| Package | Description |
|---|---|
| picard.sam.markduplicates | |
| picard.sam.markduplicates.util |
| Class and Description |
|---|
| AbstractMarkDuplicatesCommandLineProgram
Abstract class that holds parameters and methods common to classes that perform duplicate
detection and/or marking within SAM/BAM files.
|
| AbstractOpticalDuplicateFinderCommandLineProgram
Abstract class that holds parameters and methods common to classes that optical duplicate detection.
|
| LibraryIdGenerator
A class to generate library Ids and keep duplication metrics by library IDs.
|
| OpticalDuplicateFinder
Contains methods for finding optical/co-localized/sequencing duplicates.
|
| Class and Description |
|---|
| 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.
|
| LibraryIdGenerator
A class to generate library Ids and keep duplication metrics by library IDs.
|
| OpticalDuplicateFinder
Contains methods for finding optical/co-localized/sequencing duplicates.
|
| 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
Codec for ReadEnds that just outputs the primitive fields and reads them back.
|
| ReadEndsForMarkDuplicatesMap
Interface for storing and retrieving ReadEnds objects.
|
| ReadEndsForMarkDuplicatesWithBarcodes |
| ReadEndsForMateCigar
A class to store individual records for MarkDuplicatesWithMateCigar.
|