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…input alt Converter.liftover() only handled a strand flip (target reference equal to the reverse complement of the input ref). When the assemblies simply disagree about which allele is the reference, e.g. F5 rs6025 (hg19 ref T / hg38 ref C), the hg19 ref/alt were passed through unchanged, so the variant was mapped and annotated as a different (synonymous) change and the real one was missed. Add orient_alleles_to_target_ref() covering same-strand and opposite-strand swaps, and have liftover() return a swapped flag. When a converter supplies a homozygous zygosity and the alleles were swapped, the sample is homozygous for the new reference, so the row is dropped as a non-variant.
…verters - orient_alleles_to_target_ref takes the chain strand for single-base lifts, which resolves the A/T and C/G strand-flip vs swap ambiguity. - zygosity_after_liftover reinterprets converter zygosity after a swap: hom becomes a non-variant, and a new 'ref' value (homozygous for the input assembly's reference allele, emitted by converters at sites where the assemblies disagree) becomes hom. Missing zygosity is left alone.
… homozygous for an assembly-specific reference Microarray converters only emit alleles that differ from the input assembly's reference, so a call homozygous for that reference is never reported even where the liftover target assembly has a different reference base (F5 rs6025 T/T: homozygous Factor V Leiden). Provide a shared helper that returns a zygosity 'ref' row for those sites; the converter loop turns it into a hom variant once liftover has swapped the alleles.
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2 unrelated fixes.
immutable seems to help my performance, a lot.
pool.join() fixes hanging processes