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BamUtil: clipOverlap

No change in size, 00:00, 6 March 2016
Parameters
--stats : Print some statistics on the overlaps.
--overlapsOnly : Only output overlapping read pairs
--excludeFlags : Skip records with any of the specified flags set, default 0x70C0xF0C
--unmapped : Mark records that would be completely clipped as unmapped
--noeof : Do not expect an EOF block on a bam file.

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