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r212: better heuristic to fix wrong seeding

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but not good enough. Will explore more.
This commit is contained in:
Heng Li
2017-07-27 11:24:51 -04:00
parent 371e20cc7c
commit b927838495
3 changed files with 24 additions and 12 deletions
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align.c
+14 -10
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@@ -253,16 +253,20 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
for (i = 1; i < cnt1; ++i) { // gap filling
int gap, to_patch = 0;
mm_adjust_minier(mi, qseq0, &a[as1 + i], &re, &qe);
gap = (qe - qs) - (re - rs);
if (gap < -40 || gap > 40) {
int g, j, i_next = -1;
for (j = i + 1; j < cnt1; ++j) {
if ((int32_t)a[as1 + j].y - qs > opt->max_gap || (int32_t)a[as1 + j].x - rs > opt->max_gap) break;
g = ((int32_t)a[as1 + j].y - (int32_t)a[as1 + j - 1].y) - (a[as1 + j].x - a[as1 + j - 1].x);
if (abs(gap + g) < 0.5f * abs(gap - g)) {
i_next = j;
break;
}
gap = ((int32_t)a[as1 + i].y - (int32_t)a[as1 + i - 1].y) - (a[as1 + i].x - a[as1 + i - 1].x);
if (gap < -20 || gap > 20) {
int i_next = -1, j, n_ins = 0, n_del = 0, diff, max_diff = 0;
if (gap < 0) n_del += -gap;
else n_ins += gap;
for (j = i + 1; j < cnt1 && j - i < 20; ++j) {
if ((int32_t)a[as1 + j].y - qs > opt->max_gap>>1 || (int32_t)a[as1 + j].x - rs > opt->max_gap>>1) break;
gap = ((int32_t)a[as1 + j].y - (int32_t)a[as1 + j - 1].y) - (a[as1 + j].x - a[as1 + j - 1].x);
if (gap < 0) n_del += -gap;
else n_ins += gap;
diff = n_ins + n_del - abs(n_ins - n_del);
if (diff >= 40) {
if (diff >= max_diff) max_diff = diff, i_next = j;
} else if (i_next > i) break;
}
if (i_next > i) {
i = i_next, to_patch = 1;