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 ()

Constructor & Destructor Documentation

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

inline

Definition at line 38 of file alignment_bam.cpp.

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

inline

Definition at line 100 of file alignment_bam.cpp.

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

inline

Definition at line 119 of file alignment_bam.cpp.

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

inlinevirtual

return if the stream is ok

Definition at line 48 of file alignment_bam.cpp.

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

inlinevirtual

get the next batch

Definition at line 52 of file alignment_bam.cpp.

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: