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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/libseqlib">Debian Med / libseqlib</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libseqlib/commit/820f035f0c7ab27c6473af890cf8488eeb46b972">820f035f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-18T13:04:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Avoid using non-public HTSlib headers and functions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libseqlib/commit/44476aa758fc7272314554c121b3b9f23faf758f">44476aa7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-18T13:04:41Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libseqlib/commit/722c79a3145e0a27eacf507723fc27ba433de510">722c79a3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-18T13:04:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libseqlib/commit/442e90ce2fd096b2594ec21da520c528e55ef4ce">442e90ce</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-18T13:12:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh symbols
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libseqlib/commit/ee6f2daf074a43e67f6c13d820bd80fe6838cc48">ee6f2daf</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-18T13:16:52Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">do not (Build-)Depend libhts-private-dev
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libseqlib/commit/b97d3004f6f1c5623e7bce19a0180a2d3bc432e5">b97d3004</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-18T13:18:53Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#f5558833742302653c99a42f8d1dbba987cbc288">
debian/libseqlib1.symbols
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<li class="file-stats">
<a href="#e1319e3be642ca291bf4ab694440cdeefa812d34">
<span class="new-file">
+
debian/patches/fix_private_htslib_usage.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/libseqlib/compare/64f09e6893b9f58cd90c14fe94af1a497eb18a57...b97d3004f6f1c5623e7bce19a0180a2d3bc432e5#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">libseqlib (1.1.2+dfsg-5) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Avoid using non-public HTSlib headers and functions</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="plaintext"> and do not (Build-)Depend libhts-private-dev</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Closes: #946924</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> * Standards-Version: 4.4.1</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="plaintext"> * Set upstream metadata fields: Bug-Database.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Refresh symbols</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 18 Dec 2019 14:17:13 +0100</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">libseqlib (1.1.2+dfsg-4) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"> * Adapt symbols to new version of gcc</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/libseqlib/compare/64f09e6893b9f58cd90c14fe94af1a497eb18a57...b97d3004f6f1c5623e7bce19a0180a2d3bc432e5#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" 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="6" 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">@@ -6,14 +6,14 @@ Priority: optional</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> d-shlibs,</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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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> pkg-config,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> libhts-<span class="idiff left right">private-</span>dev,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> libhts-dev,</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libcurl4-openssl-dev | libcurl4-dev,</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> zlib1g-dev,</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libfml-dev (>= 0.1-3),</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="plaintext"> libbwa-dev (>= 0.7.15-3),</span>
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<td class="diff-line-num old_line" data-linenumber="14" 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">
14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libjsoncpp-dev,</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="plaintext"> libssw-dev</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">0</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">1</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/libseqlib</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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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/libseqlib.git</span>
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<td class="diff-line-num 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">
19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Homepage: https://github.com/walaj/SeqLib</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" 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="43" 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">@@ -43,7 +43,6 @@ Depends: libseqlib1 (= ${binary:Version}),</td>
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43
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> libhts-dev (>= 1.3.2-3),</span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> libhts-private-dev,</span>
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> libjsoncpp-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="48" 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">
48
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> libbwa-dev,</span>
</pre>
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49
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> libfml-dev,</span>
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<br>
</li>
<li id="f5558833742302653c99a42f8d1dbba987cbc288">
<a href="https://salsa.debian.org/med-team/libseqlib/compare/64f09e6893b9f58cd90c14fe94af1a497eb18a57...b97d3004f6f1c5623e7bce19a0180a2d3bc432e5#f5558833742302653c99a42f8d1dbba987cbc288"><strong>debian/libseqlib1.symbols</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="126" 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="126" 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">@@ -126,10 +126,10 @@ libseqlib.so.1 libseqlib1 #MINVER#</td>
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126
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="plaintext"> _ZN6SeqLib8tostringIjEENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_@Base 1.1.1+dfsg</span>
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127
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="plaintext"> _ZN6SeqLib9AddCommasIiEENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_@Base 1.1.1+dfsg</span>
</pre>
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128
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="plaintext"> _ZN6SeqLib9BamHeader21ConstructName2IDTableEv@Base 1.1.1+dfsg</span>
</pre>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="plaintext"> _ZN6SeqLib9BamHeaderC1EPK9<span class="idiff left right">bam_hdr_t@Base 1.1.1</span>+dfsg</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"> _ZN6SeqLib9BamHeaderC1EPK9<span class="idiff left right">sam_hdr_t@Base 1.1.2</span>+dfsg</span>
</pre>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="plaintext"> _ZN6SeqLib9BamHeaderC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 1.1.1+dfsg</span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="plaintext"> _ZN6SeqLib9BamHeaderC1ERKSt6vectorINS_14HeaderSequenceESaIS2_EE@Base 1.1.1+dfsg</span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="plaintext"> _ZN6SeqLib9BamHeaderC2EPK9<span class="idiff left right">bam_hdr_t@Base 1.1.1</span>+dfsg</span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> _ZN6SeqLib9BamHeaderC2EPK9<span class="idiff left right">sam_hdr_t@Base 1.1.2</span>+dfsg</span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="plaintext"> _ZN6SeqLib9BamHeaderC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 1.1.1+dfsg</span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="plaintext"> _ZN6SeqLib9BamHeaderC2ERKSt6vectorINS_14HeaderSequenceESaIS2_EE@Base 1.1.1+dfsg</span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="plaintext"> _ZN6SeqLib9BamHeaderD1Ev@Base 1.1.1+dfsg</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">@@ -306,18 +306,18 @@ libseqlib.so.1 libseqlib1 #MINVER#</td>
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="plaintext"> _ZNSt19_Sp_counted_deleterIP7htsFile14htsFile_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EED0Ev@Base 1.1.1+dfsg</span>
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="plaintext"> _ZNSt19_Sp_counted_deleterIP7htsFile14htsFile_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EED1Ev@Base 1.1.1+dfsg</span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext"> _ZNSt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE10_M_destroyEv@Base 1.1.2+dfsg</span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext"> _ZNSt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE14_M_get_deleterERKSt9type_info@Base 1.1.2+dfsg</span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext"> _ZNSt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EED0Ev@Base 1.1.2+dfsg</span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext"> _ZNSt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EED1Ev@Base 1.1.2+dfsg</span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext"> _ZNSt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EED2Ev@Base 1.1.2+dfsg</span>
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="plaintext"> _ZNSt4pairIKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEN6SeqLib4_BamEED1Ev@Base 1.1.1+dfsg</span>
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="plaintext"> _ZNSt4pairIKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEN6SeqLib4_BamEED2Ev@Base 1.1.1+dfsg</span>
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="plaintext"> _ZNSt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEN6SeqLib4_BamEED1Ev@Base 1.1.1+dfsg</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">@@ -412,8 +412,8 @@ libseqlib.so.1 libseqlib1 #MINVER#</td>
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412
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412
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="plaintext"> _ZTISt19_Sp_counted_deleterIP11__hts_idx_t10idx_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg</span>
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413
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413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="plaintext"> _ZTISt19_Sp_counted_deleterIP6bam1_tN6SeqLib11free_deleteESaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg</span>
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414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="plaintext"> _ZTISt19_Sp_counted_deleterIP7htsFile14htsFile_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg</span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="plaintext"> _ZTISt19_Sp_counted_deleterIP9bam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg</span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="plaintext"> _ZTISt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.2+dfsg</span>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="plaintext"> _ZTS10idx_delete@Base 1.1.1+dfsg</span>
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418
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="plaintext"> _ZTS14bam_hdr_delete@Base 1.1.1+dfsg</span>
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="plaintext"> _ZTS14htsFile_delete@Base 1.1.1+dfsg</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">@@ -428,8 +428,8 @@ libseqlib.so.1 libseqlib1 #MINVER#</td>
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428
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428
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="plaintext"> _ZTSSt19_Sp_counted_deleterIP11__hts_idx_t10idx_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg</span>
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429
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="plaintext"> _ZTSSt19_Sp_counted_deleterIP6bam1_tN6SeqLib11free_deleteESaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg</span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="plaintext"> _ZTSSt19_Sp_counted_deleterIP7htsFile14htsFile_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg</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">@@ -437,5 +437,5 @@ libseqlib.so.1 libseqlib1 #MINVER#</td>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="plaintext"> _ZTVSt19_Sp_counted_deleterIP6bam1_tN6SeqLib11free_deleteESaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg</span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="plaintext"> _ZTVSt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.2+dfsg</span></pre>
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<li id="e1319e3be642ca291bf4ab694440cdeefa812d34">
<a href="https://salsa.debian.org/med-team/libseqlib/compare/64f09e6893b9f58cd90c14fe94af1a497eb18a57...b97d3004f6f1c5623e7bce19a0180a2d3bc432e5#e1319e3be642ca291bf4ab694440cdeefa812d34"><strong>debian/patches/fix_private_htslib_usage.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: John Marshall <John.W.Marshall@glasgow.ac.uk></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Date: Tue Dec 17 19:10:47 2019 +0000</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Origin: https://github.com/walaj/SeqLib/commit/3fc64616a64adfcaf5271ae24f35e443ce822faf.patch</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/946924</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Description: Avoid using non-public HTSlib headers and functions</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> Only headers in htslib/*.h are part of HTSlib's public API; cram/*.h</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> in particular are not. Fortunately SeqLib only uses one function from</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> cram/cram_io.h, and that is easily replaced with a public equivalent.</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"> Instead use `hts_set_fai_filename()`, which strdups the string given to</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> it itself; `cram_set_option(fp->fp.cram, CRAM_OPT_REFERENCE, ...)` would</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> also be an option, but it's better to avoid `fp->fp.cram` as poking into</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> an htsFile's insides is also not supported by HTSlib.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff">--- a/SeqLib/BamWalker.h</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/SeqLib/BamWalker.h</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -11,11 +11,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> #define INT32_MAX 0x7fffffffL</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> </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;">-extern "C" {</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include "htslib/cram/cram.h"</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include "htslib/cram/cram_io.h"</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> struct idx_delete {</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> void operator()(hts_idx_t* x) { if (x) hts_idx_destroy(x); }</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/BamReader.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/BamReader.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="p">@@ -186,9 +186,7 @@</span> BamReader::BamReader() {}</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> // open cram reference</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> if (!m_cram_reference.empty()) {</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char * m_cram_reference_cstr = strdup(m_cram_reference.c_str());</span></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;">- int ret = cram_load_reference(fp->fp.cram, m_cram_reference_cstr);</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- free(m_cram_reference_cstr);</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int ret = hts_set_fai_filename(fp.get(), m_cram_reference.c_str());</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> if (ret < 0) </span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> throw std::invalid_argument("Could not read reference genome " + m_cram_reference + " for CRAM opt");</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> }</span></pre>
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<a href="https://salsa.debian.org/med-team/libseqlib/compare/64f09e6893b9f58cd90c14fe94af1a497eb18a57...b97d3004f6f1c5623e7bce19a0180a2d3bc432e5#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -7,4 +7,5 @@ dynamic_lib.patch</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">use_debian_packaged_jsoncpp.patch</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">use_debian_packaged_ssw.patch</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">pkg-config.patch</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">use_private_htslib_headers.patch</span></pre>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"># use_private_htslib_headers.patch</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">fix_private_htslib_usage.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/libseqlib/compare/64f09e6893b9f58cd90c14fe94af1a497eb18a57...b97d3004f6f1c5623e7bce19a0180a2d3bc432e5#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Author: Jeremiah Wala and Rameen Beroukhim</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> Title: ></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> sequence assembly</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> Journal: Bioinformatics</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Year: 2016</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> DOI: 10.1093/bioinformatics/btw741</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> PMID: 28011768</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> URL: "https://academic.oup.com/bioinformatics/article-abstract/doi/\</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> 10.1093/bioinformatics/btw741/2571356/\</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> SeqLib-a-C-API-for-rapid-BAM-manipulation-sequence"</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Author: Jeremiah Wala and Rameen Beroukhim</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Title: ></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> sequence assembly</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Journal: Bioinformatics</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Year: 2016</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> DOI: 10.1093/bioinformatics/btw741</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> PMID: 28011768</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> URL: https://academic.oup.com/bioinformatics/article-abstract/doi/10.1093/bioinformatics/btw741/2571356/SeqLib-a-C-API-for-rapid-BAM-manipulation-sequence</span>
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13
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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">
11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Registry:</span>
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<td class="diff-line-num old old_line" data-linenumber="14" 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">
14
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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC14" class="line" lang="plaintext"> - Name: OMICtools</span>
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<td class="diff-line-num old old_line" data-linenumber="15" 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">
15
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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC15" class="line" lang="plaintext"> Entry: OMICS_14682</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="16" 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">
16
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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC16" class="line" lang="plaintext"> - Name: SciCrunch</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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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC17" class="line" lang="plaintext"> Entry: NA</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="18" 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">
18
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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC18" class="line" lang="plaintext"> - Name: bio.tools</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="19" 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">
19
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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC19" class="line" lang="plaintext"> Entry: NA</span></pre>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">- Name: OMICtools</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> Entry: OMICS_14682</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">- Name: SciCrunch</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> Entry: NA</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">- Name: bio.tools</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Entry: NA</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Bug-Database: https://github.com/walaj/SeqLib/issues</span></pre>
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