bigdatagenomics/adam — pull request #199 by fnothaft (2014-04-02 19:45:07+00:00)
Title: Updating pileup conversion code to convert sequences that use the X and = (EQ) CIGAR operators

This update patches the pileup converter to allow for the conversion of reads that use the X and = CIGAR operators instead of the M operator for alignment matches. The X and = CIGAR operators provide additional information (specifically, = is *base* match, X is *base* mismatch) for alignment blocks that are an alignment match.