the read is paired in sequencing, no matter whether it is mapped in a pair

#define BAM_FPAIRED 1 

the read is mapped in a proper pair

#define BAM_FPROPER_PAIR 2 

the read itself is unmapped; conflictive with BAM_FPROPER_PAIR

#define BAM_FUNMAP 4 

the mate is unmapped

#define BAM_FMUNMAP 8 

the read is mapped to the reverse strand

#define BAM_FREVERSE 16 

the mate is mapped to the reverse strand

#define BAM_FMREVERSE 32 

this is read1

#define BAM_FREAD1 64 

this is read2

#define BAM_FREAD2 128 

not primary alignment

#define BAM_FSECONDARY 256 

QC failure

#define BAM_FQCFAIL 512 

optical or PCR duplicate

#define BAM_FDUP 1024 

defautl mask for pileup

#define BAM_DEF_MASK  

CIGAR: match

#define BAM_CMATCH 0 

CIGAR: insertion to the reference

#define BAM_CINS 1 

CIGAR: deletion from the reference

#define BAM_CDEL 2 

CIGAR: skip on the reference (e.g. spliced alignment)

#define BAM_CREF_SKIP 3 

CIGAR: clip on the read with clipped sequence present in qseq

#define BAM_CSOFT_CLIP 4 

CIGAR: clip on the read with clipped sequence trimmed off

#define BAM_CHARD_CLIP 5 

CIGAR: padding

#define BAM_CPAD 6 

Get the CIGAR array

#define bam1_cigar(b)  

Parameters

b

pointer to an alignment

Return Value

pointer to the CIGAR array

Discussion

In the CIGAR array, each element is a 32-bit integer. The lower 4 bits gives a CIGAR operation and the higher 28 bits keep the length of a CIGAR.

Get the name of the query

#define bam1_qname(b)  

Parameters

b

pointer to an alignment

Return Value

pointer to the name string, null terminated

Get query sequence

#define bam1_seq(b)  

Parameters

b

pointer to an alignment

Return Value

pointer to sequence

Discussion

Each base is encoded in 4 bits: 1 for A, 2 for C, 4 for G, 8 for T and 15 for N. Two bases are packed in one byte with the base at the higher 4 bits having smaller coordinate on the read. It is recommended to use bam1_seqi() macro to get the base.

Get query quality

#define bam1_qual(b)  

Parameters

b

pointer to an alignment

Return Value

pointer to quality string

Get a base on read

#define bam1_seqi(s, i)  

Parameters

s

Query sequence returned by bam1_seq()

i

The i-th position, 0-based

Return Value

4-bit integer representing the base.

Get query sequence and quality

#define bam1_aux(b)  

Parameters

b

pointer to an alignment

Return Value

pointer to the concatenated auxiliary data

Round an integer to the next closest power-2 integer.

#define kroundup32(x)  

Parameters

x

integer to be rounded (in place)

Discussion

x will be modified.

Initiate a pointer to bam1_t struct

#define bam_init1()  

Free the memory allocated for an alignment.

#define bam_destroy1(b) do { \ 
    free((b)->data); free(b); \ 
    } while (0) 

Parameters

b

pointer to an alignment

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