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bug fix for bubble scanning

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chhylp123
2021-04-23 20:40:43 -04:00
parent a5b29b00bd
commit 7b07e355b7
8 changed files with 183 additions and 97 deletions
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Purge_Dups.cpp
+7 -3
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@@ -5156,7 +5156,7 @@ void collect_purge_trans_cov(ma_ug_t *ug, hap_overlaps_list* ha, hap_cov_t *cov,
void purge_dups(ma_ug_t *ug, asg_t *read_g, ma_sub_t* coverage_cut, ma_hit_t_alloc* sources,
ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, kvec_asg_arc_t_warp* edge, float density,
uint32_t purege_minLen, int max_hang, int min_ovlp, float drop_ratio, uint32_t just_contain,
uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans)
uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans, uint32_t collect_p_trans_f)
{
p_g_t *pg = NULL;
asg_t* nsg = ug->g;
@@ -5235,16 +5235,20 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans)
normalize_hap_overlaps_advance(&all_ovlp, &back_all_ovlp, ug, read_g, reverse_sources, ruIndex);
if(collect_p_trans && collect_p_trans_f == 0)
{
collect_purge_trans_cov(ug, &all_ovlp, cov, position_index);
}
if(asm_opt.polyploidy <= 2)
{
mc_solve(&all_ovlp, cov->t_ch, NULL, ug, read_g, 0.8, R_INF.trio_flag, 1, NULL, 1, NULL, NULL);
///pt_solve(&all_ovlp, cov->t_ch, ug, read_g, 0.8, R_INF.trio_flag);
}
if(collect_p_trans)
if(collect_p_trans && collect_p_trans_f == 1)
{
collect_purge_trans_cov(ug, &all_ovlp, cov, position_index);
///goto end_coverage;
}
pg = init_p_g_t(ug, cov, read_g);