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variant calling

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chhylp123
2021-04-10 21:58:53 -04:00
parent 3218618bb4
commit 8f733750c4
5 changed files with 789 additions and 115 deletions
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hic.cpp
+3 -3
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@@ -2616,7 +2616,7 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag)
if(ug->g->seq[v>>1].del) continue;
if(asg_arc_n(ug->g, v) < 2) continue;
if((bub->index[v]&(uint32_t)3) != 0) continue;
if(asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, NULL, NULL, NULL, 0))
if(asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, NULL, NULL, NULL, 0, 0))
{
//beg is v, end is b.S.a[0]
//note b.b include end, does not include beg
@@ -2637,7 +2637,7 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag)
for (v = 0; v < n_vtx; ++v)
{
if((bub->index[v]&(uint32_t)3) !=2) continue;
if(asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, &pathLen, NULL, NULL, 0))
if(asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, &pathLen, NULL, NULL, 0, 0))
{
//note b.b include end, does not include beg
i = b.b.n + 1;
@@ -2669,7 +2669,7 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag)
if((bub->num.a[k]>>31) == 0) bub->s_bub++;
v = (bub->num.a[k]<<1)>>1;
bub->num.a[k] = bub->list.n;
if(asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, &pathLen, NULL, NULL, 0))
if(asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, &pathLen, NULL, NULL, 0, 0))
{
kv_push(uint64_t, bub->pathLen, pathLen);
//beg is v, end is b.S.a[0]