clintval / vartovcf / 37140549661

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feat: write per-strand allele depths as FORMAT ADF and ADR (#111)

ADF and ADR are the forward and reverse halves of AD (Number=R), from VarDict's RefFwd, RefRev, AltFwd and AltRev columns: strand is the read's SAM 0x10 flag. They follow AD's rules, so REF is missing for Complex calls and is the only value on reference-only rows; AD, ADF and ADR now share one helper. They replace the four keys var2vcf_valid.pl writes for the same counts (FORMAT RD and ALD, INFO REFBIAS and VARBIAS) with the pair bcftools uses.

16 of 16 new or added lines in 2 files covered. (100.0%)

573 of 589 relevant lines covered (97.28%)

27.38 hits per line