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backup; NOT working yet

This commit is contained in:
Heng Li 2017-06-23 19:21:47 -04:00
parent 4fea3d778a
commit d75b5b4e8a
2 changed files with 34 additions and 13 deletions
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46
align.c
View File

@ -31,18 +31,25 @@ static inline void mm_seq_rev(uint32_t len, uint8_t *seq)
static void mm_append_cigar(mm_reg1_t *r, uint32_t n_cigar, uint32_t *cigar) // TODO: this calls the libc realloc()
{
if (n_cigar == 0) return;
if (r->cigar == 0) {
uint32_t m_cigar = n_cigar + 2;
kroundup32(m_cigar);
r->cigar = (mm_cigar_t*)malloc(m_cigar * 4);
r->cigar->n = 0, r->cigar->m = m_cigar;
} else if (r->cigar->n + n_cigar > r->cigar->m - 2) {
r->cigar->m = r->cigar->n + n_cigar + 2;
kroundup32(r->cigar->m);
r->cigar->m = r->cigar->n + n_cigar;
r->cigar = (mm_cigar_t*)realloc(r->cigar, r->cigar->m * 4);
}
memcpy(r->cigar->cigar + r->cigar->n, cigar, n_cigar * 4);
r->cigar->n += n_cigar;
if (r->cigar->n > 0 && (r->cigar->cigar[r->cigar->n-1]&0xf) == (cigar[0]&0xf)) { // same CIGAR op at the boundary
r->cigar->cigar[r->cigar->n-1] += cigar[0]>>4<<4;
if (n_cigar > 1) memcpy(r->cigar->cigar + r->cigar->n, cigar + 1, (n_cigar - 1) * 4);
r->cigar->n += n_cigar - 1;
} else {
memcpy(r->cigar->cigar + r->cigar->n, cigar, n_cigar * 4);
r->cigar->n += n_cigar;
}
}
static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, uint8_t *qseq0[2], mm_reg1_t *r, mm_reg1_t *r2, mm128_t *a, ksw_extz_t *ez)
@ -50,7 +57,8 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
int32_t rid = a[r->as].x<<1>>33, rev = a[r->as].x>>63;
uint8_t *tseq, *qseq;
int32_t i, k, l, rs0, re0, qs0, qe0;
int32_t rs, re, qs, qe, ret;
int32_t rs, re, qs, qe;
int32_t rs1, qs1;
int8_t mat[25];
ksw_gen_simple_mat(5, mat, opt->a, opt->b);
@ -83,34 +91,46 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
if (qs > 0 && rs > 0) { // left extension
uint32_t ql = qs - qs0, tl = rs - rs0;
qseq = &qseq0[rev][qs0];
ret = mm_idx_getseq(mi, rid, rs0, rs, tseq);
assert(ret > 0);
mm_idx_getseq(mi, rid, rs0, rs, tseq);
mm_seq_rev(ql, qseq);
mm_seq_rev(tl, tseq);
#if 0
fprintf(stderr, "===> [-1] %d-%d %c (%s:%d-%d) <===\n", qs0, qs, "+-"[rev], mi->seq[rid].name, rs0, rs);
for (k = 0; k < tl; ++k) fputc("ACGTN"[tseq[k]], stderr); fputc('\n', stderr);
for (k = 0; k < ql; ++k) fputc("ACGTN"[qseq[k]], stderr); fputc('\n', stderr);
#endif
ksw_extz2_sse(km, ql, qseq, tl, tseq, 5, mat, opt->q, opt->e, (int)(opt->bw * 1.5 + .499), opt->zdrop, KSW_EZ_EXTZ_ONLY|KSW_EZ_RIGHT|KSW_EZ_REV_CIGAR, ez);
mm_seq_rev(ql, qseq);
mm_append_cigar(r, ez->n_cigar, ez->cigar);
}
for (i = 0; i < r->cigar->n; ++i) fprintf(stderr, "%d%c", r->cigar->cigar[i]>>4, "MID"[r->cigar->cigar[i]&0xf]); fputc('\n', stderr);
/*
for (i = 1; i < r->cnt; ++i) {
rs1 = rs - (ez->max_t + 1);
qs1 = qs - (ez->max_q + 1);
} else rs1 = rs, qs1 = qs;
fprintf(stderr, "%d,%d\n", rs1, qs1); for (i = 0; i < r->cigar->n; ++i) fprintf(stderr, "%d%c", r->cigar->cigar[i]>>4, "MID"[r->cigar->cigar[i]&0xf]); fputc('\n', stderr);
for (i = 1; i < r->cnt; ++i) { // gap filling
re = (int32_t)a[r->as + i].x + 1;
qe = (int32_t)a[r->as + i].y + 1;
if (i == r->cnt - 1 || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
qseq = &qseq0[rev][qs];
tseq = &tseq0[rs - rs0];
#if 0
mm_idx_getseq(mi, rid, rs, re, tseq);
#if 1
fprintf(stderr, "===> [%d] %d-%d %c (%s:%d-%d) <===\n", i, qs, qe, "+-"[rev], mi->seq[rid].name, rs, re);
for (k = 0; k < re - rs; ++k) fputc("ACGTN"[tseq[k]], stderr); fputc('\n', stderr);
for (k = 0; k < qe - qs; ++k) fputc("ACGTN"[qseq[k]], stderr); fputc('\n', stderr);
#endif
ksw_extz2_sse(km, qe-qs, qseq, re-rs, tseq, 5, mat, opt->q, opt->e, (int)(opt->bw * 1.5 + .499), opt->zdrop, KSW_EZ_DYN_BAND, ez);
if (ez->score == KSW_NEG_INF) { // truncated by Z-drop
} else {
mm_append_cigar(r, ez->n_cigar, ez->cigar);
}
for (i = 0; i < r->cigar->n; ++i) fprintf(stderr, "%d%c", r->cigar->cigar[i]>>4, "MID"[r->cigar->cigar[i]&0xf]); fputc('\n', stderr);
rs = re, qs = qe;
}
}
*/
if (i == r->cnt) {
}
// fprintf(stderr, "%d,%d\n", rs1, qs1); for (i = 0; i < r->cigar->n; ++i) fprintf(stderr, "%d%c", r->cigar->cigar[i]>>4, "MID"[r->cigar->cigar[i]&0xf]); fputc('\n', stderr);
kfree(km, tseq);
}

1
map.c
View File

@ -385,6 +385,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
r->re - r->rs > r->qe - r->qs? r->re - r->rs : r->qe - r->qs, r->cnt);
if (r->parent == j) printf("\tss:i:%d", r->subsc);
putchar('\n');
free(r->cigar);
}
free(s->reg[i]);
free(s->seq[i].seq); free(s->seq[i].name);