GATKSAMRecord clippedRead = clipper.clipRead(clippingRepresentation);
if (outputBam != null) {
outputBam.addAlignment(clippedRead);
} else {
out.println(clippedRead.format());
}
data.nTotalReads++;
data.nTotalBases += clipper.getRead().getReadLength();
if (clipper.wasClipped()) {