| Interface | Description |
|---|---|
| ReadEndsForMarkDuplicatesMap |
Interface for storing and retrieving ReadEnds objects.
|
| Class | Description |
|---|---|
| AbstractMarkDuplicatesCommandLineProgram |
Abstract class that holds parameters and methods common to classes that perform duplicate
detection and/or marking within SAM/BAM/CRAM files.
|
| AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator |
Little class used to package up a header and an iterable/iterator.
|
| AbstractOpticalDuplicateFinderCommandLineProgram |
Abstract class that holds parameters and methods common to classes that optical duplicate detection.
|
| DiskBasedReadEndsForMarkDuplicatesMap |
Disk-based implementation of ReadEndsForMarkDuplicatesMap.
|
| GATKDuplicationMetrics |
Metrics that are calculated during the process of marking duplicates
within a stream of SAMRecords.
|
| LibraryIdGenerator |
A class to generate library Ids and keep duplication metrics by library IDs.
|
| ReadEnds |
Little struct-like class to hold read pair (and fragment) end data for duplicate marking.
|
| ReadEndsForMarkDuplicates |
Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar
|
| ReadEndsForMarkDuplicatesCodec |
Codec for ReadEnds that just outputs the primitive fields and reads them back.
|
| ReadsKey |
Encodes a unique key for read, read pairs and fragments.
|
| SamRecordWithOrdinalAndSetDuplicateReadFlag |
This class sets the duplicate read flag as the result state when examining sets of records.
|
| SerializableOpticalDuplicatesFinder |
An intermediate class flagged as being serializable so that the Picard OpticalDuplicateFinder can be serialized despite
it not being marked as such.
|
| Enum | Description |
|---|---|
| MarkDuplicatesScoringStrategy |
This class helps us compute and compare duplicate scores, which are used for selecting the non-duplicate
during duplicate marking (see MarkDuplicatesGATK).
|