Package | Description |
---|---|
picard.sam.markduplicates.util |
Modifier and Type | Class and Description |
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class |
PhysicalLocationForMateCigar
Stores the minimal information needed for optical duplicate detection.
|
class |
ReadEnds
Little struct-like class to hold read pair (and fragment) end data for duplicate marking.
|
class |
ReadEndsForMarkDuplicates
Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar
|
class |
ReadEndsForMateCigar
A class to store individual records for MarkDuplicatesWithMateCigar.
|
Modifier and Type | Method and Description |
---|---|
boolean |
OpticalDuplicateFinder.addLocationInformation(String readName,
OpticalDuplicateFinder.PhysicalLocation loc)
Method used to extract tile/x/y from the read name and add it to the PhysicalLocation so that it
can be used later to determine optical duplication
|
Modifier and Type | Method and Description |
---|---|
boolean[] |
OpticalDuplicateFinder.findOpticalDuplicates(List<? extends OpticalDuplicateFinder.PhysicalLocation> list)
Finds which reads within the list of duplicates are likely to be optical duplicates of
one another.
|
Constructor and Description |
---|
PhysicalLocationForMateCigar(OpticalDuplicateFinder.PhysicalLocation rec) |