cram_samtools.h File Reference

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

Go to the source code of this file.

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)

Typedefs
typedef bam1_t	bam_seq_t

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))

Definition at line 53 of file cram_samtools.h.

#define bam_bin

(

b)

(b)->core.bin

Definition at line 46 of file cram_samtools.h.

#define bam_blk_size

(

b)

((b)->l_data)

Definition at line 35 of file cram_samtools.h.

#define bam_cigar

(

b)

bam_get_cigar((b))

Definition at line 52 of file cram_samtools.h.

#define bam_cigar_len

(

b)

(b)->core.n_cigar

Definition at line 44 of file cram_samtools.h.

#define bam_dup

(

b)

bam_copy1(bam_init1(), (b))

Definition at line 55 of file cram_samtools.h.

#define bam_flag

(

b)

(b)->core.flag

Definition at line 45 of file cram_samtools.h.

#define bam_free

(

b)

bam_destroy1((b))

Definition at line 57 of file cram_samtools.h.

#define bam_ins_size

(

b)

(b)->core.isize

Definition at line 42 of file cram_samtools.h.

#define bam_map_qual

(

b)

(b)->core.qual

Definition at line 47 of file cram_samtools.h.

#define bam_mate_pos

(

b)

(b)->core.mpos

Definition at line 40 of file cram_samtools.h.

#define bam_mate_ref

(

b)

(b)->core.mtid

Definition at line 41 of file cram_samtools.h.

#define bam_name

(

b)

bam_get_qname((b))

Definition at line 49 of file cram_samtools.h.

#define bam_name_len

(

b)

(b)->core.l_qname

Definition at line 48 of file cram_samtools.h.

#define bam_pos

(

b)

(b)->core.pos

Definition at line 39 of file cram_samtools.h.

#define bam_qual

(

b)

bam_get_qual((b))

Definition at line 50 of file cram_samtools.h.

#define bam_ref

(

b)

(b)->core.tid

Definition at line 38 of file cram_samtools.h.

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

Definition at line 59 of file cram_samtools.h.

#define bam_seq

(

b)

bam_get_seq((b))

Definition at line 51 of file cram_samtools.h.

#define bam_seq_len

(

b)

(b)->core.l_qseq

Definition at line 43 of file cram_samtools.h.

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

Definition at line 36 of file cram_samtools.h.

Typedef Documentation

typedef bam1_t bam_seq_t

Definition at line 75 of file cram_samtools.h.

Enumeration Type Documentation

enum cigar_op

Enumerator
BAM_CMATCH_
BAM_CINS_
BAM_CDEL_
BAM_CREF_SKIP_
BAM_CSOFT_CLIP_
BAM_CHARD_CLIP_
BAM_CPAD_
BAM_CBASE_MATCH
BAM_CBASE_MISMATCH

Definition at line 63 of file cram_samtools.h.

Function Documentation

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
	)

Definition at line 41 of file cram_samtools.c.

SAM_hdr* bam_header_to_cram

(

bam_hdr_t *

h)

Definition at line 142 of file cram_samtools.c.

bam_hdr_t* cram_header_to_bam

(

SAM_hdr *

h)

Definition at line 120 of file cram_samtools.c.