sam.h

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/*  sam.h -- SAM and BAM file I/O and manipulation.

    Copyright (C) 2008, 2009, 2013-2014 Genome Research Ltd.
    Copyright (C) 2010, 2012, 2013 Broad Institute.

    Author: Heng Li <lh3@sanger.ac.uk>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.  */

#ifndef HTSLIB_SAM_H
#define HTSLIB_SAM_H

#include <stdint.h>
#include "hts.h"

/**********************
 *** SAM/BAM header ***
 **********************/

typedef struct {
    int32_t n_targets, ignore_sam_err;
    uint32_t l_text;
    uint32_t *target_len;
    int8_t *cigar_tab;
    char **target_name;
    char *text;
    void *sdict;
} bam_hdr_t;

/****************************
 *** CIGAR related macros ***
 ****************************/

#define BAM_CMATCH      0
#define BAM_CINS        1
#define BAM_CDEL        2
#define BAM_CREF_SKIP   3
#define BAM_CSOFT_CLIP  4
#define BAM_CHARD_CLIP  5
#define BAM_CPAD        6
#define BAM_CEQUAL      7
#define BAM_CDIFF       8
#define BAM_CBACK       9

#define BAM_CIGAR_STR   "MIDNSHP=XB"
#define BAM_CIGAR_SHIFT 4
#define BAM_CIGAR_MASK  0xf
#define BAM_CIGAR_TYPE  0x3C1A7

#define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)
#define bam_cigar_oplen(c) ((c)>>BAM_CIGAR_SHIFT)
#define bam_cigar_opchr(c) (BAM_CIGAR_STR[bam_cigar_op(c)])
#define bam_cigar_gen(l, o) ((l)<<BAM_CIGAR_SHIFT|(o))

/* bam_cigar_type returns a bit flag with:
 *   bit 1 set if the cigar operation consumes the query
 *   bit 2 set if the cigar operation consumes the reference
 *
 * For reference, the unobfuscated truth table for this function is:
 * BAM_CIGAR_TYPE  QUERY  REFERENCE
 * --------------------------------
 * BAM_CMATCH      1      1
 * BAM_CINS        1      0
 * BAM_CDEL        0      1
 * BAM_CREF_SKIP   0      1
 * BAM_CSOFT_CLIP  1      0
 * BAM_CHARD_CLIP  0      0
 * BAM_CPAD        0      0
 * BAM_CEQUAL      1      1
 * BAM_CDIFF       1      1
 * BAM_CBACK       0      0
 * --------------------------------
 */
#define bam_cigar_type(o) (BAM_CIGAR_TYPE>>((o)<<1)&3) // bit 1: consume query; bit 2: consume reference

#define BAM_FPAIRED        1

#define BAM_FPROPER_PAIR   2

#define BAM_FUNMAP         4

#define BAM_FMUNMAP        8

#define BAM_FREVERSE      16

#define BAM_FMREVERSE     32

#define BAM_FREAD1        64

#define BAM_FREAD2       128

#define BAM_FSECONDARY   256

#define BAM_FQCFAIL      512

#define BAM_FDUP        1024

#define BAM_FSUPPLEMENTARY 2048

/*************************
 *** Alignment records ***
 *************************/

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;

typedef struct {
    bam1_core_t core;
    int l_data, m_data;
    uint8_t *data;
#ifndef BAM_NO_ID
    uint64_t id;
#endif
} bam1_t;

#define bam_is_rev(b) (((b)->core.flag&BAM_FREVERSE) != 0)

#define bam_is_mrev(b) (((b)->core.flag&BAM_FMREVERSE) != 0)

#define bam_get_qname(b) ((char*)(b)->data)

#define bam_get_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname))

#define bam_get_seq(b)   ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname)

#define bam_get_qual(b)  ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1))

#define bam_get_aux(b)   ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1) + (b)->core.l_qseq)

#define bam_get_l_aux(b) ((b)->l_data - ((b)->core.n_cigar<<2) - (b)->core.l_qname - (b)->core.l_qseq - (((b)->core.l_qseq + 1)>>1))

#define bam_seqi(s, i) ((s)[(i)>>1] >> ((~(i)&1)<<2) & 0xf)

/**************************
 *** Exported functions ***
 **************************/

#ifdef __cplusplus
extern "C" {
#endif

    /***************
     *** BAM I/O ***
     ***************/

    bam_hdr_t *bam_hdr_init(void);
    bam_hdr_t *bam_hdr_read(BGZF *fp);
    int bam_hdr_write(BGZF *fp, const bam_hdr_t *h);
    void bam_hdr_destroy(bam_hdr_t *h);
    int bam_name2id(bam_hdr_t *h, const char *ref);
    bam_hdr_t* bam_hdr_dup(const bam_hdr_t *h0);

    bam1_t *bam_init1(void);
    void bam_destroy1(bam1_t *b);
    int bam_read1(BGZF *fp, bam1_t *b);
    int bam_write1(BGZF *fp, const bam1_t *b);
    bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc);
    bam1_t *bam_dup1(const bam1_t *bsrc);

    int bam_cigar2qlen(int n_cigar, const uint32_t *cigar);
    int bam_cigar2rlen(int n_cigar, const uint32_t *cigar);

    int32_t bam_endpos(const bam1_t *b);

    int   bam_str2flag(const char *str);    
    char *bam_flag2str(int flag);   
    /*************************
     *** BAM/CRAM indexing ***
     *************************/

    // These BAM iterator functions work only on BAM files.  To work with either
    // BAM or CRAM files use the sam_index_load() & sam_itr_*() functions.
    #define bam_itr_destroy(iter) hts_itr_destroy(iter)
    #define bam_itr_queryi(idx, tid, beg, end) sam_itr_queryi(idx, tid, beg, end)
    #define bam_itr_querys(idx, hdr, region) sam_itr_querys(idx, hdr, region)
    #define bam_itr_next(htsfp, itr, r) hts_itr_next((htsfp)->fp.bgzf, (itr), (r), 0)

    // Load .csi or .bai BAM index file.
    #define bam_index_load(fn) hts_idx_load((fn), HTS_FMT_BAI)

    int bam_index_build(const char *fn, int min_shift);

    // Load BAM (.csi or .bai) or CRAM (.crai) index file.
    hts_idx_t *sam_index_load(htsFile *fp, const char *fn);

    #define sam_itr_destroy(iter) hts_itr_destroy(iter)
    hts_itr_t *sam_itr_queryi(const hts_idx_t *idx, int tid, int beg, int end);
    hts_itr_t *sam_itr_querys(const hts_idx_t *idx, bam_hdr_t *hdr, const char *region);
    #define sam_itr_next(htsfp, itr, r) hts_itr_next((htsfp)->fp.bgzf, (itr), (r), (htsfp))

    /***************
     *** SAM I/O ***
     ***************/

    #define sam_open(fn, mode) (hts_open((fn), (mode)))
    #define sam_close(fp) hts_close(fp)

    int sam_open_mode(char *mode, const char *fn, const char *format);

    typedef htsFile samFile;
    bam_hdr_t *sam_hdr_parse(int l_text, const char *text);
    bam_hdr_t *sam_hdr_read(samFile *fp);
    int sam_hdr_write(samFile *fp, const bam_hdr_t *h);

    int sam_parse1(kstring_t *s, bam_hdr_t *h, bam1_t *b);
    int sam_format1(const bam_hdr_t *h, const bam1_t *b, kstring_t *str);
    int sam_read1(samFile *fp, bam_hdr_t *h, bam1_t *b);
    int sam_write1(samFile *fp, const bam_hdr_t *h, const bam1_t *b);

    /*************************************
     *** Manipulating auxiliary fields ***
     *************************************/

    uint8_t *bam_aux_get(const bam1_t *b, const char tag[2]);
    int32_t bam_aux2i(const uint8_t *s);
    double bam_aux2f(const uint8_t *s);
    char bam_aux2A(const uint8_t *s);
    char *bam_aux2Z(const uint8_t *s);

    void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data);
    int bam_aux_del(bam1_t *b, uint8_t *s);

#ifdef __cplusplus
}
#endif

/**************************
 *** Pileup and Mpileup ***
 **************************/

#if !defined(BAM_NO_PILEUP)

typedef struct {
    bam1_t *b;
    int32_t qpos;
    int indel, level;
    uint32_t is_del:1, is_head:1, is_tail:1, is_refskip:1, aux:28;
} bam_pileup1_t;

typedef int (*bam_plp_auto_f)(void *data, bam1_t *b);

struct __bam_plp_t;
typedef struct __bam_plp_t *bam_plp_t;

struct __bam_mplp_t;
typedef struct __bam_mplp_t *bam_mplp_t;

#ifdef __cplusplus
extern "C" {
#endif

    bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data);
    void bam_plp_destroy(bam_plp_t iter);
    int bam_plp_push(bam_plp_t iter, const bam1_t *b);
    const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp);
    const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp);
    void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt);
    void bam_plp_reset(bam_plp_t iter);

    bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data);
    void bam_mplp_init_overlaps(bam_mplp_t iter);
    void bam_mplp_destroy(bam_mplp_t iter);
    void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt);
    int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);

#ifdef __cplusplus
}
#endif

#endif // ~!defined(BAM_NO_PILEUP)

#endif