From d84f6c6e6d421085bb508a1cb381476d197833b0 Mon Sep 17 00:00:00 2001
From: Ted Wong <tedwong@smallchess.com>
Date: Tue, 21 Nov 2017 21:05:12 +1100
Subject: [PATCH 1/2] Added a function and constant for checking supplementary
 BAM alignments.

---
 src/api/BamAlignment.cpp | 8 ++++++++
 src/api/BamAlignment.h   | 1 +
 src/api/BamConstants.h   | 1 +
 3 files changed, 10 insertions(+)

diff --git a/src/api/BamAlignment.cpp b/src/api/BamAlignment.cpp
index 8173dcf3..ce76e201 100644
--- a/src/api/BamAlignment.cpp
+++ b/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
 */
diff --git a/src/api/BamAlignment.h b/src/api/BamAlignment.h
index 6491807f..9a12be7b 100644
--- a/src/api/BamAlignment.h
+++ b/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
diff --git a/src/api/BamConstants.h b/src/api/BamConstants.h
index 973c13b1..3cea09f5 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 BAM_ALIGNMENT_SUPPLEMENTARY = 0x0800;
 
 // CIGAR constants
 const char* const BAM_CIGAR_LOOKUP = "MIDNSHP=X";

From adeac92ba179a960b18979cbf85b41c4ffd3be64 Mon Sep 17 00:00:00 2001
From: Ted Wong <tedwong@smallchess.com>
Date: Tue, 21 Nov 2017 21:17:34 +1100
Subject: [PATCH 2/2] Added functions for randomly access BAM files by
 pointers.

---
 src/api/BamReader.cpp                | 20 ++++++++++++++++++++
 src/api/BamReader.h                  |  6 ++++++
 src/api/internal/bam/BamReader_p.cpp | 10 ++++++++++
 src/api/internal/bam/BamReader_p.h   |  3 +++
 4 files changed, 39 insertions(+)

diff --git a/src/api/BamReader.cpp b/src/api/BamReader.cpp
index 56e6c395..c1ce0917 100644
--- a/src/api/BamReader.cpp
+++ b/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.
 
diff --git a/src/api/BamReader.h b/src/api/BamReader.h
index 1991a67f..91053e70 100644
--- a/src/api/BamReader.h
+++ b/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
     // ----------------------
diff --git a/src/api/internal/bam/BamReader_p.cpp b/src/api/internal/bam/BamReader_p.cpp
index 25ca1844..254ec1cf 100644
--- a/src/api/internal/bam/BamReader_p.cpp
+++ b/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()
 {
diff --git a/src/api/internal/bam/BamReader_p.h b/src/api/internal/bam/BamReader_p.h
index fdcd8f8c..5b0e8468 100644
--- a/src/api/internal/bam/BamReader_p.h
+++ b/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;