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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>
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<strong><a href="https://salsa.debian.org/med-team/libucsc/commit/f4c0312891721f36cd4354389fbd0bd9ce4da016">f4c03128</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-19T14:00:09+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add missing Build-Depends, use Debian packaged htslib
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<span class="new-file">
+
debian/patches/series
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<li class="file-stats">
<a href="#e9ffd79035f20df75689c726e3780374ee2ad4f4">
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+
debian/patches/use_debian_packaged_htslib.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/libucsc/commit/f4c0312891721f36cd4354389fbd0bd9ce4da016#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,4 +4,4 @@ libucsc (0.0+git20180518.91029f67+dfsg-1) UNRELEASED; urgency=medium</td>
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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:</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="LC5" class="line" lang="plaintext"> https://github.com/ucscGenomeBrowser/kent/issues/13</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="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Tue, 05 Jul 2016 15:09:25</span> +0200</span></pre>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Sat, 19 May 2018 13:59:04</span> +0200</span></pre>
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</li>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/libucsc/commit/f4c0312891721f36cd4354389fbd0bd9ce4da016#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,9 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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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">Uploaders: Andreas Tille <tille@debian.org></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="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> libhts-dev,</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="plaintext"> libssl-dev</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="plaintext">Standards-Version: 4.1.4</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="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/libucsc</span>
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<td class="diff-line-num new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/libucsc.git</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/libucsc/commit/f4c0312891721f36cd4354389fbd0bd9ce4da016#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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<li id="e9ffd79035f20df75689c726e3780374ee2ad4f4">
<a href="https://salsa.debian.org/med-team/libucsc/commit/f4c0312891721f36cd4354389fbd0bd9ce4da016#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"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/inc/bamFile.h</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/inc/bamFile.h</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -11,7 +11,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> #ifndef _IOLIB</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> #define _IOLIB 2</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> #endif</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;">-#include "htslib/sam.h"</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;">+#include <htslib/sam.h></span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> typedef samFile samfile_t;</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> typedef hts_idx_t bam_index_t;</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> typedef bam_hdr_t bam_header_t;</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/inc/common.mk</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/inc/common.mk</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -18,7 +18,7 @@ ifneq (,$(findstring -,$(MACHTYPE)))</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+HG_INC+=-I../inc </span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> # to check for Mac OSX Darwin specifics:</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> UNAME_S := $(shell uname -s)</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -259,7 +259,7 @@ ifeq (${ZLIB},)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> endif</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> #global external libraries</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-L += $(kentSrc)/htslib/libhts.a</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+L += -lhts</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> L+=${PNGLIB} ${ZLIB} ${MLIB}</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> HG_INC+=${PNGINCL}</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/lib/knetUdc.c</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/lib/knetUdc.c</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -8,7 +8,7 @@</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> #include "common.h"</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> #include "udc.h"</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> #include "knetUdc.h"</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include "htslib/knetfile.h"</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <htslib/knetfile.h></span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> static char *udcCacheDir = NULL;</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/lib/linefile.c</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/lib/linefile.c</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -15,7 +15,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> #include "localmem.h"</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> #include "cheapcgi.h"</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> #include "udc.h"</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include "htslib/tbx.h"</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <htslib/tbx.h></span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> char *getFileNameFromHdrSig(char *m)</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> /* Check if header has signature of supported compression stream,</span></pre>
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<a href="https://salsa.debian.org/med-team/libucsc/commit/f4c0312891721f36cd4354389fbd0bd9ce4da016#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" 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">@@ -16,7 +16,4 @@ include /usr/share/dpkg/default.mk</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> dh $@</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">#get-orig-source:</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"># . debian/get-orig-source</span></pre>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> dh $@ --sourcedirectory=src/lib</span></pre>
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