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change max coverage of pri-range

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chhylp123
2020-07-18 17:40:58 -04:00
parent 88ab801717
commit 952471657f
5 changed files with 76 additions and 51 deletions
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Overlaps.cpp
+28 -8
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@@ -13503,14 +13503,25 @@ kvec_asg_arc_t_warp* new_rtg_edges)
purge_dups(*ug, read_g, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges,
asm_opt.purge_simi_rate, asm_opt.purge_overlap_len, max_hang, min_ovlp, bubble_dist,
drop_ratio, 1, 1);
if(asm_opt.recover_atg_cov_min == -1024 || asm_opt.recover_atg_cov_max == -1024)
if(asm_opt.recover_atg_cov_min == -1024)
{
asm_opt.recover_atg_cov_max = asm_opt.hom_global_coverage/HOM_PEAK_RATE;
asm_opt.recover_atg_cov_min = asm_opt.recover_atg_cov_max * 0.8;
asm_opt.recover_atg_cov_max = asm_opt.recover_atg_cov_max * 1.2;
///asm_opt.recover_atg_cov_max = asm_opt.recover_atg_cov_max * 1.2;
asm_opt.recover_atg_cov_max = INT32_MAX;
}
fprintf(stderr, "[M::%s] primary contig coverage range: [%d, %d]\n",
__func__, asm_opt.recover_atg_cov_min, asm_opt.recover_atg_cov_max);
if(asm_opt.recover_atg_cov_max != INT32_MAX)
{
fprintf(stderr, "[M::%s] primary contig coverage range: [%d, %d]\n",
__func__, asm_opt.recover_atg_cov_min, asm_opt.recover_atg_cov_max);
}
else
{
fprintf(stderr, "[M::%s] primary contig coverage range: [%d, infinity]\n",
__func__, asm_opt.recover_atg_cov_min);
}
///primary_flag = get_utg_attributes(*ug, read_g, coverage_cut, sources, ruIndex);
@@ -22643,15 +22654,24 @@ kvec_asg_arc_t_warp* new_rtg_edges)
}
}
if(asm_opt.recover_atg_cov_min == -1024 || asm_opt.recover_atg_cov_max == -1024)
if(asm_opt.recover_atg_cov_min == -1024)
{
asm_opt.recover_atg_cov_max = asm_opt.hom_global_coverage/HOM_PEAK_RATE;
asm_opt.recover_atg_cov_min = asm_opt.recover_atg_cov_max * 0.8;
asm_opt.recover_atg_cov_max = asm_opt.recover_atg_cov_max * 1.2;
///asm_opt.recover_atg_cov_max = asm_opt.recover_atg_cov_max * 1.2;
asm_opt.recover_atg_cov_max = INT32_MAX;
}
fprintf(stderr, "[M::%s] primary contig coverage range: [%d, %d]\n",
__func__, asm_opt.recover_atg_cov_min, asm_opt.recover_atg_cov_max);
if(asm_opt.recover_atg_cov_max != INT32_MAX)
{
fprintf(stderr, "[M::%s] primary contig coverage range: [%d, %d]\n",
__func__, asm_opt.recover_atg_cov_min, asm_opt.recover_atg_cov_max);
}
else
{
fprintf(stderr, "[M::%s] primary contig coverage range: [%d, infinity]\n",
__func__, asm_opt.recover_atg_cov_min);
}
recover_utg_by_coverage(ug, read_g, coverage_cut, sources, ruIndex);