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nvbio::alndiff::BAMAlignmentStream Struct Reference

Detailed description

Definition at line 36 of file alignment_bam.cpp.

Inheritance diagram for nvbio::alndiff::BAMAlignmentStream:
nvbio::alndiff::AlignmentStream

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)
inline

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 
)
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

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 
)
inlinevirtual

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: