Uses of Interface
picard.sam.util.PhysicalLocation

Packages that use PhysicalLocation

Package	Description
picard.sam.markduplicates.util
picard.sam.util

Uses of PhysicalLocation in picard.sam.markduplicates.util

Classes in picard.sam.markduplicates.util that implement PhysicalLocation

Modifier and Type	Class and Description
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	ReadEndsForMarkDuplicatesWithBarcodes
class	ReadEndsForMateCigar A class to store individual records for MarkDuplicatesWithMateCigar.

Methods in picard.sam.markduplicates.util with parameters of type PhysicalLocation

Modifier and Type	Method and Description
boolean[]	OpticalDuplicateFinder.findOpticalDuplicates(java.util.List<? extends PhysicalLocation> list, PhysicalLocation keeper) Finds which reads within the list of duplicates that are likely to be optical/co-localized duplicates of one another.

Method parameters in picard.sam.markduplicates.util with type arguments of type PhysicalLocation

Modifier and Type	Method and Description
boolean[]	OpticalDuplicateFinder.findOpticalDuplicates(java.util.List<? extends PhysicalLocation> list, PhysicalLocation keeper) Finds which reads within the list of duplicates that are likely to be optical/co-localized duplicates of one another.

Constructors in picard.sam.markduplicates.util with parameters of type PhysicalLocation

Constructor and Description
PhysicalLocationForMateCigar(PhysicalLocation rec)

Uses of PhysicalLocation in picard.sam.util

Classes in picard.sam.util that implement PhysicalLocation

Modifier and Type	Class and Description
class	PhysicalLocationInt Small class that provides access to the physical location information about a cluster.
class	PhysicalLocationShort Small class that provides access to the physical location information about a cluster.

Methods in picard.sam.util with parameters of type PhysicalLocation

Modifier and Type	Method and Description
boolean	ReadNameParser.addLocationInformation(java.lang.String readName, PhysicalLocation loc) Method used to extract tile/x/y from the read name and add it to the PhysicalLocationShort so that it can be used later to determine optical duplication