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r763: fine control long join flank len (#128)

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Heng Li
2018-03-29 14:16:58 -04:00
parent 2d7ec75d50
commit ee4cd089f7
5 changed files with 10 additions and 4 deletions
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hit.c
+4 -3
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@@ -304,7 +304,7 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_r
for (i = n_aux - 1; i >= 1; --i) {
mm_reg1_t *r0 = &regs[(int32_t)aux[i-1]], *r1 = &regs[(int32_t)aux[i]];
mm128_t *a0e, *a1s;
int max_gap, min_gap, sc_thres;
int max_gap, min_gap, sc_thres, min_flank_len;
// test
if (r0->as + r0->cnt != r1->as) continue; // not adjacent in a[]
@@ -318,8 +318,9 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_r
if (max_gap > opt->max_join_long || min_gap > opt->max_join_short) continue;
sc_thres = (int)((float)opt->min_join_flank_sc / opt->max_join_long * max_gap + .499);
if (r0->score < sc_thres || r1->score < sc_thres) continue; // require good flanking chains
if (r0->re - r0->rs < max_gap>>1 || r0->qe - r0->qs < max_gap>>1) continue; // require enough flanking length
if (r1->re - r1->rs < max_gap>>1 || r1->qe - r1->qs < max_gap>>1) continue;
min_flank_len = (int)(max_gap * opt->min_join_flank_ratio);
if (r0->re - r0->rs < min_flank_len || r0->qe - r0->qs < min_flank_len) continue; // require enough flanking length
if (r1->re - r1->rs < min_flank_len || r1->qe - r1->qs < min_flank_len) continue;
// all conditions satisfied; join
a[r1->as].y |= MM_SEED_LONG_JOIN;