Fix some bugs in LeftAlignAndTrimVariants #9305
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A few different bugs in LeftAlignAndTrimVariants.
First, only indels will have their alleles trimmed. This PR changes this so that alleles trimming will happen for MNPs if possible as well.
Additionally, when multiple variants occur at the same location (either due to splitting multiallelics before running LeftAlignAndTrimVariants, or running with
--split-multi-allelics), the tool will not currently behave correctly. Only the first variant processed at a location will be correctly left aligned and trimmed, other variants can only currently be left aligned up to the base following the left aligned start of the first processed variant in the set.This PR fixes both issues, so that:
Also adds tests of these types of edge cases.