| Class | Description |
|---|---|
| EstimateLibraryComplexity |
Attempts to estimate library complexity from sequence alone.
|
| MarkDuplicates |
A better duplication marking algorithm that handles all cases including clipped
and gapped alignments.
|
| MarkDuplicatesWithMateCigar |
An even better duplication marking algorithm that handles all cases including clipped
and gapped alignments.
|
| MarkDuplicatesWithMateCigarIterator |
This will iterate through a coordinate sorted SAM file (iterator) and either mark or
remove duplicates as appropriate.
|