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nvbio::io::AlignmentData Struct Reference

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

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 Alignmentaln
 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::SequenceDataHostread_data_batch_p
const HostCigarArraycigar_array_p
const HostMdsArraymds_array_p
uint32 read_offset
 the offset of the read from the start of read_data More...
uint32 read_len
 length of the
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 Cigarcigar
 CIGAR for this alignment. More...
uint32 cigar_pos
uint32 cigar_len
 CIGAR length. More...
const uint8mds_vec
 MDS vector. More...

Member Typedef Documentation

Definition at line 52 of file output_priv.h.

Definition at line 51 of file output_priv.h.

Definition at line 53 of file output_priv.h.

Constructor & Destructor Documentation

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

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 

Definition at line 103 of file output_priv.h.

Member Function Documentation

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

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: