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nvbio::io::SequenceDataFile_SAM Struct Reference

Detailed description

SequenceDataFile from a BAM file

Definition at line 82 of file sequence_sam.h.

#include <sequence_sam.h>

Inheritance diagram for nvbio::io::SequenceDataFile_SAM:
nvbio::io::SequenceDataFile nvbio::io::SequenceDataInputStream

Public Types

enum  { LINE_BUFFER_INIT_SIZE = 1024 }
enum  SortOrder { SortOrder_unknown, SortOrder_unsorted, SortOrder_queryname, SortOrder_coordinate }
- Public Types inherited from nvbio::io::SequenceDataFile
enum  FileState {

Public Methods

 SequenceDataFile_SAM (const char *read_file_name, const SequenceDataFile::Options &options)
virtual int nextChunk (struct SequenceDataEncoder *output, uint32 max_reads, uint32 max_bps)
virtual bool rewind ()
bool init (void)
- Public Methods inherited from nvbio::io::SequenceDataFile
virtual ~SequenceDataFile ()
virtual int next (struct SequenceDataEncoder *encoder, const uint32 batch_size, const uint32 batch_bps)
virtual bool is_ok (void)
- Public Methods inherited from nvbio::io::SequenceDataInputStream
virtual ~SequenceDataInputStream ()

Public Members

std::vector< std::string > sq_names
std::vector< uint64sq_lengths

Additional Inherited Members

- Static Public Members inherited from nvbio::io::SequenceDataFile
static const uint32 LONG_READ = 32*1024
- Proteced Methods inherited from nvbio::io::SequenceDataFile
 SequenceDataFile (const Options &options)
- Protected Members inherited from nvbio::io::SequenceDataFile
Options m_options
uint32 m_loaded
FileState m_file_state

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