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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/libucsc">Debian Med / libucsc</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libucsc/commit/6eba386e173fc491d5d8c113017c8dc1ee8037ff">6eba386e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-05T08:52:34Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Leave htslib in for the moment since upstream sticks to version 1.3
</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#e9ffd79035f20df75689c726e3780374ee2ad4f4">
debian/patches/use_debian_packaged_htslib.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/libucsc/commit/6eba386e173fc491d5d8c113017c8dc1ee8037ff#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">libucsc (0.0+git20180<span class="idiff left right">518.91029f67</span>+dfsg-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">libucsc (0.0+git20180<span class="idiff left right">904.0e87e322</span>+dfsg-1) UNRELEASED; urgency=medium</span>
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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="LC2" class="line" lang="plaintext"></span>
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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="plaintext"> * Initial release (Closes: #xxxxxx)</span>
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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">
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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="LC4" class="line" lang="plaintext"> Does not build due to usage of htslib 1.3:</span>
</pre>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/libucsc/commit/6eba386e173fc491d5d8c113017c8dc1ee8037ff#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" 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="17" 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">@@ -17,7 +17,8 @@ Files-Excluded:</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> src/d*</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> src/f*</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> src/g*</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> src/h*</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> src/hca</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> src/hg</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> src/idbQuery</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> src/index</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> src/intronerator</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/libucsc/commit/6eba386e173fc491d5d8c113017c8dc1ee8037ff#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">use_debian_packaged_htslib.patch</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right"># </span>use_debian_packaged_htslib.patch</span></pre>
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<li id="e9ffd79035f20df75689c726e3780374ee2ad4f4">
<a href="https://salsa.debian.org/med-team/libucsc/commit/6eba386e173fc491d5d8c113017c8dc1ee8037ff#e9ffd79035f20df75689c726e3780374ee2ad4f4"><strong>debian/patches/use_debian_packaged_htslib.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff">Last-Update: Sat, 19 May 2018 13:59:04 +0200</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff">Description: Use Debian packaged htslib</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> This patch is deactivated since upstream sticks to version 1.3</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/src/inc/bamFile.h</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/src/inc/bamFile.h</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" 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="32" 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">@@ -31,7 +32,7 @@ Description: Use Debian packaged htslib</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-L += $(kentSrc)/htslib/libhts.a</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+L += -lhts</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> L+=${PNGLIB} ${<span class="idiff left right">ZLIB} ${M</span>LIB}</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> L+=${PNGLIB} ${<span class="idiff left right">MLIB} ${Z</span>LIB}</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> HG_INC+=${PNGINCL}</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/lib/knetUdc.c</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/lib/knetUdc.c</span></span>
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