picard.sam.markduplicates.util

Class OpticalDuplicateFinder

java.lang.Object

picard.sam.markduplicates.util.OpticalDuplicateFinder

public class OpticalDuplicateFinder
extends Object

Contains methods for finding optical duplicates.

Author:

Tim Fennell, Nils Homer

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	OpticalDuplicateFinder.PhysicalLocation Small interface that provides access to the physical location information about a cluster.

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_OPTICAL_DUPLICATE_DISTANCE
static String	DEFAULT_READ_NAME_REGEX
int	opticalDuplicatePixelDistance
String	readNameRegex

Constructor Summary

Constructors

Constructor and Description
OpticalDuplicateFinder()
OpticalDuplicateFinder(int opticalDuplicatePixelDistance)
OpticalDuplicateFinder(String readNameRegex)
OpticalDuplicateFinder(String readNameRegex, int opticalDuplicatePixelDistance)
OpticalDuplicateFinder(String readNameRegex, int opticalDuplicatePixelDistance, Log log)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	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
boolean[]	findOpticalDuplicates(List<? extends OpticalDuplicateFinder.PhysicalLocation> list) Finds which reads within the list of duplicates are likely to be optical duplicates of one another.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT_READ_NAME_REGEX

public static final String DEFAULT_READ_NAME_REGEX

DEFAULT_OPTICAL_DUPLICATE_DISTANCE

public static final int DEFAULT_OPTICAL_DUPLICATE_DISTANCE

See Also:

Constant Field Values

readNameRegex

public String readNameRegex

opticalDuplicatePixelDistance

public int opticalDuplicatePixelDistance

Constructor Detail

OpticalDuplicateFinder

public OpticalDuplicateFinder()

OpticalDuplicateFinder

public OpticalDuplicateFinder(int opticalDuplicatePixelDistance)

OpticalDuplicateFinder

public OpticalDuplicateFinder(String readNameRegex)

OpticalDuplicateFinder

public OpticalDuplicateFinder(String readNameRegex,
                      int opticalDuplicatePixelDistance)

OpticalDuplicateFinder

public OpticalDuplicateFinder(String readNameRegex,
                      int opticalDuplicatePixelDistance,
                      Log log)

Method Detail

addLocationInformation

public boolean 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

Parameters:

readName - the name of the read/cluster

loc - the object to add tile/x/y to

Returns:

true if the read name contained the information in parsable form, false otherwise

findOpticalDuplicates

public boolean[] findOpticalDuplicates(List<? extends OpticalDuplicateFinder.PhysicalLocation> list)

Finds which reads within the list of duplicates are likely to be optical duplicates of one another.

Note: this method will perform a sort() of the list; if it is imperative that the list be unmodified a copy of the list should be passed to this method.

Parameters:

list - a list of reads that are determined to be duplicates of one another

Returns:

a boolean[] of the same length as the incoming list marking which reads are optical duplicates