MultiVariantWalkerGroupedOnStart doesn't handle reads correctly
closed | Created 2019-07-08 | Last updated 2019-09-12| Posted by davidbenjamin | See in Github

VariantWalker bug

When MultiVariantWalkerGroupedOnStart finds a variant that does not share a start with the currentVariants, it processes that group of variants. However, it does so using the readsContext of the found variant with a different start and not that of the group of processed variants. Furthermore, in afterTraverse it processes any remaining variants with an empty ReadsContext, which is just wrong.

This has not been caught before because no existing implementations use reads.

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