broadinstitute/picard — pull request #90 by gbggrant (2014-10-06 13:56:54+00:00)
Title: Improvement to handle 'mismatching' ref alleles for indel comparison conditions

If ref allele in truth does not match ref allele in call, then verify first that the shorter ref allele string is the prefix of the longer, and then
append the remainder of the longer ref allele (i.e. that which follows the prefix) onto the shorter's ref and genotype alleles.