BAM file handler

typedef RAZF *bamFile;  

BAM file handler

typedef BGZF *bamFile;  

BAM file handler

typedef RAZF *bamFile;  

Structure for the alignment header.

typedef struct { 
    int32_t n_targets; 
    char **target_name; 
    uint32_t *target_len; 
    void *hash, *rg2lib; 
    int l_text; 
    char *text; 
} bam_header_t;  

Fields

n_targets

number of reference sequences

target_name

names of the reference sequences

target_len

lengths of the referene sequences

hash

hash table for fast name lookup

rg2lib

hash table for @RG-ID -> LB lookup

l_text

length of the plain text in the header

text

plain text

Discussion

Field hash points to null by default. It is a private member.

Structure for core alignment information.

typedef struct { 
    int32_t tid; 
    int32_t pos; 
    uint32_t bin:16, qual:8, l_qname:8; 
    uint32_t flag:16, n_cigar:16; 
    int32_t l_qseq; 
    int32_t mtid; 
    int32_t mpos; 
    int32_t isize; 
} bam1_core_t;  

Fields

tid

chromosome ID, defined by bam_header_t

pos

0-based leftmost coordinate

strand

strand; 0 for forward and 1 otherwise

bin

bin calculated by bam_reg2bin()

qual

mapping quality

l_qname

length of the query name

flag

bitwise flag

n_cigar

number of CIGAR operations

l_qseq

length of the query sequence (read)

Structure for one alignment.

typedef struct { 
    bam1_core_t core; 
    int l_aux, data_len, m_data; 
    uint8_t *data; 
} bam1_t;  

Fields

core

core information about the alignment

l_aux

length of auxiliary data

data_len

current length of bam1_t::data

m_data

maximum length of bam1_t::data

data

all variable-length data, concatenated; structure: cigar-qname-seq-qual-aux

Discussion

Notes:

1. qname is zero tailing and core.l_qname includes the tailing '\0'.
2. l_qseq is calculated from the total length of an alignment block on reading or from CIGAR.

TAM file handler

typedef struct __tamFile_t *tamFile;  

Structure for one alignment covering the pileup position.

typedef struct { 
    bam1_t *b; 
    int32_t qpos; 
    int indel, level; 
    uint32_t is_del:1, is_head:1, is_tail:1; 
} bam_pileup1_t;  

Fields

b

pointer to the alignment

qpos

position of the read base at the pileup site, 0-based

indel

indel length; 0 for no indel, positive for ins and negative for del

is_del

1 iff the base on the padded read is a deletion

level

the level of the read in the "viewer" mode

Discussion

See also bam_plbuf_push() and bam_lplbuf_push(). The difference between the two functions is that the former does not set bam_pileup1_t::level, while the later does. Level helps the implementation of alignment viewers, but calculating this has some overhead.

pileup buffer

typedef struct __bam_plbuf_t bam_plbuf_t;  

Type of function to be called by bam_plbuf_push().

typedef int ( *bam_pileup_f)(
    uint32_t tid,
    uint32_t pos,
    int n,
    const bam_pileup1_t *pl,
    void *data);  

Parameters

tid

chromosome ID as is defined in the header

pos

start coordinate of the alignment, 0-based

n

number of elements in pl array

pl

array of alignments

data

user provided data

Discussion

See also bam_plbuf_push(), bam_plbuf_init() and bam_pileup1_t.

Type of function to be called by bam_fetch().

typedef int ( *bam_fetch_f)(
    const bam1_t *b,
    void *data);  

Parameters

b

the alignment

data

user provided data

© Genome Research Ltd. Last Updated: Saturday, June 13, 2009