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bwtaln.h
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bwtaln.h
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#ifndef BWTALN_H
#define BWTALN_H
#include <stdint.h>
#include "bwt.h"
#include "hash.h"
#define BWA_TYPE_NO_MATCH 0
#define BWA_TYPE_UNIQUE 1
#define BWA_TYPE_REPEAT 2
#define BWA_TYPE_MATESW 3
#define SAM_FPD 1 // paired
#define SAM_FPP 2 // properly paired
#define SAM_FSU 4 // self-unmapped
#define SAM_FMU 8 // mate-unmapped
#define SAM_FSR 16 // self on the reverse strand
#define SAM_FMR 32 // mate on the reverse strand
#define SAM_FR1 64 // this is read one
#define SAM_FR2 128 // this is read two
#define SAM_FSC 256 // secondary alignment
#define BWA_AVG_ERR 0.02
#define BWA_MIN_RDLEN 35 // for read trimming
#define BWA_MAX_BCLEN 63 // maximum barcode length; 127 is the maximum
#ifndef bns_pac
#define bns_pac(pac, k) ((pac)[(k)>>2] >> ((~(k)&3)<<1) & 3)
#endif
#define FROM_M 0
#define FROM_I 1
#define FROM_D 2
#define FROM_S 3
#define SAI_MAGIC "SAI\1"
typedef struct {
bwtint_t w;
int bid;
} bwt_width_t;
typedef struct {
uint64_t n_mm:8, n_gapo:8, n_gape:8, score:20, n_ins:10, n_del:10;
bwtint_t k, l;
} bwt_aln1_t;
typedef uint16_t bwa_cigar_t;
/* rgoya: If changing order of bytes, beware of operations like:
* s->cigar[0] += s->full_len - s->len;
*/
#define CIGAR_OP_SHIFT 14
#define CIGAR_LN_MASK 0x3fff
#define __cigar_op(__cigar) ((__cigar)>>CIGAR_OP_SHIFT)
#define __cigar_len(__cigar) ((__cigar)&CIGAR_LN_MASK)
#define __cigar_create(__op, __len) ((__op)<<CIGAR_OP_SHIFT | (__len))
typedef struct {
uint32_t n_cigar:15, gap:8, mm:8, strand:1;
int ref_shift;
bwtint_t pos;
bwa_cigar_t *cigar;
} bwt_multi1_t;
typedef struct {
char *name;
ubyte_t *seq, *rseq, *qual;
uint32_t len:20, strand:1, type:2, dummy:1, extra_flag:8;
uint32_t n_mm:8, n_gapo:8, n_gape:8, mapQ:8;
int score;
int clip_len;
// alignments in SA coordinates
int n_aln;
bwtint_t index;
bwt_aln1_t *aln;
// multiple hits
int n_multi;
bwt_multi1_t *multi;
// alignment information
bwtint_t sa, pos;
uint64_t c1:28, c2:28, seQ:8; // number of top1 and top2 hits; single-end mapQ
int ref_shift;
int n_cigar;
bwa_cigar_t *cigar;
// for multi-threading only
int tid;
// barcode
char bc[BWA_MAX_BCLEN + 1]; // null terminated; up to BWA_MAX_BCLEN bases
// NM and MD tags
uint32_t full_len:20, nm:12;
char *md;
uint64_t read_num; // number of the read seq in the given fastq file
} bwa_seq_t;
#define BWA_MODE_GAPE 0x01
#define BWA_MODE_COMPREAD 0x02
#define BWA_MODE_LOGGAP 0x04
#define BWA_MODE_CFY 0x08
#define BWA_MODE_NONSTOP 0x10
#define BWA_MODE_BAM 0x20
#define BWA_MODE_BAM_SE 0x40
#define BWA_MODE_BAM_READ1 0x80
#define BWA_MODE_BAM_READ2 0x100
#define BWA_MODE_IL13 0x200
typedef struct {
int s_mm, s_gapo, s_gape;
int mode; // bit 24-31 are the barcode length
int indel_end_skip, max_del_occ, max_entries;
float fnr;
int max_diff, max_gapo, max_gape;
int max_seed_diff, seed_len;
int n_threads;
int max_top2;
int trim_qual;
} gap_opt_t;
#define BWA_PET_STD 1
typedef struct {
int max_isize, force_isize;
int max_occ;
int n_multi, N_multi;
int type, is_sw, is_preload;
double ap_prior;
} pe_opt_t;
struct __bwa_seqio_t;
typedef struct __bwa_seqio_t bwa_seqio_t;
bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
#ifdef __cplusplus
extern "C" {
#endif
gap_opt_t *gap_init_opt();
void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt);
bwa_seqio_t *bwa_seq_open(const char *fn);
bwa_seqio_t *bwa_bam_open(const char *fn, int which);
void bwa_seq_close(bwa_seqio_t *bs);
void seq_reverse(int len, ubyte_t *seq, int is_comp);
bwa_seq_t *bwa_read_seq(bwa_seqio_t *seq, int n_needed, int *n, int mode, int trim_qual);
bwa_seq_t *bwa_read_seq2(bwa_seqio_t *seq, int n_needed, int *n, int mode, int trim_qual, bwa_seq_t *seqs);
void bwa_free_read_seq(int n_seqs, bwa_seq_t *seqs);
int bwa_cal_maxdiff(int l, double err, double thres);
void bwa_cal_sa_reg_gap(int tid, bwt_t *const bwt, int n_seqs, bwa_seq_t *seqs, const gap_opt_t *opt);
void bwa_cal_sa_reg_gap2(int tid, bwt_t *const bwt, int n_seqs, bwa_seq_t *seqs, const gap_opt_t *opt);
void bwa_cs2nt_core(bwa_seq_t *p, bwtint_t l_pac, ubyte_t *pac);
#ifdef __cplusplus
}
#endif
#endif