All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
Public Methods | Public Members | List of all members
nvbio::alndiff::BAMAlignmentStream Struct Reference

Detailed description

Definition at line 36 of file alignment_bam.cpp.

Inheritance diagram for nvbio::alndiff::BAMAlignmentStream:

Public Methods

 BAMAlignmentStream (const char *file_name)
bool is_ok ()
uint32 next_batch (const uint32 count, Alignment *batch)
void analyze_cigar (const std::vector< BamTools::CigarOp > &cigar, Alignment *aln)
void analyze_md (const char *md, Alignment *aln)
- Public Methods inherited from nvbio::alndiff::AlignmentStream
virtual ~AlignmentStream ()

Public Members

BamTools::BamReader m_bam_reader
uint32 m_offset

Constructor & Destructor Documentation

nvbio::alndiff::BAMAlignmentStream::BAMAlignmentStream ( const char *  file_name)

Definition at line 38 of file alignment_bam.cpp.

Member Function Documentation

void nvbio::alndiff::BAMAlignmentStream::analyze_cigar ( const std::vector< BamTools::CigarOp > &  cigar,
Alignment aln 

Definition at line 100 of file alignment_bam.cpp.

void nvbio::alndiff::BAMAlignmentStream::analyze_md ( const char *  md,
Alignment aln 

Definition at line 119 of file alignment_bam.cpp.

bool nvbio::alndiff::BAMAlignmentStream::is_ok ( void  )

return if the stream is ok

Reimplemented from nvbio::alndiff::AlignmentStream.

Definition at line 48 of file alignment_bam.cpp.

uint32 nvbio::alndiff::BAMAlignmentStream::next_batch ( const uint32  count,
Alignment batch 

get the next batch

Reimplemented from nvbio::alndiff::AlignmentStream.

Definition at line 52 of file alignment_bam.cpp.

Member Data Documentation

BamTools::BamReader nvbio::alndiff::BAMAlignmentStream::m_bam_reader

Definition at line 143 of file alignment_bam.cpp.

uint32 nvbio::alndiff::BAMAlignmentStream::m_offset

Definition at line 144 of file alignment_bam.cpp.

The documentation for this struct was generated from the following file: