ReadsIODetail

Detailed Description

Classes
struct	nvbio::io::ReadDataFile_BAM
struct	nvbio::io::ReadDataFile_FASTQ_parser
struct	nvbio::io::ReadDataFile_FASTQ_gz
struct	nvbio::io::ReadDataFile
struct	nvbio::io::ReadDataFile_TXT
struct	nvbio::io::ReadDataFile_TXT_gz

Macros
#define	GZREAD(field)
#define	GZFWD(bytes)   gzseek(fp, (bytes), SEEK_CUR)
#define	GZSKIP(field)   gzseek(fp, sizeof(field), SEEK_CUR)

Functions
	nvbio::io::ReadDataFile_BAM::ReadDataFile_BAM (const char *read_file_name, const uint32 max_reads, const uint32 max_read_len, const ReadEncoding flags)
bool	nvbio::io::ReadDataFile_BAM::init (void)
virtual int	nvbio::io::ReadDataFile_BAM::nextChunk (ReadDataRAM *output, uint32 max_reads, uint32 max_bps)
virtual int	nvbio::io::ReadDataFile_FASTQ_parser::nextChunk (ReadDataRAM *output, uint32 max_reads, uint32 max_bps)
	nvbio::io::ReadDataFile_FASTQ_gz::ReadDataFile_FASTQ_gz (const char *read_file_name, const QualityEncoding qualities, const uint32 max_reads, const uint32 max_read_len, const ReadEncoding flags)
virtual FileState	nvbio::io::ReadDataFile_FASTQ_gz::fillBuffer (void)
virtual int	nvbio::io::ReadDataFile_TXT::nextChunk (ReadDataRAM *output, uint32 max_reads, uint32 max_bps)
	nvbio::io::ReadDataFile_TXT_gz::ReadDataFile_TXT_gz (const char *read_file_name, const QualityEncoding qualities, const uint32 max_reads, const uint32 max_read_len, const ReadEncoding flags, const uint32 buffer_size=64536u)
virtual FileState	nvbio::io::ReadDataFile_TXT_gz::fillBuffer (void)

Macro Definition Documentation

#define GZFWD

(

bytes)

gzseek(fp, (bytes), SEEK_CUR)

Definition at line 105 of file bam.cpp.

#define GZREAD

(

field)

Value:

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

Definition at line 98 of file bam.cpp.

#define GZSKIP

(

field)

gzseek(fp, sizeof(field), SEEK_CUR)

Definition at line 109 of file bam.cpp.

Function Documentation

ReadDataFile_TXT::FileState nvbio::io::ReadDataFile_TXT_gz::fillBuffer ( void  )

virtual

Implements nvbio::io::ReadDataFile_TXT.

Definition at line 156 of file reads_txt.cpp.

ReadDataFile_FASTQ_parser::FileState nvbio::io::ReadDataFile_FASTQ_gz::fillBuffer ( void  )

virtual

Implements nvbio::io::ReadDataFile_FASTQ_parser.

Definition at line 232 of file reads_fastq.cpp.

bool nvbio::io::ReadDataFile_BAM::init

(

void

)

initialize the stream

Definition at line 112 of file bam.cpp.

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

virtual

read the next chunk

Implements nvbio::io::ReadDataFile.

Definition at line 169 of file bam.cpp.

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

protectedvirtual

Implements nvbio::io::ReadDataFile.

Definition at line 46 of file reads_txt.cpp.

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

protectedvirtual

Implements nvbio::io::ReadDataFile.

Definition at line 47 of file reads_fastq.cpp.

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

constructor

Definition at line 49 of file bam.cpp.

nvbio::io::ReadDataFile_FASTQ_gz::ReadDataFile_FASTQ_gz	(	const char *	read_file_name,
		const QualityEncoding	qualities,
		const uint32	max_reads,
		const uint32	max_read_len,
		const ReadEncoding	flags
	)

Definition at line 213 of file reads_fastq.cpp.

nvbio::io::ReadDataFile_TXT_gz::ReadDataFile_TXT_gz	(	const char *	read_file_name,
		const QualityEncoding	qualities,
		const uint32	max_reads,
		const uint32	max_read_len,
		const ReadEncoding	flags,
		const uint32	buffer_size = 64536u
	)

Definition at line 138 of file reads_txt.cpp.