bam_io.h File Reference

#include <htslib/sam.h>
#include <htslib/hts.h>
#include <htslib/bgzf.h>
#include "assembly_types.h"

Go to the source code of this file.

Classes
struct	BAM_header
struct	BAM_alignment_header
struct	BAM_alignment_record
struct	BAM_alignment_batch_raw
struct	BAM_CRQ_index
struct	BAM_NAUX_index
struct	BAM_alignment_batch_SoA
struct	HTSBAMReader
struct	HTSBAMWriter

Macros
#define	H_BATCH_SIZE_ALLOC   10000000U
#define	ALNREC_SIZE_ALLOC   512

Typedefs
typedef nvbio::vector < device_tag, BAM_CRQ_index >	D_VectorCRQIndex
typedef nvbio::vector < host_tag, BAM_CRQ_index >	H_VectorCRQIndex

Enumerations
enum	BAM_field_masks {   BAM_NAMES = 1, BAM_CIGARS = 2, BAM_READS = 4, BAM_QUALITIES = 8,   BAM_FLAGS = 16, BAM_POSITIONS = 32, BAM_REFIDS = 64, BAM_MAPQ = 128,   BAM_AUX = 256, BAM_BIN = 512, BAM_ALL = 0xFFFF }
enum	BAM_alignment_flags {   BAM_FLAGS_PAIRED = 1, BAM_FLAGS_PROPER_PAIR = 2, BAM_FLAGS_UNMAPPED = 4, BAM_FLAGS_MATE_UNMAPPED = 8,   BAM_FLAGS_REVERSE = 16, BAM_FLAGS_MATE_REVERSE = 32, BAM_FLAGS_READ_1 = 64, BAM_FLAGS_READ_2 = 128,   BAM_FLAGS_SECONDARY = 256, BAM_FLAGS_QC_FAILED = 512, BAM_FLAGS_DUPLICATE = 1024 }

Macro Definition Documentation

#define ALNREC_SIZE_ALLOC   512

Definition at line 145 of file bam_io.h.

#define H_BATCH_SIZE_ALLOC   10000000U

Definition at line 144 of file bam_io.h.

Typedef Documentation

typedef nvbio::vector<device_tag, BAM_CRQ_index> D_VectorCRQIndex

Definition at line 147 of file bam_io.h.

typedef nvbio::vector<host_tag, BAM_CRQ_index> H_VectorCRQIndex

Definition at line 148 of file bam_io.h.

Enumeration Type Documentation

enum BAM_alignment_flags

Enumerator
BAM_FLAGS_PAIRED
BAM_FLAGS_PROPER_PAIR
BAM_FLAGS_UNMAPPED
BAM_FLAGS_MATE_UNMAPPED
BAM_FLAGS_REVERSE
BAM_FLAGS_MATE_REVERSE
BAM_FLAGS_READ_1
BAM_FLAGS_READ_2
BAM_FLAGS_SECONDARY
BAM_FLAGS_QC_FAILED
BAM_FLAGS_DUPLICATE

Definition at line 102 of file bam_io.h.

enum BAM_field_masks

Enumerator
BAM_NAMES
BAM_CIGARS
BAM_READS
BAM_QUALITIES
BAM_FLAGS
BAM_POSITIONS
BAM_REFIDS
BAM_MAPQ
BAM_AUX
BAM_BIN
BAM_ALL

Definition at line 87 of file bam_io.h.