[med-svn] [Git][med-team/bamtools][master] 2 commits: Refresh patch

[Andreas Tille]

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 <tille at debian.org>  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 <domibel at debian.org>
  # 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 <tille at debian.org>
+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.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200527/b55b2210/attachment-0001.html>