# picard.sam.markduplicates.util

## Interfaces

- ReadEndsForMarkDuplicatesMap

## Classes

- AbstractMarkDuplicatesCommandLineProgram
- AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
- AbstractOpticalDuplicateFinderCommandLineProgram
- DiskBasedReadEndsForMarkDuplicatesMap
- LibraryIdGenerator
- MarkQueue
- OpticalDuplicateFinder
- PhysicalLocationForMateCigar
- PhysicalLocationForMateCigarSet
- ReadEnds
- ReadEndsForMarkDuplicates
- ReadEndsForMarkDuplicatesCodec
- ReadEndsForMarkDuplicatesWithBarcodes
- ReadEndsForMarkDuplicatesWithBarcodesCodec
- ReadEndsForMateCigar
- SamRecordWithOrdinalAndSetDuplicateReadFlag