Skip non-primary alignments by default.  If default is overridden, exceptions may result for paired reads with non-primary alignments.
Skip non-primary alignments by default.  If default is overridden, exceptions may result for paired reads with non-primary alignments.

alecw/picard,nh13/picard,nh13/picard,broadinstitute/picard,broadinstitute/picard,alecw/picard,broadinstitute/picard,annkupi/picard,annkupi/picard,broadinstitute/picard,nh13/picard,nh13/picard,broadinstitute/picard,annkupi/picard,annkupi/picard,alecw/picard,alecw/picard