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more accurate purging

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chhylp123
2021-03-26 18:07:30 -04:00
parent d89a630ff3
commit 24a19d7976
4 changed files with 446 additions and 138 deletions
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hic.cpp
+11 -10
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@@ -2678,17 +2678,17 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *het_flag)
for (i = 0; i < ug->g->n_seq; i++)
{
if((bub->index[i]>>2) == 0)
if((bub->index[i]>>2) == 0)
{
bub->index[i] = (uint32_t)-1;
bub->index[i] = (uint32_t)-1; ///hom
}
else
{
if((bub->index[i]>>2) == 1)
if((bub->index[i]>>2) == 1)
{
bub->index[i] = P_het(*bub); ///potential het
}
else
else
{
bub->index[i] = M_het(*bub); ///must het
}
@@ -2705,11 +2705,11 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *het_flag)
n_occ += ug->u.a[a[v]>>1].n;
}
if((pathLen*2) >= ug->g->seq[beg>>1].len && (pathLen*2) >= ug->g->seq[sink>>1].len)
{
bub->index[(beg>>1)] = (uint32_t)-1;
bub->index[(sink>>1)] = (uint32_t)-1;
}
// if((pathLen*2) >= ug->g->seq[beg>>1].len && (pathLen*2) >= ug->g->seq[sink>>1].len)
// {
// bub->index[(beg>>1)] = (uint32_t)-1;
// bub->index[(sink>>1)] = (uint32_t)-1;
// }
if(n_occ > 3)
{
@@ -2749,7 +2749,7 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *het_flag)
if(bub->index[i] == M_het(*bub)) bub->index[i] = P_het(*bub);
if(bub->index[i] > P_het(*bub))
{
if(het_flag && het_flag[i] == 1)
if(het_flag && het_flag[i])
{
bub->index[i] = P_het(*bub);
}
@@ -2769,6 +2769,7 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *het_flag)
}
bub->b_g = NULL;
bub->b_ug = NULL;
build_bub_graph(ug, bub);
}