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UL g-alignment-v1

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chhylp123
2022-03-26 18:51:46 -04:00
parent 95eb2de2b9
commit 75f8048b18
3 changed files with 70 additions and 15 deletions
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6
Process_Read.cpp
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@@ -1007,7 +1007,7 @@ void append_ul_t(all_ul_t *x, uint64_t *rid, char* id, int64_t id_l, char* str,
if(ovlp < 0) {///push original bases
kv_pushp(uc_block_t, p->bb, &b);
b->hid = 0/**x->mm**/; b->rev = 0; b->base = 1; b->pchain = 0;
b->hid = 0/**x->mm**/; b->rev = 0; b->base = 1; b->pchain = 0; b->el = 0;
b->qe = maxs; b->qs = b->qe + ovlp; bl += (b->qe-b->qs);
o_l = (b->qs >= UL_FLANK?UL_FLANK:b->qs);
o_r = ((str_l-b->qe)>=UL_FLANK?UL_FLANK:(str_l-b->qe));
@@ -1020,7 +1020,7 @@ void append_ul_t(all_ul_t *x, uint64_t *rid, char* id, int64_t id_l, char* str,
///push ovlp bases
kv_pushp(uc_block_t, p->bb, &b);
b->hid = (z->tn<<1)>>1; b->rev = z->rev; b->base = 0;
b->hid = (z->tn<<1)>>1; b->rev = z->rev; b->base = 0; b->el = 1;
b->pchain = ((z->tn&((uint32_t)(0x80000000)))?1:0);
b->qs = z->qs; b->qe = z->qe;
b->ts = z->ts; b->te = z->te;
@@ -1031,7 +1031,7 @@ void append_ul_t(all_ul_t *x, uint64_t *rid, char* id, int64_t id_l, char* str,
if(st > 0) {///push original bases
kv_pushp(uc_block_t, p->bb, &b);
b->hid = 0/**x->mm**/; b->rev = 0; b->base = 1; b->pchain = 0;
b->hid = 0/**x->mm**/; b->rev = 0; b->base = 1; b->pchain = 0; b->el = 0;
b->qe = st; b->qs = 0; bl += (b->qe-b->qs);
o_l = (b->qs >= UL_FLANK?UL_FLANK:b->qs);
o_r = ((str_l-b->qe)>=UL_FLANK?UL_FLANK:(str_l-b->qe));