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Classes | Public Methods | List of all members
nvbio::io::SamOutput Struct Reference

Detailed description

Definition at line 43 of file output_sam.h.

#include <output_sam.h>

Inheritance diagram for nvbio::io::SamOutput:
nvbio::io::OutputFile

Public Methods

 SamOutput (const char *file_name, AlignmentType alignment_type, BNT bnt)
 
 ~SamOutput ()
 
void header ()
 
void process (struct HostOutputBatchSE &batch)
 
void process (struct HostOutputBatchPE &batch)
 
void close (void)
 Flush and close the output file. More...
 
template<>
void write_tag (const char *name, const char *value)
 
- Public Methods inherited from nvbio::io::OutputFile
virtual ~OutputFile ()
 
void set_program (const char *_pg_id, const char *_pg_name, const char *_pg_version, const char *_pg_args)
 
void set_rg (const char *_rg_id, const char *_rg_string)
 
virtual void configure_mapq_evaluator (int mapq_filter)
 
virtual IOStatsget_aggregate_statistics (void)
 Returns aggregate I/O statistics for this object. More...
 

Additional Inherited Members

- Static Public Methods inherited from nvbio::io::OutputFile
static OutputFileopen (const char *file_name, AlignmentType aln_type, BNT bnt)
 
- Proteced Methods inherited from nvbio::io::OutputFile
 OutputFile (const char *file_name, AlignmentType alignment_type, BNT bnt)
 
- Protected Members inherited from nvbio::io::OutputFile
const char * file_name
 Name of the file we're writing. More...
 
AlignmentType alignment_type
 The type of alignment we're running (single or paired-end) More...
 
BNT bnt
 Reference genome data handle. More...
 
int mapq_filter
 The current mapping quality filter: reads with a mapq below this value will be marked as not aligned. More...
 
IOStats iostats
 I/O statistics. More...
 
std::string pg_id
 
std::string pg_name
 
std::string pg_version
 
std::string pg_args
 
std::string rg_id
 
std::string rg_string
 

Constructor & Destructor Documentation

nvbio::io::SamOutput::SamOutput ( const char *  file_name,
AlignmentType  alignment_type,
BNT  bnt 
)

Definition at line 37 of file output_sam.cpp.

nvbio::io::SamOutput::~SamOutput ( )

Definition at line 53 of file output_sam.cpp.

Member Function Documentation

void nvbio::io::SamOutput::close ( void  )
virtual

Flush and close the output file.

Reimplemented from nvbio::io::OutputFile.

Definition at line 574 of file output_sam.cpp.

void nvbio::io::SamOutput::header ( )
inlinevirtual

write the header out

Reimplemented from nvbio::io::OutputFile.

Definition at line 96 of file output_sam.h.

void nvbio::io::SamOutput::process ( struct HostOutputBatchSE batch)
virtual

Process a set of alignment results for the current batch.

Parameters
batchHandle to the buffers containing the alignment results

Reimplemented from nvbio::io::OutputFile.

Definition at line 535 of file output_sam.cpp.

void nvbio::io::SamOutput::process ( struct HostOutputBatchPE batch)
virtual

Process a set of alignment results for the current batch.

Parameters
batchHandle to the buffers containing the alignment results

Reimplemented from nvbio::io::OutputFile.

Definition at line 554 of file output_sam.cpp.

template<>
void nvbio::io::SamOutput::write_tag ( const char *  name,
const char *  value 
)

Definition at line 148 of file output_sam.cpp.


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