Detailed description

Definition at line 82 of file sequence_sam.h.

Inheritance diagram for nvbio::io::SequenceDataFile_SAM:

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 { FILE_NOT_READY, FILE_OPEN_FAILED, FILE_OK, FILE_EOF, FILE_STREAM_ERROR, FILE_PARSE_ERROR }

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 ()

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

Related Functions inherited from nvbio::io::SequenceDataInputStream
int	next (const Alphabet alphabet, SequenceDataHost data, SequenceDataInputStream stream, const uint32 batch_size, const uint32 batch_bps=uint32(-1))

int	append (const Alphabet alphabet, SequenceDataHost data, SequenceDataInputStream stream, const uint32 batch_size, const uint32 batch_bps=uint32(-1))

int	skip (SequenceDataInputStream *stream, const uint32 batch_size)

SequenceDataInputStream *	open_sequence_file (const char *sequence_file_name, const QualityEncoding qualities=Phred33, const uint32 max_seqs=uint32(-1), const uint32 max_sequence_len=uint32(-1), const SequenceEncoding flags=FORWARD, const uint32 trim3=0, const uint32 trim5=0)

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

Public Types