Changes

--stats        : Print some statistics on the overlaps.

--stats        : Print some statistics on the overlaps.

--overlapsOnly : Only output overlapping read pairs

--overlapsOnly : Only output overlapping read pairs

--excludeFlags : Skip records with any of the specified flags set, default 0x70C

--excludeFlags : Skip records with any of the specified flags set, default 0xF0C

                 --unmapped    : Mark records that would be completely clipped as unmapped

                 --unmapped    : Mark records that would be completely clipped as unmapped

  --noeof        : Do not expect an EOF block on a bam file.

  --noeof        : Do not expect an EOF block on a bam file.