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--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 0x70C
--unmapped : Mark records that would be completely clipped as unmapped
--noeof : Do not expect an EOF block on a bam file.
--params : Print the parameter settings to stderr
--params : Print the parameter settings to stderr
Clipping By Coordinate Optional Parameters:
Clipping By Coordinate Optional Parameters:
