Detailed description

Definition at line 72 of file sam.h.

#include <sam.h>

Inheritance diagram for nvbio::io::ReadDataFile_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::ReadDataFile
enum	FileState { FILE_NOT_READY, FILE_OPEN_FAILED, FILE_OK, FILE_EOF, FILE_STREAM_ERROR, FILE_PARSE_ERROR }

Public Methods
	ReadDataFile_SAM (const char *read_file_name, const uint32 max_reads, const uint32 max_read_len, const ReadEncoding flags)

virtual int	nextChunk (ReadDataRAM *output, uint32 max_reads, uint32 max_bps)

bool	init (void)

Public Methods inherited from nvbio::io::ReadDataFile
virtual	~ReadDataFile ()

virtual ReadData *	next (const uint32 batch_size, const uint32 batch_bps)

virtual bool	is_ok (void)

Public Methods inherited from nvbio::io::ReadDataStream
	ReadDataStream (uint32 truncate_read_len=uint32(-1))

virtual	~ReadDataStream ()

Additional Inherited Members
Static Public Members inherited from nvbio::io::ReadDataFile
static const uint32	LONG_READ = 32*1024

Proteced Methods inherited from nvbio::io::ReadDataFile
	ReadDataFile (const uint32 max_reads, const uint32 truncate_read_len, const ReadEncoding flags)

Protected Members inherited from nvbio::io::ReadDataFile
uint32	m_max_reads

ReadEncoding	m_flags

uint32	m_loaded

FileState	m_file_state

Member Enumeration Documentation

anonymous enum

Enumerator
LINE_BUFFER_INIT_SIZE

Definition at line 74 of file sam.h.

Definition at line 76 of file sam.h.

nvbio::io::ReadDataFile_SAM::ReadDataFile_SAM	(	const char *	read_file_name,
		const uint32	max_reads,
		const uint32	max_read_len,
		const ReadEncoding	flags
	)

Definition at line 38 of file sam.cpp.

bool nvbio::io::ReadDataFile_SAM::init ( void )

Definition at line 150 of file sam.cpp.

int nvbio::io::ReadDataFile_SAM::nextChunk	(	ReadDataRAM *	output,
		uint32	max_reads,
		uint32	max_bps
	)

virtual

Definition at line 347 of file sam.cpp.

std::vector<uint64> nvbio::io::ReadDataFile_SAM::sq_lengths

Definition at line 118 of file sam.h.

std::vector<std::string> nvbio::io::ReadDataFile_SAM::sq_names

Definition at line 117 of file sam.h.

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