clintval / vartovcf / 37143489586

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github

feat: write VarDict's strand-bias Fisher p-value as FORMAT STRAND_BIAS_FISHER_P (#116)

STRAND_BIAS_FISHER_P is VarDict's SBF column: the two-sided Fisher exact p-value that the ALT reads' forward/reverse split differs from the REF reads' split, rounded by VarDict to 5 decimals. It is FORMAT, Number=A, missing when there is no ALT allele, and sits next to ADF and ADR, which hold the table's counts. VarDict's odds ratio is not written: it codes zero cells as 0 or Inf, and ADF and ADR show its direction directly.

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

617 of 634 relevant lines covered (97.32%)

29.18 hits per line