clintval / vartovcf / 37140276540

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github

feat: write FORMAT AF as AD[1] / DP at full precision, clamped to [0, 1] (#110)

VarDict's AF column is rounded half-even to 4 decimals, so a one-read call at a depth above 20,000 reads 0. FORMAT AF is now the ALT depth over DP, computed in double precision and stored as a VCF Float, which keeps about 7 significant digits at any magnitude (one read in a million writes 1e-06). It is clamped to [0, 1] because VarDict's ALT count can exceed DP, and is missing without an ALT allele or when DP is 0. GT's 1/1 threshold now reads this AF, so GT and AF always agree.

10 of 10 new or added lines in 2 files covered. (100.0%)

561 of 577 relevant lines covered (97.23%)

25.73 hits per line