NVBIO
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
Classes | Macros | Typedefs | Enumerations
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

Definition at line 147 of file bam_io.h.

Definition at line 148 of file bam_io.h.

Enumeration Type Documentation

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.

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.