Changes to SamLocusIterator to a) check the mapping quality only once per sam record instead of at every base and b) add the ability to filter out non-PF reads during pileup construction.
Changes to SamLocusIterator to a) check the mapping quality only once per sam record instead of at every base and b) add the ability to filter out non-PF reads during pileup construction.

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