Package | Description |
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picard.sam.markduplicates.util |
Modifier and Type | Class and Description |
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class |
ReadEndsForMarkDuplicates
Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar
|
class |
ReadEndsForMarkDuplicatesWithBarcodes |
class |
ReadEndsForMateCigar
A class to store individual records for MarkDuplicatesWithMateCigar.
|
Modifier and Type | Method and Description |
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java.util.Set<ReadEnds> |
MarkQueue.getLocations(ReadEndsForMateCigar current)
Returns the nonDuplicateReadEndsSet of read ends that should be considered for tracking optical duplicates.
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java.util.Set<ReadEnds> |
PhysicalLocationForMateCigarSet.getReadEnds()
Gets the set of read ends
|
java.util.Set<ReadEnds> |
ReadEndsForMateCigar.getReadEndSetForOpticalDuplicates()
Gets the read ends for optical duplicate tracking
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Modifier and Type | Method and Description |
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static void |
AbstractMarkDuplicatesCommandLineProgram.trackOpticalDuplicates(java.util.List<? extends ReadEnds> ends,
ReadEnds keeper,
OpticalDuplicateFinder opticalDuplicateFinder,
LibraryIdGenerator libraryIdGenerator)
Looks through the set of reads and identifies how many of the duplicates are
in fact optical duplicates, and stores the data in the instance level histogram.
|
Modifier and Type | Method and Description |
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static void |
AbstractMarkDuplicatesCommandLineProgram.trackOpticalDuplicates(java.util.List<? extends ReadEnds> ends,
ReadEnds keeper,
OpticalDuplicateFinder opticalDuplicateFinder,
LibraryIdGenerator libraryIdGenerator)
Looks through the set of reads and identifies how many of the duplicates are
in fact optical duplicates, and stores the data in the instance level histogram.
|