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r93: fixed various small issues

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This commit is contained in:
Heng Li
2017-06-28 10:35:21 -04:00
parent cdc2a1e29f
commit bcd9b1c621
4 changed files with 64 additions and 23 deletions
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align.c
+41 -6
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@@ -30,6 +30,7 @@ static void mm_reg_split(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *
{
if (n <= 0 || n >= r->cnt) return;
*r2 = *r;
r2->id = -1;
r2->p = 0;
r2->cnt = r->cnt - n;
r2->score = (int32_t)(r->score * ((float)r2->cnt / r->cnt) + .499);
@@ -243,7 +244,11 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
r->p->score += ez->max;
re1 = rs + (ez->max_t + 1);
qe1 = qs + (ez->max_q + 1);
mm_reg_split(r, r2, j + 1, qlen, a);
if (r->cnt - (j + 1) >= opt->min_cnt) {
mm_reg_split(r, r2, j + 1, qlen, a);
if (j + 1 < opt->min_cnt)
r2->id = r->id, r->id = -1;
}
break;
} else { // FIXME: in rare cases, r->p can be NULL, which leads to a segfault
r->p->score += ez->score;
@@ -252,7 +257,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
}
}
if (r2->cnt == 0 && qe < qe0 && re < re0) { // right extension
if (i == r->cnt && qe < qe0 && re < re0) { // right extension
qseq = &qseq0[rev][qe];
mm_idx_getseq(mi, rid, re, re0, tseq);
ksw_extz2_sse(km, qe0 - qe, qseq, re0 - re, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, KSW_EZ_EXTZ_ONLY, ez);
@@ -276,11 +281,11 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int *n_regs_, mm_reg1_t *regs, mm128_t *a)
{
extern unsigned char seq_nt4_table[256];
int i, r, n_regs = *n_regs_;
int32_t i, r, n_regs = *n_regs_;
uint8_t *qseq0[2];
ksw_extz_t ez;
memset(&ez, 0, sizeof(ksw_extz_t));
// encode the query sequence
qseq0[0] = (uint8_t*)kmalloc(km, qlen);
qseq0[1] = (uint8_t*)kmalloc(km, qlen);
for (i = 0; i < qlen; ++i) {
@@ -288,6 +293,8 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
qseq0[1][qlen - 1 - i] = qseq0[0][i] < 4? 3 - qseq0[0][i] : 4;
}
// align through seed hits
memset(&ez, 0, sizeof(ksw_extz_t));
for (r = 0; r < n_regs; ++r) {
mm_reg1_t r2;
mm_align1(km, opt, mi, qlen, qseq0, &regs[r], &r2, a, &ez);
@@ -299,8 +306,36 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
++n_regs;
}
}
*n_regs_ = n_regs;
kfree(km, qseq0[0]); kfree(km, qseq0[1]);
kfree(km, ez.cigar);
kfree(km, qseq0[0]); kfree(km, qseq0[1]); kfree(km, ez.cigar);
// filter
for (r = i = 0; r < n_regs; ++r) {
mm_reg1_t *reg = &regs[r];
int flt = 0;
if (reg->p->blen - reg->p->n_ambi - reg->p->n_diff < opt->min_chain_score) flt = 1;
else if (reg->cnt < opt->min_cnt) flt = 1;
else if (reg->p->score < opt->min_dp_score) flt = 1;
if (flt) free(reg->p);
else if (i < r) regs[i++] = regs[r]; // NB: this also move the regs[r].p pointer
else ++i;
}
// remap mm_reg1_t::{id,parent}
if (i < n_regs || n_regs != *n_regs_) { // there are region splits or drops
int32_t *id;
n_regs = i;
id = (int32_t*)kmalloc(km, *n_regs_ * 4);
for (r = 0; r < *n_regs_; ++r) id[r] = -1;
for (r = 0; r < n_regs; ++r) {
if (regs[r].id >= 0) id[regs[r].id] = r;
regs[r].id = r;
}
for (r = 0; r < n_regs; ++r)
if (regs[r].parent >= 0)
regs[r].parent = id[regs[r].parent];
kfree(km, id);
}
*n_regs_ = n_regs;
return regs;
}