Added a function and constant for checking supplementary BAM alignments.

src/api/BamAlignment.cpp

@@ -734,6 +734,14 @@ bool BamAlignment::HasTag(const std::string& tag) const
     return FindTag(tag, pTagData, tagDataLength, numBytesParsed);
 }
 
+/*! \fn bool BamAlignment::IsSupplementary() const
+    \return \c true if this read is supplementary
+*/
+bool BamAlignment::IsSupplementary() const
+{
+    return ((AlignmentFlag & Constants::BAM_ALIGNMENT_SUPPLEMENTARY) != 0);
+}
+
 /*! \fn bool BamAlignment::IsDuplicate() const
     \return \c true if this read is a PCR duplicate
 */

src/api/BamAlignment.h

@@ -48,6 +48,7 @@ class API_EXPORT BamAlignment
     bool IsMateMapped() const;         // returns true if alignment's mate is mapped
     bool IsMateReverseStrand() const;  // returns true if alignment's mate mapped to reverse strand
     bool IsPaired() const;             // returns true if alignment part of paired-end read
+    bool IsSupplementary() const;      // returns true if this read is supplementary
     bool IsPrimaryAlignment() const;   // returns true if reported position is primary alignment
     bool IsProperPair()
         const;  // returns true if alignment is part of read that satisfied paired-end resolution

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 BAM_ALIGNMENT_SUPPLEMENTARY = 0x0800;
 
 // CIGAR constants
 const char* const BAM_CIGAR_LOOKUP = "MIDNSHP=X";

src/api/BamReader.cpp

@@ -306,6 +306,26 @@ bool BamReader::OpenIndex(const std::string& indexFilename)
     return d->OpenIndex(indexFilename);
 }
 
+/*! \fn bool BamReader::GetPointer()
+    \brief Returns the current file pointer.
+
+    Useful for going back to previous alignments with SetPointer().
+
+    \returns \c file pointer
+    \sa SetPointer()
+*/
+
+int64_t BamReader::GetPointer() const
+{
+	return d->GetPointer();
+}
+
+// set the current file pointer
+void BamReader::SetPointer(int64_t i)
+{
+	d->SetPointer(i);
+}
+
 /*! \fn bool BamReader::Rewind()
     \brief Returns the internal file pointer to the first alignment record.
 

src/api/BamReader.h

@@ -54,6 +54,12 @@ class API_EXPORT BamReader
     bool SetRegion(const int& leftRefID, const int& leftPosition, const int& rightRefID,
                    const int& rightPosition);
 
+    // returns current file pointer
+	int64_t GetPointer() const; 
+
+	// set the current file pointer
+	void SetPointer(int64_t);
+
     // ----------------------
     // access alignment data
     // ----------------------

src/api/internal/bam/BamReader_p.cpp

@@ -423,6 +423,16 @@ bool BamReaderPrivate::OpenIndex(const std::string& indexFilename)
     }
 }
 
+int64_t BamReaderPrivate::GetPointer() const
+{
+	return m_stream.Tell();
+}
+
+void BamReaderPrivate::SetPointer(int64_t position)
+{
+     m_stream.Seek(position);	
+}
+
 // returns BAM file pointer to beginning of alignment data
 bool BamReaderPrivate::Rewind()
 {

src/api/internal/bam/BamReader_p.h

@@ -54,6 +54,9 @@ class BamReaderPrivate
     bool GetNextAlignment(BamAlignment& alignment);
     bool GetNextAlignmentCore(BamAlignment& alignment);
 
+	int64_t GetPointer() const;
+	void SetPointer(int64_t);
+
     // access auxiliary data
     std::string GetHeaderText() const;
     const SamHeader& GetConstSamHeader() const;