333;">htslib</span><span class="p">/</span><span class="n" style="color: #333;">issues</span><span class="p">/</span><span class="m" style="color: #099;">695</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC12" 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;">Fri</span><span class="p">,</span> <span class="m" style="color: #099;">27</span> <span class="n" style="color: #333;">Apr</span> <span class="m" style="color: #099;">2018</span> <span class="m" style="color: #099;">17</span><span class="p">:</span><span class="m" style="color: #099;">16</span><span class="p">:</span><span class="m" style="color: #099;">43</span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="mosel"></span>
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<a href="https://salsa.debian.org/med-team/htslib/compare/8aaefae6089e0b5fd6ce0c73961a86e409b39550...3c62e7eb2a2e5d5feeec2f9e709364a1cb55ba5c#320e0a1f712271d8a80729a499fdcfd9c66d5fb3"><strong>debian/libhts2.symbols</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">@@ -274,7 +274,7 @@ libhts.so.2 libhts2 #MINVER#</td>
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274
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="plaintext"> cram_decoder_init@Base 1.0</span>
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="plaintext"> cram_dependent_data_series@Base 1.2.1</span>
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276
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="plaintext"> cram_dopen@Base 1.0</span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="plaintext"> cram_drain_rqueue@Base 1.8<span class="idiff left right">-1</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext"> cram_drain_rqueue@Base 1.8</span>
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278
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="plaintext"> cram_encode_compression_header@Base 1.0</span>
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279
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279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="plaintext"> cram_encode_container@Base 1.0</span>
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280
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="plaintext"> cram_encode_slice_header@Base 1.0</span>
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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">@@ -341,7 +341,6 @@ libhts.so.2 libhts2 #MINVER#</td>
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341
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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="plaintext"> cram_new_container@Base 1.0</span>
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342
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342
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="plaintext"> cram_new_metrics@Base 1.0</span>
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343
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="plaintext"> cram_new_slice@Base 1.0</span>
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344
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="plaintext">#MISSING: 1.8-1# cram_nop_decode_reset@Base 1.4.1</span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="plaintext"> cram_open@Base 1.0</span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="plaintext"> cram_put_bam_seq@Base 1.0</span>
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347
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="plaintext"> cram_read_SAM_hdr@Base 1.0</span>
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<li id="d15f1d345f7f44c5504b59d09021db9079b73869">
<a href="https://salsa.debian.org/med-team/htslib/compare/8aaefae6089e0b5fd6ce0c73961a86e409b39550...3c62e7eb2a2e5d5feeec2f9e709364a1cb55ba5c#d15f1d345f7f44c5504b59d09021db9079b73869"><strong>debian/patches/fix_pkg-config.patch</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: This patch is deactivated</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"> --> see https://bugs.debian.org/881170</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> debian/patches/fix_pkg-config.patch is incorrect</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> .</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> Cflags are just pointing to system default include dir. However, files are in</span>
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<td class="diff-line-num old old_line" data-linenumber="6" 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">
6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> subdirectory which cram/*.h input files are kept in. To be found pkg-config</span>
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<td class="diff-line-num old old_line" data-linenumber="7" 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">
7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> needs to point to this dir</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff">Last-Update: Thu, 09 Feb 2017 13:39:57 +0100</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"><span class="gd" style="color: #000; background-color: #fdd;">--- a/htslib.pc.in</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;">+++ b/htslib.pc.in</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,7 +9,7 @@ static_libs=@static_LIBS@</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> Name: htslib</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> Description: C library for high-throughput sequencing data formats</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> Version: @-PACKAGE_VERSION@</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Cflags: -I${includedir}</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Cflags: -I${includedir}/htslib</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> Libs: -L${libdir} -lhts</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> Libs.private: -L${libdir} @private_LIBS@ -lhts -lm -lpthread</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> Requires.private: zlib @pc_requires@</span></pre>
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