Detailed description

Definition at line 49 of file output_priv.h.

#include <output_priv.h>

Public Types
typedef io::SequenceDataHost	read_data_type

typedef io::SequenceDataAccess < DNA_N >	read_access_type

typedef read_access_type::sequence_stream_type	read_type

Public Methods
	AlignmentData ()

	AlignmentData (const Alignment _aln, const uint32 _mapq, const uint32 _aln_id, const uint32 _read_id, const io::SequenceDataHost read_data_batch, const HostCigarArray cigar_array, const HostMdsArray mds_array)

Static Public Methods
static AlignmentData	invalid (void)

Public Members
bool	valid
	set to true if this is a valid alignment More...

const Alignment *	aln
	the alignment itself More...

uint32	aln_id
	the alignment index More...

uint32	read_id
	the read id of this alignment within the batch More...

uint32	mapq
	the mapping quality score More...

const io::SequenceDataHost *	read_data_batch_p

const HostCigarArray *	cigar_array_p

const HostMdsArray *	mds_array_p

uint32	read_offset
	the offset of the read from the start of read_data More...

uint32	read_len
	length of the read More...

const char *	read_name
	read name More...

read_type	read_data
	the iterator for the read data, acts as an array of uint8 More...

const char *	qual
	quality data More...

const Cigar *	cigar
	CIGAR for this alignment. More...

uint32	cigar_pos

uint32	cigar_len
	CIGAR length. More...

const uint8 *	mds_vec
	MDS vector. More...

Member Typedef Documentation

typedef io::SequenceDataAccess<DNA_N> nvbio::io::AlignmentData::read_access_type

Definition at line 52 of file output_priv.h.

typedef io::SequenceDataHost nvbio::io::AlignmentData::read_data_type

Definition at line 51 of file output_priv.h.

typedef read_access_type::sequence_stream_type nvbio::io::AlignmentData::read_type

Definition at line 53 of file output_priv.h.

Constructor & Destructor Documentation

nvbio::io::AlignmentData::AlignmentData ( )

inline

Definition at line 86 of file output_priv.h.

nvbio::io::AlignmentData::AlignmentData	(	const Alignment *	_aln,
		const uint32	_mapq,
		const uint32	_aln_id,
		const uint32	_read_id,
		const io::SequenceDataHost *	read_data_batch,
		const HostCigarArray *	cigar_array,
		const HostMdsArray *	mds_array
	)

inline

Definition at line 103 of file output_priv.h.

Member Function Documentation

static AlignmentData nvbio::io::AlignmentData::invalid ( void )

inlinestatic

Definition at line 138 of file output_priv.h.

Member Data Documentation

const Alignment* nvbio::io::AlignmentData::aln

the alignment itself

Definition at line 56 of file output_priv.h.

uint32 nvbio::io::AlignmentData::aln_id

the alignment index

Definition at line 57 of file output_priv.h.

const Cigar* nvbio::io::AlignmentData::cigar

CIGAR for this alignment.

Definition at line 80 of file output_priv.h.

const HostCigarArray* nvbio::io::AlignmentData::cigar_array_p

Definition at line 66 of file output_priv.h.

uint32 nvbio::io::AlignmentData::cigar_len

CIGAR length.

Definition at line 83 of file output_priv.h.

uint32 nvbio::io::AlignmentData::cigar_pos

the position of the cigar in the cigar array for this batch (should really not be here, only used to get the BNT)

Definition at line 81 of file output_priv.h.

uint32 nvbio::io::AlignmentData::mapq

the mapping quality score

Definition at line 59 of file output_priv.h.

const HostMdsArray* nvbio::io::AlignmentData::mds_array_p

Definition at line 67 of file output_priv.h.

const uint8* nvbio::io::AlignmentData::mds_vec

MDS vector.

Definition at line 84 of file output_priv.h.

const char* nvbio::io::AlignmentData::qual

quality data

Definition at line 78 of file output_priv.h.

read_type nvbio::io::AlignmentData::read_data

the iterator for the read data, acts as an array of uint8

Definition at line 77 of file output_priv.h.

const io::SequenceDataHost* nvbio::io::AlignmentData::read_data_batch_p

Definition at line 65 of file output_priv.h.

uint32 nvbio::io::AlignmentData::read_id

the read id of this alignment within the batch

Definition at line 58 of file output_priv.h.

uint32 nvbio::io::AlignmentData::read_len

length of the read

Definition at line 74 of file output_priv.h.

const char* nvbio::io::AlignmentData::read_name

read name

Definition at line 75 of file output_priv.h.

uint32 nvbio::io::AlignmentData::read_offset

the offset of the read from the start of read_data

Definition at line 73 of file output_priv.h.

bool nvbio::io::AlignmentData::valid

set to true if this is a valid alignment

Definition at line 55 of file output_priv.h.

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

E:/git/nvbio/nvbio/io/output/output_priv.h

Detailed description

Public Types

Public Methods

Static Public Methods

Public Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation