hammerlab/guacamole — pull request #61 by arahuja (2014-05-12 17:31:30+00:00)
Title: Cigar offsets incorrectly jumps full length of elements

The current cigar element offsets are incorrect - while we are searching for the next cigar element the indices jump by the complete length of the cigar element, when we may already be offset by some amount into the cigar element.

This PR only contains failing tests for now - not sure how we should handle this. Currently at any given locus we don't have information on whether the current element consumes read and/or reference bases so we don't know whether to subtract off the offset from either. We could save this information around, but then the next issue is currently we define a read position for deletion element and I'm not sure what the interpretation of a read position for a deletion element is.