| Interface | Description |
|---|---|
| OpticalDuplicateFinder.PhysicalLocation |
Small interface that provides access to the physical location information about a cluster.
|
| 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 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.
|
| LibraryIdGenerator |
A class to generate library Ids and keep duplication metrics by library IDs.
|
| MarkQueue |
This is the mark queue.
|
| OpticalDuplicateFinder |
Contains methods for finding optical duplicates.
|
| PhysicalLocationForMateCigar |
Stores the minimal information needed for optical duplicate detection.
|
| PhysicalLocationForMateCigarSet |
This stores records that are comparable for detecting optical duplicates.
|
| 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 |
Coded for ReadEnds that just outputs the primitive fields and reads them back.
|
| ReadEndsForMarkDuplicatesWithBarcodes | |
| ReadEndsForMarkDuplicatesWithBarcodesCodec |
Created by nhomer on 9/13/15.
|
| ReadEndsForMateCigar |
A class to store individual records for MarkDuplicatesWithMateCigar.
|
| SamRecordWithOrdinalAndSetDuplicateReadFlag |
This class sets the duplicate read flag as the result state when examining sets of records.
|