clintval / vartovcf / 37142105471

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feat: write VarDict's high-quality ALT read count as FORMAT HICNT (#112)

HICNT is VarDict's HiCnt column: the ALT reads whose mean base quality over the allele's bases is at least VarDict's -q, which is the count VarDict's own minimum-reads rule (-r) tests. It is FORMAT, Number=A, and missing when there is no ALT allele. VarDict's HiCov and HiAF are not written: HiCov sums HiCnt over only the non-insertion alleles that start at the position, so it is not a depth, and HiAF divided by it reads 1 for a 50% insertion.

8 of 8 new or added lines in 2 files covered. (100.0%)

580 of 596 relevant lines covered (97.32%)

27.73 hits per line