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update for r350

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chhylp123
2021-07-26 00:16:00 -04:00
parent b14f894160
commit 321acb2d8a
12 changed files with 241 additions and 130 deletions
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Purge_Dups.cpp
+4 -5
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@@ -5267,11 +5267,7 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans, uint32_t colle
hap_alignment_struct_pip hap_buf;
long long k_mer_only, coverage_only;
if(asm_opt.pur_global_coverage != -1)
{
hap_buf.cov_threshold = asm_opt.pur_global_coverage;
}
else if(asm_opt.hom_global_coverage != -1)
if(asm_opt.hom_global_coverage != -1)
{
hap_buf.cov_threshold = (asm_opt.hom_global_coverage_set?
(((double)asm_opt.hom_global_coverage)*((double)HOM_PEAK_RATE)):(asm_opt.hom_global_coverage));
@@ -5325,6 +5321,9 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans, uint32_t colle
}
}
if(asm_opt.hom_global_coverage == -1) asm_opt.hom_global_coverage = hap_buf.cov_threshold;
if(asm_opt.pur_global_coverage != -1) hap_buf.cov_threshold = asm_opt.pur_global_coverage;
fprintf(stderr, "[M::%s] homozygous read coverage threshold: %d\n", __func__, asm_opt.hom_global_coverage_set?
asm_opt.hom_global_coverage:(int)(((double)asm_opt.hom_global_coverage)/((double)HOM_PEAK_RATE)));
fprintf(stderr, "[M::%s] purge duplication coverage threshold: %lld\n", __func__, hap_buf.cov_threshold);
if(just_coverage) goto end_coverage;