Detailed Description

Namespaces
	nvbio::io

Classes
struct	nvbio::io::SequenceDataFile_BAM

struct	nvbio::io::SequenceDataFile_FASTA_gz

struct	nvbio::io::SequenceDataOutputFile_FASTA

struct	nvbio::io::SequenceDataFile_FASTQ_parser

struct	nvbio::io::SequenceDataFile_FASTQ_gz

struct	nvbio::io::SequenceDataOutputFile_FASTQ

struct	nvbio::io::SequenceDataFile

struct	nvbio::io::SequenceDataFile_SAM

struct	nvbio::io::SequenceDataFile_TXT

struct	nvbio::io::SequenceDataFile_TXT_gz

struct	nvbio::io::SequenceDataOutputFile_TXT

Macros
#define	GZREAD(field)

#define	GZFWD(bytes) gzseek(fp, (bytes), SEEK_CUR)

#define	GZSKIP(field) gzseek(fp, sizeof(field), SEEK_CUR)

Enumerations
enum	nvbio::io::AlignmentFlags { nvbio::io::SAMFlag_MultipleSegments = 0x1, nvbio::io::SAMFlag_AllSegmentsAligned = 0x2, nvbio::io::SAMFlag_SegmentUnmapped = 0x4, nvbio::io::SAMFlag_NextSegmentUnmapped = 0x8, nvbio::io::SAMFlag_ReverseComplemented = 0x10, nvbio::io::SAMFlag_NextSegmentReverseComplemented = 0x20, nvbio::io::SAMFlag_FirstSegment = 0x40, nvbio::io::SAMFlag_LastSegment = 0x80, nvbio::io::SAMFlag_SecondaryAlignment = 0x100, nvbio::io::SAMFlag_FailedQC = 0x200, nvbio::io::SAMFlag_Duplicate = 0x400, nvbio::io::SAMFlag_MultipleSegments = 0x1, nvbio::io::SAMFlag_AllSegmentsAligned = 0x2, nvbio::io::SAMFlag_SegmentUnmapped = 0x4, nvbio::io::SAMFlag_NextSegmentUnmapped = 0x8, nvbio::io::SAMFlag_ReverseComplemented = 0x10, nvbio::io::SAMFlag_NextSegmentReverseComplemented = 0x20, nvbio::io::SAMFlag_FirstSegment = 0x40, nvbio::io::SAMFlag_LastSegment = 0x80, nvbio::io::SAMFlag_SecondaryAlignment = 0x100, nvbio::io::SAMFlag_FailedQC = 0x200, nvbio::io::SAMFlag_Duplicate = 0x400 }

enum	{ nvbio::io::SequenceDataFile_SAM::LINE_BUFFER_INIT_SIZE = 1024 }

enum	nvbio::io::SequenceDataFile_SAM::SortOrder { nvbio::io::SequenceDataFile_SAM::SortOrder_unknown, nvbio::io::SequenceDataFile_SAM::SortOrder_unsorted, nvbio::io::SequenceDataFile_SAM::SortOrder_queryname, nvbio::io::SequenceDataFile_SAM::SortOrder_coordinate }

Functions
	nvbio::io::SequenceDataFile_SAM::SequenceDataFile_SAM (const char *read_file_name, const SequenceDataFile::Options &options)

virtual int	nvbio::io::SequenceDataFile_SAM::nextChunk (struct SequenceDataEncoder *output, uint32 max_reads, uint32 max_bps)

virtual bool	nvbio::io::SequenceDataFile_SAM::rewind ()

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

	nvbio::io::SequenceDataFile_BAM::SequenceDataFile_BAM (const char *read_file_name, const SequenceDataFile::Options &options)

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

virtual bool	nvbio::io::SequenceDataFile_BAM::rewind ()

virtual int	nvbio::io::SequenceDataFile_BAM::nextChunk (struct SequenceDataEncoder *output, uint32 max_reads, uint32 max_bps)

	nvbio::io::SequenceDataFile_FASTA_gz::SequenceDataFile_FASTA_gz (const char *read_file_name, const SequenceDataFile::Options &options)

bool	nvbio::io::SequenceDataFile_FASTA_gz::rewind ()

int	nvbio::io::SequenceDataFile_FASTA_gz::nextChunk (SequenceDataEncoder *output, uint32 max_reads, uint32 max_bps)

	nvbio::io::SequenceDataOutputFile_FASTA::SequenceDataOutputFile_FASTA (const char file_name, const char compressor, const char *options)

void	nvbio::io::SequenceDataOutputFile_FASTA::next (const SequenceDataHost &sequence_data)

bool	nvbio::io::SequenceDataOutputFile_FASTA::is_ok ()

virtual int	nvbio::io::SequenceDataFile_FASTQ_parser::nextChunk (struct SequenceDataEncoder *output, uint32 max_reads, uint32 max_bps)

	nvbio::io::SequenceDataFile_FASTQ_gz::SequenceDataFile_FASTQ_gz (const char *read_file_name, const SequenceDataFile::Options &options)

	nvbio::io::SequenceDataFile_FASTQ_gz::~SequenceDataFile_FASTQ_gz ()

virtual FileState	nvbio::io::SequenceDataFile_FASTQ_gz::fillBuffer (void)

virtual bool	nvbio::io::SequenceDataFile_FASTQ_gz::rewind ()

	nvbio::io::SequenceDataOutputFile_FASTQ::SequenceDataOutputFile_FASTQ (const char file_name, const char compressor, const char *options)

void	nvbio::io::SequenceDataOutputFile_FASTQ::next (const SequenceDataHost &sequence_data)

bool	nvbio::io::SequenceDataOutputFile_FASTQ::is_ok ()

virtual int	nvbio::io::SequenceDataFile_TXT::nextChunk (struct SequenceDataEncoder *output, uint32 max_reads, uint32 max_bps)

	nvbio::io::SequenceDataFile_TXT_gz::SequenceDataFile_TXT_gz (const char *read_file_name, const Options &options, const uint32 buffer_size=64536u)

	nvbio::io::SequenceDataFile_TXT_gz::~SequenceDataFile_TXT_gz ()

virtual bool	nvbio::io::SequenceDataFile_TXT_gz::rewind ()

virtual FileState	nvbio::io::SequenceDataFile_TXT_gz::fillBuffer (void)

	nvbio::io::SequenceDataOutputFile_TXT::SequenceDataOutputFile_TXT (const char file_name, const char compressor, const char *options)

void	nvbio::io::SequenceDataOutputFile_TXT::next (const SequenceDataHost &sequence_data)

bool	nvbio::io::SequenceDataOutputFile_TXT::is_ok ()

Variables
std::vector< std::string >	nvbio::io::SequenceDataFile_SAM::sq_names

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

Macro Definition Documentation

#define GZFWD ( bytes) gzseek(fp, (bytes), SEEK_CUR)

Definition at line 105 of file sequence_bam.cpp.

#define GZREAD ( field)

Value:

if (readData(&(field), sizeof(field)) == false) {           \
        return error;                                           \
    }

Definition at line 98 of file sequence_bam.cpp.

#define GZSKIP ( field) gzseek(fp, sizeof(field), SEEK_CUR)

Definition at line 109 of file sequence_bam.cpp.

Enumeration Type Documentation

anonymous enum

Enumerator
LINE_BUFFER_INIT_SIZE

Definition at line 84 of file sequence_sam.h.

enum nvbio::io::AlignmentFlags

flag comments come from SAMtools spec a better explanation is available at: http://genome.sph.umich.edu/wiki/SAM#What_Information_Does_SAM.2FBAM_Have_for_an_Alignment

Enumerator
SAMFlag_MultipleSegments
SAMFlag_AllSegmentsAligned
SAMFlag_SegmentUnmapped
SAMFlag_NextSegmentUnmapped
SAMFlag_ReverseComplemented
SAMFlag_NextSegmentReverseComplemented
SAMFlag_FirstSegment
SAMFlag_LastSegment
SAMFlag_SecondaryAlignment
SAMFlag_FailedQC
SAMFlag_Duplicate
SAMFlag_MultipleSegments
SAMFlag_AllSegmentsAligned
SAMFlag_SegmentUnmapped
SAMFlag_NextSegmentUnmapped
SAMFlag_ReverseComplemented
SAMFlag_NextSegmentReverseComplemented
SAMFlag_FirstSegment
SAMFlag_LastSegment
SAMFlag_SecondaryAlignment
SAMFlag_FailedQC
SAMFlag_Duplicate

Definition at line 53 of file sequence_sam.h.

enum nvbio::io::SequenceDataFile_SAM::SortOrder

Enumerator
SortOrder_unknown
SortOrder_unsorted
SortOrder_queryname
SortOrder_coordinate

Definition at line 86 of file sequence_sam.h.

Function Documentation

SequenceDataFile_TXT::FileState nvbio::io::SequenceDataFile_TXT_gz::fillBuffer ( void )

virtual

fill the buffer

Implements nvbio::io::SequenceDataFile_TXT.

Definition at line 242 of file sequence_txt.cpp.

SequenceDataFile_FASTQ_parser::FileState nvbio::io::SequenceDataFile_FASTQ_gz::fillBuffer ( void )

virtual

Implements nvbio::io::SequenceDataFile_FASTQ_parser.

Definition at line 327 of file sequence_fastq.cpp.

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

initialize the stream

Definition at line 112 of file sequence_bam.cpp.

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

Definition at line 148 of file sequence_sam.cpp.

bool nvbio::io::SequenceDataOutputFile_FASTA::is_ok ( void )

virtual

return whether the stream is ok

Implements nvbio::io::SequenceDataOutputStream.

Definition at line 245 of file sequence_fasta.cpp.

bool nvbio::io::SequenceDataOutputFile_TXT::is_ok ( void )

virtual

return whether the stream is ok

Implements nvbio::io::SequenceDataOutputStream.

Definition at line 330 of file sequence_txt.cpp.

bool nvbio::io::SequenceDataOutputFile_FASTQ::is_ok ( void )

virtual

return whether the stream is ok

Implements nvbio::io::SequenceDataOutputStream.

Definition at line 458 of file sequence_fastq.cpp.

void nvbio::io::SequenceDataOutputFile_FASTA::next ( const SequenceDataHost & sequence_data)

virtual

next batch

Implements nvbio::io::SequenceDataOutputStream.

Definition at line 227 of file sequence_fasta.cpp.

void nvbio::io::SequenceDataOutputFile_TXT::next ( const SequenceDataHost & sequence_data)

virtual

next batch

Implements nvbio::io::SequenceDataOutputStream.

Definition at line 312 of file sequence_txt.cpp.

void nvbio::io::SequenceDataOutputFile_FASTQ::next ( const SequenceDataHost & sequence_data)

virtual

next batch

Implements nvbio::io::SequenceDataOutputStream.

Definition at line 440 of file sequence_fastq.cpp.

int nvbio::io::SequenceDataFile_FASTA_gz::nextChunk	(	SequenceDataEncoder *	output,
		uint32	max_reads,
		uint32	max_bps
	)

virtual

get a chunk of reads

Implements nvbio::io::SequenceDataFile.

Definition at line 153 of file sequence_fasta.cpp.

int nvbio::io::SequenceDataFile_BAM::nextChunk	(	struct SequenceDataEncoder *	output,
		uint32	max_reads,
		uint32	max_bps
	)

virtual

read the next chunk

Implements nvbio::io::SequenceDataFile.

Definition at line 182 of file sequence_bam.cpp.

int nvbio::io::SequenceDataFile_TXT::nextChunk	(	struct SequenceDataEncoder *	output,
		uint32	max_reads,
		uint32	max_bps
	)

protectedvirtual

Implements nvbio::io::SequenceDataFile.

Definition at line 47 of file sequence_txt.cpp.

int nvbio::io::SequenceDataFile_FASTQ_parser::nextChunk	(	struct SequenceDataEncoder *	output,
		uint32	max_reads,
		uint32	max_bps
	)

protectedvirtual

Implements nvbio::io::SequenceDataFile.

Definition at line 48 of file sequence_fastq.cpp.

int nvbio::io::SequenceDataFile_SAM::nextChunk	(	struct SequenceDataEncoder *	output,
		uint32	max_reads,
		uint32	max_bps
	)

virtual

load the next chunk

Implements nvbio::io::SequenceDataFile.

Definition at line 364 of file sequence_sam.cpp.

bool nvbio::io::SequenceDataFile_BAM::rewind ( void )

virtual

rewind the file

Implements nvbio::io::SequenceDataInputStream.

Definition at line 170 of file sequence_bam.cpp.

bool nvbio::io::SequenceDataFile_FASTA_gz::rewind ( void )

virtual

rewind the file

Implements nvbio::io::SequenceDataInputStream.

Definition at line 141 of file sequence_fasta.cpp.

bool nvbio::io::SequenceDataFile_SAM::rewind ( void )

virtual

rewind the file

Implements nvbio::io::SequenceDataInputStream.

Definition at line 345 of file sequence_sam.cpp.

bool nvbio::io::SequenceDataFile_TXT_gz::rewind ( void )

virtual

rewind the file

Implements nvbio::io::SequenceDataInputStream.

Definition at line 227 of file sequence_txt.cpp.

bool nvbio::io::SequenceDataFile_FASTQ_gz::rewind ( void )

virtual

rewind the file

Implements nvbio::io::SequenceDataInputStream.

Definition at line 356 of file sequence_fastq.cpp.

nvbio::io::SequenceDataFile_BAM::SequenceDataFile_BAM	(	const char *	read_file_name,
		const SequenceDataFile::Options &	options
	)

constructor

Definition at line 50 of file sequence_bam.cpp.

nvbio::io::SequenceDataFile_FASTA_gz::SequenceDataFile_FASTA_gz	(	const char *	read_file_name,
		const SequenceDataFile::Options &	options
	)

constructor

Definition at line 126 of file sequence_fasta.cpp.

nvbio::io::SequenceDataFile_FASTQ_gz::SequenceDataFile_FASTQ_gz	(	const char *	read_file_name,
		const SequenceDataFile::Options &	options
	)

Definition at line 305 of file sequence_fastq.cpp.

nvbio::io::SequenceDataFile_SAM::SequenceDataFile_SAM	(	const char *	read_file_name,
		const SequenceDataFile::Options &	options
	)

constructor

Definition at line 39 of file sequence_sam.cpp.

nvbio::io::SequenceDataFile_TXT_gz::SequenceDataFile_TXT_gz	(	const char *	read_file_name,
		const Options &	options,
		const uint32	buffer_size = `64536u`
	)

Definition at line 204 of file sequence_txt.cpp.

nvbio::io::SequenceDataOutputFile_FASTA::SequenceDataOutputFile_FASTA	(	const char *	file_name,
		const char *	compressor,
		const char *	options
	)

constructor

Definition at line 169 of file sequence_fasta.cpp.

nvbio::io::SequenceDataOutputFile_FASTQ::SequenceDataOutputFile_FASTQ	(	const char *	file_name,
		const char *	compressor,
		const char *	options
	)

constructor

Definition at line 373 of file sequence_fastq.cpp.

nvbio::io::SequenceDataOutputFile_TXT::SequenceDataOutputFile_TXT	(	const char *	file_name,
		const char *	compressor,
		const char *	options
	)

constructor

Definition at line 270 of file sequence_txt.cpp.

nvbio::io::SequenceDataFile_FASTQ_gz::~SequenceDataFile_FASTQ_gz ( )

Definition at line 320 of file sequence_fastq.cpp.

nvbio::io::SequenceDataFile_TXT_gz::~SequenceDataFile_TXT_gz ( )

Definition at line 220 of file sequence_txt.cpp.

Variable Documentation

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

Definition at line 129 of file sequence_sam.h.

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

Definition at line 128 of file sequence_sam.h.

Detailed Description

Namespaces

Classes

Macros

Enumerations

Functions

Variables

Macro Definition Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation