IO

Detailed Description

Modules
	FM-Index I/O
	Read data input
	Sequence Data Input
	Output
	Utils

Namespaces
	nvbio::io

Classes
struct	nvbio::io::Cigar
struct	nvbio::io::Alignment
struct	nvbio::io::AlignmentCompare
struct	nvbio::io::BestAlignments
struct	nvbio::io::PairedAlignments
struct	nvbio::io::BestPairedAlignments
struct	nvbio::io::has_second
struct	nvbio::io::has_second_paired
struct	nvbio::io::has_second_unpaired
struct	nvbio::io::is_paired
struct	nvbio::io::is_unpaired
struct	nvbio::io::is_concordant
struct	nvbio::io::is_discordant
struct	nvbio::io::is_not_concordant
struct	nvbio::io::is_aligned
class	nvbio::io::BufferedTextFile
struct	nvbio::OutputStream
struct	nvbio::GZOutputFile
struct	nvbio::LZ4OutputFile

Enumerations
enum	nvbio::io::MDS_OP {   nvbio::io::MDS_MATCH = 0, nvbio::io::MDS_MISMATCH = 1, nvbio::io::MDS_INSERTION = 2, nvbio::io::MDS_DELETION = 3,   nvbio::io::MDS_INVALID = 4 }

Functions
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::io::distinct_alignments (const uint32 pos1, const bool rc1, const uint32 pos2, const bool rc2, const uint32 dist)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::io::distinct_alignments (const uint32 apos1, const uint32 opos1, const bool arc1, const bool orc1, const uint32 apos2, const uint32 opos2, const bool arc2, const bool orc2, const uint32 dist)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::io::distinct_alignments (const Alignment &p1, const Alignment &p2, const uint32 dist=1)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::io::distinct_alignments (const PairedAlignments &p1, const PairedAlignments &p2)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::io::distinct_alignments (const PairedAlignments &p1, const PairedAlignments &p2, const uint32 dist)
	nvbio::io::BufferedTextFile::BufferedTextFile (const char *fname, char record_separator= '\n', size_t buffer_size=256 *1024)
	nvbio::io::BufferedTextFile::~BufferedTextFile ()
bool	nvbio::io::BufferedTextFile::fill_buffer (void)
bool	nvbio::io::BufferedTextFile::buffer_full (void)
bool	nvbio::io::BufferedTextFile::buffer_empty (void)
char *	nvbio::io::BufferedTextFile::next_record (char **line_end)
OutputStream *	nvbio::open_output_file (const char *file_name, const char *compressor, const char *options)

Enumeration Type Documentation

enum nvbio::io::MDS_OP

The list of MD string operations

Enumerator
MDS_MATCH
MDS_MISMATCH
MDS_INSERTION
MDS_DELETION
MDS_INVALID

Definition at line 46 of file alignments.h.

Function Documentation

bool nvbio::io::BufferedTextFile::buffer_empty ( void  )

inline

Definition at line 116 of file bufferedtextfile.h.

bool nvbio::io::BufferedTextFile::buffer_full ( void  )

inline

Definition at line 111 of file bufferedtextfile.h.

nvbio::io::BufferedTextFile::BufferedTextFile ( const char *  fname, char  record_separator = '\n', size_t  buffer_size = 256 * 1024  )

inline

Definition at line 58 of file bufferedtextfile.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::io::distinct_alignments	(	const uint32	pos1,
		const bool	rc1,
		const uint32	pos2,
		const bool	rc2,
		const uint32	dist
	)

Definition at line 35 of file alignments_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::io::distinct_alignments	(	const uint32	apos1,
		const uint32	opos1,
		const bool	arc1,
		const bool	orc1,
		const uint32	apos2,
		const uint32	opos2,
		const bool	arc2,
		const bool	orc2,
		const uint32	dist
	)

Definition at line 66 of file alignments_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::io::distinct_alignments	(	const Alignment &	p1,
		const Alignment &	p2,
		const uint32	dist = 1
	)

Definition at line 90 of file alignments_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::io::distinct_alignments	(	const PairedAlignments &	p1,
		const PairedAlignments &	p2
	)

Definition at line 105 of file alignments_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::io::distinct_alignments	(	const PairedAlignments &	p1,
		const PairedAlignments &	p2,
		const uint32	dist
	)

Definition at line 121 of file alignments_inl.h.

bool nvbio::io::BufferedTextFile::fill_buffer ( void  )

inline

Definition at line 81 of file bufferedtextfile.h.

char* nvbio::io::BufferedTextFile::next_record ( char **  line_end)

inline

Definition at line 122 of file bufferedtextfile.h.

OutputStream * nvbio::open_output_file	(	const char *	file_name,
		const char *	compressor,
		const char *	options
	)

output file factory method

Definition at line 140 of file output_stream.cpp.

nvbio::io::BufferedTextFile::~BufferedTextFile ( )

inline

Definition at line 71 of file bufferedtextfile.h.