#include "htslib/sam.h"
#include "cram/sam_header.h"

Macros
#define	bam_blk_size(b) ((b)->l_data)

#define	bam_set_blk_size(b, v) ((b)->data_len = (v))

#define	bam_ref(b) (b)->core.tid

#define	bam_pos(b) (b)->core.pos

#define	bam_mate_pos(b) (b)->core.mpos

#define	bam_mate_ref(b) (b)->core.mtid

#define	bam_ins_size(b) (b)->core.isize

#define	bam_seq_len(b) (b)->core.l_qseq

#define	bam_cigar_len(b) (b)->core.n_cigar

#define	bam_flag(b) (b)->core.flag

#define	bam_bin(b) (b)->core.bin

#define	bam_map_qual(b) (b)->core.qual

#define	bam_name_len(b) (b)->core.l_qname

#define	bam_name(b) bam_get_qname((b))

#define	bam_qual(b) bam_get_qual((b))

#define	bam_seq(b) bam_get_seq((b))

#define	bam_cigar(b) bam_get_cigar((b))

#define	bam_aux(b) bam_get_aux((b))

#define	bam_dup(b) bam_copy1(bam_init1(), (b))

#define	bam_free(b) bam_destroy1((b))

#define	bam_reg2bin(beg, end) hts_reg2bin((beg),(end),14,5)

Enumerations
enum	cigar_op { BAM_CMATCH_ =BAM_CMATCH, BAM_CINS_ =BAM_CINS, BAM_CDEL_ =BAM_CDEL, BAM_CREF_SKIP_ =BAM_CREF_SKIP, BAM_CSOFT_CLIP_ =BAM_CSOFT_CLIP, BAM_CHARD_CLIP_ =BAM_CHARD_CLIP, BAM_CPAD_ =BAM_CPAD, BAM_CBASE_MATCH =BAM_CEQUAL, BAM_CBASE_MISMATCH =BAM_CDIFF }

Functions
bam_hdr_t *	cram_header_to_bam (SAM_hdr *h)

SAM_hdr *	bam_header_to_cram (bam_hdr_t *h)

int	bam_construct_seq (bam_seq_t *bp, size_t extra_len, const char qname, size_t qname_len, int flag, int rname, int pos, int end, int mapq, uint32_t ncigar, const uint32_t cigar, int mrnm, int mpos, int isize, int len, const char seq, const char *qual)

Macro Definition Documentation

#define bam_aux ( b ) bam_get_aux((b))

#define bam_bin ( b ) (b)->core.bin

#define bam_blk_size ( b ) ((b)->l_data)

#define bam_cigar ( b ) bam_get_cigar((b))

#define bam_cigar_len ( b ) (b)->core.n_cigar

#define bam_dup ( b ) bam_copy1(bam_init1(), (b))

#define bam_flag ( b ) (b)->core.flag

#define bam_free ( b ) bam_destroy1((b))

#define bam_ins_size ( b ) (b)->core.isize

#define bam_map_qual ( b ) (b)->core.qual

#define bam_mate_pos ( b ) (b)->core.mpos

#define bam_mate_ref ( b ) (b)->core.mtid

#define bam_name ( b ) bam_get_qname((b))

#define bam_name_len ( b ) (b)->core.l_qname

#define bam_pos ( b ) (b)->core.pos

#define bam_qual ( b ) bam_get_qual((b))

#define bam_ref ( b ) (b)->core.tid

#define bam_seq ( b ) bam_get_seq((b))

#define bam_seq_len ( b ) (b)->core.l_qseq

Typedef Documentation

SAM_hdr* bam_header_to_cram ( bam_hdr_t * h )

bam_hdr_t* cram_header_to_bam ( SAM_hdr * h )