Incorrect labelling of transversions in vcfclassify

[smottarella]

Hi,

When running vcfclassify, the qualification for any variant being labelled a transversion is that it does not qualify as a transition, but this approach incorrectly labels every non-transition a transversion, including insertions, deletions, and all non-specific alternate alleles. One solution is to create an isTransversion(ref, alt) method and have the hasTransversion call the new isTransversion method in place of !isTransition(ref, alt). A simple copy of the isTransition method with this conditional clause will work:

if ((ref == "A" && (alt == "C" || alt == "T")) || (ref == "C" && (alt == "A" || alt == "G")) || (ref == "G" && (alt == "C" || alt == "T")) || (ref == "T" && (alt == "A" || alt == "G")))

Thanks