| 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.
|
| Enum | Description |
|---|---|
| MarkDuplicates.DuplicateTaggingPolicy |
Enum used to control how duplicates are flagged in the DT optional tag on each read.
|
| MarkDuplicates.DuplicateType |
Enum for the possible values that a duplicate read can be tagged with in the DT attribute.
|