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, 00:00, 6 March 2016
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| --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. |