Andreas Tille pushed to branch master at Debian Med / bamtools
Commits: 46dc9f03 by Andreas Tille at 2020-05-27T09:42:47+02:00 Refresh patch - - - - - 130504f9 by Andreas Tille at 2020-05-27T10:35:46+02:00 Add IsSupplementaryAlignment() patch from bamtools code copy shipped with tiddit - - - - - 4 changed files: - debian/changelog - debian/patches/0008_Cmake_Test.patch - debian/patches/series - + debian/patches/tiddit.patch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +bamtools (2.5.1+dfsg-6) UNRELEASED; urgency=medium + + * Add IsSupplementaryAlignment() patch from bamtools code copy shipped + with tiddit + + -- Andreas Tille <[email protected]> Wed, 27 May 2020 09:59:29 +0200 + bamtools (2.5.1+dfsg-5) unstable; urgency=medium * Ignore one test that is known to fail on ppc64el architecture ===================================== debian/patches/0008_Cmake_Test.patch ===================================== @@ -13,7 +13,7 @@ Author: Dominique Belhachemi <[email protected]> # on macOS, MACOSX_RPATH is enabled by default on more recent versions # of CMake. Disable this behaviour, and let user enable it if need be. cmake_policy( SET CMP0042 OLD ) -@@ -98,3 +100,11 @@ include_directories("${CMAKE_BINARY_DIR} +@@ -97,3 +99,11 @@ include_directories( src ) # list subdirectories to build in add_subdirectory( src ) ===================================== debian/patches/series ===================================== @@ -4,3 +4,4 @@ doxygen-tweak 0006-Doxygen-reproducibility 0008_Cmake_Test.patch spelling +tiddit.patch ===================================== debian/patches/tiddit.patch ===================================== @@ -0,0 +1,41 @@ +Description: Add IsSupplementaryAlignment() patch from bamtools code copy + shipped with tiddit +Author: Andreas Tille <[email protected]> +Last-Update: Wed, 27 May 2020 09:59:29 +0200 + +--- a/src/api/BamAlignment.h ++++ b/src/api/BamAlignment.h +@@ -53,6 +53,7 @@ public: + const; // returns true if alignment is part of read that satisfied paired-end resolution + bool IsReverseStrand() const; // returns true if alignment mapped to reverse strand + bool IsSecondMate() const; // returns true if alignment is second mate on read ++ bool IsSupplementaryAlignment(void) const; // Additional patch by tiddit package + + // manipulate alignment flags + public: +--- a/src/api/BamConstants.h ++++ b/src/api/BamConstants.h +@@ -43,6 +43,7 @@ const int BAM_ALIGNMENT_READ_2 = 0x0080; + const int BAM_ALIGNMENT_SECONDARY = 0x0100; + const int BAM_ALIGNMENT_QC_FAILED = 0x0200; + const int BAM_ALIGNMENT_DUPLICATE = 0x0400; ++const int SUPPLEMENTARY = 0x0800; // Additional patch by tiddit package + + // CIGAR constants + const char* const BAM_CIGAR_LOOKUP = "MIDNSHP=X"; +--- a/src/api/BamAlignment.cpp ++++ b/src/api/BamAlignment.cpp +@@ -822,6 +822,13 @@ bool BamAlignment::IsSecondMate() const + return ((AlignmentFlag & Constants::BAM_ALIGNMENT_READ_2) != 0); + } + ++/*! \fn bool BamAlignment::IsSupplementaryAlignment() const ++ \return \c true if ailgnment is supplementary (This is an additional patch by tiddit package) ++ */ ++bool BamAlignment::IsSupplementaryAlignment(void) const { ++ return ( (AlignmentFlag & Constants::SUPPLEMENTARY) != 0 ); ++} ++ + /*! \fn bool BamAlignment::IsValidSize(const std::string& tag, const std::string& type) const + \internal + View it on GitLab: https://salsa.debian.org/med-team/bamtools/-/compare/303e4ac0e1d12f4cade7623aba5feb39d8495a7f...130504f9b81c0bfe865a9da2a3feb30e62052463 -- View it on GitLab: https://salsa.debian.org/med-team/bamtools/-/compare/303e4ac0e1d12f4cade7623aba5feb39d8495a7f...130504f9b81c0bfe865a9da2a3feb30e62052463 You're receiving this email because of your account on salsa.debian.org.
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