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