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#include <limits.h>
#include "bwa.h"
#include "bwamem.h"
#include "bntseq.h"
#include "kstring.h"
/***************************
* SMEM iterator interface *
***************************/
struct __smem_i {
const bwt_t *bwt;
const uint8_t *query;
int start, len;
int min_intv, max_len;
uint64_t max_intv;
bwtintv_v *matches; // matches; to be returned by smem_next()
bwtintv_v *sub; // sub-matches inside the longest match; temporary
bwtintv_v *tmpvec[2]; // temporary arrays
};
smem_i *smem_itr_init(const bwt_t *bwt)
{
smem_i *itr;
itr = calloc(1, sizeof(smem_i));
itr->bwt = bwt;
itr->tmpvec[0] = calloc(1, sizeof(bwtintv_v));
itr->tmpvec[1] = calloc(1, sizeof(bwtintv_v));
itr->matches = calloc(1, sizeof(bwtintv_v));
itr->sub = calloc(1, sizeof(bwtintv_v));
itr->min_intv = 1;
itr->max_len = INT_MAX;
itr->max_intv = 0;
return itr;
}
void smem_itr_destroy(smem_i *itr)
{
free(itr->tmpvec[0]->a); free(itr->tmpvec[0]);
free(itr->tmpvec[1]->a); free(itr->tmpvec[1]);
free(itr->matches->a); free(itr->matches);
free(itr->sub->a); free(itr->sub);
free(itr);
}
void smem_set_query(smem_i *itr, int len, const uint8_t *query)
{
itr->query = query;
itr->start = 0;
itr->len = len;
}
void smem_config(smem_i *itr, int min_intv, int max_len, uint64_t max_intv)
{
itr->min_intv = min_intv;
itr->max_len = max_len;
itr->max_intv = max_intv;
}
const bwtintv_v *smem_next(smem_i *itr)
{
int ori_start;
itr->tmpvec[0]->n = itr->tmpvec[1]->n = itr->matches->n = itr->sub->n = 0;
if (itr->start >= itr->len || itr->start < 0) return 0;
while (itr->start < itr->len && itr->query[itr->start] > 3) ++itr->start; // skip ambiguous bases
if (itr->start == itr->len) return 0;
ori_start = itr->start;
itr->start = bwt_smem1a(itr->bwt, itr->len, itr->query, ori_start, itr->min_intv, itr->max_intv, itr->matches, itr->tmpvec); // search for SMEM
return itr->matches;
}
/***********************
*** Extra functions ***
***********************/
mem_alnreg_v mem_align1(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int l_seq, const char *seq_)
{ // the difference from mem_align1_core() is that this routine: 1) calls mem_mark_primary_se(); 2) does not modify the input sequence
extern mem_alnreg_v mem_align1_core(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int l_seq, char *seq, void *buf);
extern void mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a, int64_t id);
mem_alnreg_v ar;
char *seq;
seq = malloc(l_seq);
memcpy(seq, seq_, l_seq); // makes a copy of seq_
ar = mem_align1_core(opt, bwt, bns, pac, l_seq, seq, 0);
mem_mark_primary_se(opt, ar.n, ar.a, lrand48());
free(seq);
return ar;
}
static inline int get_pri_idx(double XA_drop_ratio, const mem_alnreg_t *a, int i)
{
int k = a[i].secondary_all;
if (k >= 0 && a[i].score >= a[k].score * XA_drop_ratio) return k;
return -1;
}
// Okay, returning strings is bad, but this has happened a lot elsewhere. If I have time, I need serious code cleanup.
char **mem_gen_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_alnreg_v *a, int l_query, const char *query) // ONLY work after mem_mark_primary_se()
{
int i, k, r, *cnt, tot;
kstring_t *aln = 0, str = {0,0,0};
char **XA = 0, *has_alt;
cnt = calloc(a->n, sizeof(int));
has_alt = calloc(a->n, 1);
for (i = 0, tot = 0; i < a->n; ++i) {
r = get_pri_idx(opt->XA_drop_ratio, a->a, i);
if (r >= 0) {
++cnt[r], ++tot;
if (a->a[i].is_alt) has_alt[r] = 1;
}
}
if (tot == 0) goto end_gen_alt;
aln = calloc(a->n, sizeof(kstring_t));
for (i = 0; i < a->n; ++i) {
mem_aln_t t;
if ((r = get_pri_idx(opt->XA_drop_ratio, a->a, i)) < 0) continue;
if (cnt[r] > opt->max_XA_hits_alt || (!has_alt[r] && cnt[r] > opt->max_XA_hits)) continue;
t = mem_reg2aln(opt, bns, pac, l_query, query, &a->a[i]);
str.l = 0;
kputs(bns->anns[t.rid].name, &str);
kputc(',', &str); kputc("+-"[t.is_rev], &str); kputl(t.pos + 1, &str);
kputc(',', &str);
for (k = 0; k < t.n_cigar; ++k) {
kputw(t.cigar[k]>>4, &str);
kputc("MIDSHN"[t.cigar[k]&0xf], &str);
}
kputc(',', &str); kputw(t.NM, &str);
kputc(';', &str);
free(t.cigar);
kputsn(str.s, str.l, &aln[r]);
}
XA = calloc(a->n, sizeof(char*));
for (k = 0; k < a->n; ++k)
XA[k] = aln[k].s;
end_gen_alt:
free(has_alt); free(cnt); free(aln); free(str.s);
return XA;
}
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