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Get RODBinding records that overlap endpoint of deletion, etc in GATK 1.6
I have implemented a custom walker that is attempting to intersect variants from a VCF with regions specified in a ROD. In the map function, I iterate across all variant contexts (modeled on various walkers in GATK), incorporating information from features obtained from the other RODs via RefMetaDataTracker getValues method.
I am not surprised that features that only overlap the endpoint of the current (length > 1) variant are not returned. However, I am not sure how to implement the behavior I want within the walker framework. If I am iterating across variants in a VCF, how do I get a set of features in another ROD that overlap with that variant, including those that just overlap with the end of the variant?