//throw new GATKException(String.format("Unable to align read %s to reference; count = %d",read.getReadName(),count));
System.out.printf("Unable to align read %s to reference; count = %d%n",read.getReadName(),count);
failures++;
}
Alignment foundAlignment = null;
for(Alignment[] alignmentsOfQuality: alignments) {
for(Alignment alignment: alignmentsOfQuality) {
if( read.getReadNegativeStrandFlag() != alignment.isNegativeStrand() )
continue;
if( read.getAlignmentStart() != alignment.getAlignmentStart() )