Package org.broadinstitute.gatk.utils.sam

Examples of org.broadinstitute.gatk.utils.sam.GATKSAMRecord.format()


        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()) {
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