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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bamtools">Debian Med / bamtools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bamtools/-/commit/46dc9f03d7620c671fc0b5b40709771b7404bfb6">46dc9f03</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-27T09:42:47+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bamtools/-/commit/130504f9b81c0bfe865a9da2a3feb30e62052463">130504f9</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-05-27T10:35:46+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add IsSupplementaryAlignment() patch from bamtools code copy shipped with tiddit
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#acf76687b8d6bd6257223b8ed1843a41a9b7e11f">
debian/patches/0008_Cmake_Test.patch
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#43c27734bcfab1fa28c84273d8d9e5501cedacb0">
<span class="new-file">
+
debian/patches/tiddit.patch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bamtools/-/compare/303e4ac0e1d12f4cade7623aba5feb39d8495a7f...130504f9b81c0bfe865a9da2a3feb30e62052463#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bamtools (2.5.1+dfsg-6) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> * Add IsSupplementaryAlignment() patch from bamtools code copy shipped</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"> with tiddit</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 27 May 2020 09:59:29 +0200</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">bamtools (2.5.1+dfsg-5) unstable; urgency=medium</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"> * Ignore one test that is known to fail on ppc64el architecture</span>
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<li id="acf76687b8d6bd6257223b8ed1843a41a9b7e11f">
<a href="https://salsa.debian.org/med-team/bamtools/-/compare/303e4ac0e1d12f4cade7623aba5feb39d8495a7f...130504f9b81c0bfe865a9da2a3feb30e62052463#acf76687b8d6bd6257223b8ed1843a41a9b7e11f"><strong>debian/patches/0008_Cmake_Test.patch</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" 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="13" 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">@@ -13,7 +13,7 @@ Author: Dominique Belhachemi <domibel@debian.org></td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> # on macOS, MACOSX_RPATH is enabled by default on more recent versions</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> # of CMake. Disable this behaviour, and let user enable it if need be.</span>
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<td class="diff-line-num old_line" data-linenumber="15" 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="LC15" class="line" lang="diff"> cmake_policy( SET CMP0042 OLD )</span>
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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">
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="p">@@ -9<span class="idiff left">8,3 +100,11 @@</span></span><span class="idiff right"> include_directories("${CMAKE_BINARY_DIR}</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -9<span class="idiff left">7,3 +99,11 @@</span></span><span class="idiff right"> include_directories( src )</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> # list subdirectories to build in</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> add_subdirectory( src )</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/bamtools/-/compare/303e4ac0e1d12f4cade7623aba5feb39d8495a7f...130504f9b81c0bfe865a9da2a3feb30e62052463#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">@@ -4,3 +4,4 @@ doxygen-tweak</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">0006-Doxygen-reproducibility</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">0008_Cmake_Test.patch</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">spelling</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">tiddit.patch</span></pre>
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<li id="43c27734bcfab1fa28c84273d8d9e5501cedacb0">
<a href="https://salsa.debian.org/med-team/bamtools/-/compare/303e4ac0e1d12f4cade7623aba5feb39d8495a7f...130504f9b81c0bfe865a9da2a3feb30e62052463#43c27734bcfab1fa28c84273d8d9e5501cedacb0"><strong>debian/patches/tiddit.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Add IsSupplementaryAlignment() patch from bamtools code copy</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> shipped with tiddit</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Wed, 27 May 2020 09:59:29 +0200</span></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">--- a/src/api/BamAlignment.h</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/api/BamAlignment.h</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -53,6 +53,7 @@</span> public:</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> const; // returns true if alignment is part of read that satisfied paired-end resolution</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> bool IsReverseStrand() const; // returns true if alignment mapped to reverse strand</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> bool IsSecondMate() const; // returns true if alignment is second mate on read</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;">+ bool IsSupplementaryAlignment(void) const; // Additional patch by tiddit package</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> // manipulate alignment flags</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> public:</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/api/BamConstants.h</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/api/BamConstants.h</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -43,6 +43,7 @@</span> const int BAM_ALIGNMENT_READ_2 = 0x0080;</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> const int BAM_ALIGNMENT_SECONDARY = 0x0100;</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> const int BAM_ALIGNMENT_QC_FAILED = 0x0200;</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> const int BAM_ALIGNMENT_DUPLICATE = 0x0400;</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+const int SUPPLEMENTARY = 0x0800; // Additional patch by tiddit package</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> // CIGAR constants</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> const char* const BAM_CIGAR_LOOKUP = "MIDNSHP=X";</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;">--- a/src/api/BamAlignment.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/api/BamAlignment.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -822,6 +822,13 @@</span> bool BamAlignment::IsSecondMate() const</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> return ((AlignmentFlag & Constants::BAM_ALIGNMENT_READ_2) != 0);</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+/*! \fn bool BamAlignment::IsSupplementaryAlignment() const</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;">+ \return \c true if ailgnment is supplementary (This is an additional patch by tiddit package)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ */</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bool BamAlignment::IsSupplementaryAlignment(void) const {</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return ( (AlignmentFlag & Constants::SUPPLEMENTARY) != 0 );</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</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;">+</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> /*! \fn bool BamAlignment::IsValidSize(const std::string& tag, const std::string& type) const</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> \internal</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span></pre>
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