xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-03 15:48:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

haplotype popping

Browse Source
This commit is contained in:
chhylp123
2021-05-24 19:43:50 -04:00
parent 9e6dde7fb2
commit a39f01f4d8
9 changed files with 1696 additions and 567 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Purge_Dups.cpp
+16 -14
View File
@@ -9,6 +9,7 @@
#include "kdq.h"
#include "hic.h"
#include "rcut.h"
#include "tovlp.h"
KDQ_INIT(uint64_t)
KSORT_INIT_GENERIC(uint64_t)
@@ -1689,15 +1690,16 @@ uint32_t v_in_pos, uint32_t w_in_pos, uint32_t xUnitigLen, uint32_t yUnitigLen,
return tmp;
}
void chain_trans_ovlp(hap_cov_t *cov, ma_ug_t *ug, asg_t *read_sg, buf_t* xReads, uint32_t targetBaseLen, uint32_t* xEnd)
void chain_trans_ovlp(hap_cov_t *cover, utg_trans_t *o, ma_ug_t *ug, asg_t *read_sg, buf_t* xReads, uint32_t targetBaseLen, uint32_t* xEnd)
{
ma_hit_t_alloc* reverse_sources = cov->reverse_sources;
ma_sub_t *coverage_cut = cov->coverage_cut;
int max_hang = cov->max_hang;
int min_ovlp = cov->min_ovlp;
kvec_asg_arc_t_offset* u_buffer = &(cov->u_buffer);
kvec_t_i32_warp* tailIndex = &(cov->tailIndex);
kvec_t_i32_warp* prevIndex = &(cov->prevIndex);
ma_hit_t_alloc* reverse_sources = (o? o->reverse_sources:cover->reverse_sources);
ma_sub_t *coverage_cut = (o? o->coverage_cut:cover->coverage_cut);
int max_hang = (o? o->max_hang:cover->max_hang);
int min_ovlp = (o? o->min_ovlp:cover->min_ovlp);
kvec_asg_arc_t_offset* u_buffer = (o? &(o->u_buffer):&(cover->u_buffer));
kvec_t_i32_warp* tailIndex = (o? &(o->tailIndex):&(cover->tailIndex));
kvec_t_i32_warp* prevIndex = (o? &(o->prevIndex):&(cover->prevIndex));
uint64_t *pos_idx = (o? o->pos_idx:cover->pos_idx);
ma_hit_t_alloc *xR = NULL;
ma_hit_t *h = NULL;
ma_sub_t *sq = NULL, *st = NULL;
@@ -1804,11 +1806,11 @@ void chain_trans_ovlp(hap_cov_t *cov, ma_ug_t *ug, asg_t *read_sg, buf_t* xReads
rId = t.v>>1;
if(read_sg->seq[rId].del == 1) continue;
if(cov->pos_idx[rId] == (uint64_t)-1) continue;
w = (uint32_t)(cov->pos_idx[rId]);
if(pos_idx[rId] == (uint64_t)-1) continue;
w = (uint32_t)(pos_idx[rId]);
if(rId != (w>>1)) continue;
tmp = get_xy_pos_by_pos(read_sg, &t, v, w, len, cov->pos_idx[w>>1]>>32,
tmp = get_xy_pos_by_pos(read_sg, &t, v, w, len, pos_idx[w>>1]>>32,
(uint32_t)-1, targetBaseLen, &(t.el));
if(((tmp>>32) == (uint32_t)-1) || (((uint32_t)tmp) == (uint32_t)-1)) continue;
if(t.el) continue; ///must
@@ -1905,11 +1907,11 @@ void chain_trans_ovlp(hap_cov_t *cov, ma_ug_t *ug, asg_t *read_sg, buf_t* xReads
rId = t.v>>1;
if(read_sg->seq[rId].del == 1) continue;
if(cov->pos_idx[rId] == (uint64_t)-1) continue;
w = (uint32_t)(cov->pos_idx[rId]);
if(pos_idx[rId] == (uint64_t)-1) continue;
w = (uint32_t)(pos_idx[rId]);
if(rId != (w>>1)) continue;
tmp = get_xy_pos_by_pos(read_sg, &t, v, w, len, cov->pos_idx[w>>1]>>32,
tmp = get_xy_pos_by_pos(read_sg, &t, v, w, len, pos_idx[w>>1]>>32,
(uint32_t)-1, targetBaseLen, &(t.el));
if(((tmp>>32) == (uint32_t)-1) || (((uint32_t)tmp) == (uint32_t)-1)) continue;
if(t.el) continue; ///must