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update coverage

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chhylp123
2020-07-13 22:34:26 -04:00
parent c01b593d7c
commit fda858f9e7
8 changed files with 449 additions and 104 deletions
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Purge_Dups.cpp
+22 -15
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@@ -4136,9 +4136,9 @@ uint32_t minLen, double purge_threshold)
get_contig_length(ug, read_g, &primary_bases, &alter_bases);
total_bases = primary_bases + alter_bases;
fprintf(stderr, "primary_bases: %lu\n", primary_bases);
fprintf(stderr, "alter_bases: %lu\n", alter_bases);
fprintf(stderr, "total_bases: %lu\n", total_bases);
// fprintf(stderr, "primary_bases: %lu\n", primary_bases);
// fprintf(stderr, "alter_bases: %lu\n", alter_bases);
// fprintf(stderr, "total_bases: %lu\n", total_bases);
for (v = 0; v < all_ovlp->num; v++)
@@ -4149,9 +4149,9 @@ uint32_t minLen, double purge_threshold)
}
}
purge_bases = purge_bases/2;
fprintf(stderr, "purge_bases: %lu\n", purge_bases);
///fprintf(stderr, "purge_bases: %lu\n", purge_bases);
alter_bases = alter_bases + purge_bases;
fprintf(stderr, "new alter_bases: %lu\n", alter_bases);
///fprintf(stderr, "new alter_bases: %lu\n", alter_bases);
for (v = 0; v < all_ovlp->num; v++)
@@ -4172,7 +4172,7 @@ uint32_t minLen, double purge_threshold)
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, long long bubble_dist, float drop_ratio,
uint32_t just_contain)
uint32_t just_contain, uint32_t just_coverage)
{
asg_t *purge_g = NULL;
purge_g = asg_init();
@@ -4205,12 +4205,17 @@ uint32_t just_contain)
hap_alignment_struct_pip hap_buf;
long long k_mer_only, coverage_only;
hap_buf.cov_threshold = get_read_coverage_thres(ug, read_g, ruIndex, position_index,
sources, coverage_cut, read_g->n_seq, COV_COUNT, &k_mer_only, &coverage_only);
///fprintf(stderr, "cov_threshold: %lld\n", hap_buf.cov_threshold);
if(asm_opt.hom_global_coverage != -1)
{
hap_buf.cov_threshold = asm_opt.hom_global_coverage;
}
else
{
hap_buf.cov_threshold = get_read_coverage_thres(ug, read_g, ruIndex, position_index,
sources, coverage_cut, read_g->n_seq, COV_COUNT, &k_mer_only, &coverage_only);
}
for (v = 0; v < nsg->n_seq; v++)
{
uId = v;
@@ -4256,9 +4261,9 @@ uint32_t just_contain)
hap_buf.cov_threshold = k_mer_only * HOM_PEAK_RATE;
}
}
asm_opt.hom_global_coverage = hap_buf.cov_threshold;
fprintf(stderr, "cov_threshold: %lld\n", hap_buf.cov_threshold);
if(asm_opt.hom_global_coverage == -1) asm_opt.hom_global_coverage = hap_buf.cov_threshold;
fprintf(stderr, "[M::%s] purge duplication coverage threshold: %lld\n", __func__, hap_buf.cov_threshold);
if(just_coverage) goto end_coverage;
///kt_for(asm_opt.thread_num, hap_alignment_worker, &hap_buf, nsg->n_seq);
kt_for(asm_opt.thread_num, hap_alignment_advance_worker, &hap_buf, nsg->n_seq);
@@ -4367,6 +4372,8 @@ uint32_t just_contain)
}
}
end_coverage:
uint32_t is_Unitig;
for (v = 0; v < ruIndex->len; v++)
{