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r249: make max overlap error rate CLI options

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Heng Li
2020-05-06 01:16:50 -04:00
parent 331e437c72
commit 3364a29b87
6 changed files with 56 additions and 49 deletions
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Overlaps.cpp
+3 -4
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@@ -1725,10 +1725,9 @@ ma_sub_t* coverage_cut, float shift_rate)
collect_contain(&(paf[i]), NULL, rLen, &max_left, &max_right, 0.1);
///collect_contain(&(paf[i]), &(rev_paf[i]), rLen, &max_left, &max_right, 0.1);
////shift_rate should be (FINAL_OVERLAP_ERROR_RATE*2)
////shift_rate should be (asm_opt.max_ov_diff_final*2)
///this read is a normal read
if(max_left.e > max_right.s &&
(max_left.e - max_right.s >= rLen * shift_rate))
if (max_left.e > max_right.s && (max_left.e - max_right.s >= rLen * shift_rate))
{
continue;
}
@@ -26062,7 +26061,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
///ma_hit_sub is just use to init coverage_cut,
///it seems we do not need ma_hit_cut & ma_hit_flt
ma_hit_sub(min_dp, sources, n_read, readLen, mini_overlap_length, &coverage_cut);
detect_chimeric_reads(sources, n_read, readLen, coverage_cut, FINAL_OVERLAP_ERROR_RATE*2);
detect_chimeric_reads(sources, n_read, readLen, coverage_cut, asm_opt.max_ov_diff_final * 2.0);
ma_hit_cut(sources, n_read, readLen, mini_overlap_length, &coverage_cut);
///print_binned_reads(sources, n_read, coverage_cut);
ma_hit_flt(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length);