clintval / vartovcf / 39986979359

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github

feat: restore the LOW_HICNT filter for VarDict's -r (#163)

--filter-low-hicnt labels a call LOW_HICNT when its tumor (or only) sample has fewer high-quality ALT reads (FORMAT HICNT) than the threshold, the count VarDict's own -r tests. #134 dropped it because tumor-normal rows had no HICNT; #142 recovers HICNT for both samples, and the label is not applied where it stays missing.

With --reads, a partial row split between its MNV and the reads that stayed can keep fewer high-quality reads than the -r VarDict wrote it under, so the label is computed on the reads that stayed. It also marks the candidates -p keeps below -r.

23 of 23 new or added lines in 2 files covered. (100.0%)

5803 of 5907 relevant lines covered (98.24%)

122129.83 hits per line