Add IsSupplementaryAlignment() patch from bamtools code copy

Last-Update: Wed, 27 May 2020 09:59:29 +0200

shipped with tiddit

Gbp-Pq: Name tiddit.patch

3 files changed, 9 insertions, 0 deletions

diff --git a/src/api/BamAlignment.cpp b/src/api/BamAlignment.cpp
index 8173dcf..142c8e9 100644
--- 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
 
diff --git a/src/api/BamAlignment.h b/src/api/BamAlignment.h
index 845e83a..a887a49 100644
--- 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:
diff --git a/src/api/BamConstants.h b/src/api/BamConstants.h
index 973c13b..f0f9c64 100644
--- 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";