picard.sam.markduplicates.util

Class OpticalDuplicateFinder

java.lang.Object

picard.sam.util.ReadNameParser

picard.sam.markduplicates.util.OpticalDuplicateFinder

public class OpticalDuplicateFinder
extends ReadNameParser

Contains methods for finding optical/co-localized/sequencing duplicates.

Author:

Tim Fennell, Nils Homer

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_BIG_DUPLICATE_SET_SIZE
static int	DEFAULT_OPTICAL_DUPLICATE_DISTANCE
int	opticalDuplicatePixelDistance

Fields inherited from class picard.sam.util.ReadNameParser

DEFAULT_READ_NAME_REGEX

Constructor Summary

Constructors

Constructor and Description
OpticalDuplicateFinder() Uses the default duplicate distance and the default read name regex ReadNameParser.DEFAULT_READ_NAME_REGEX.
OpticalDuplicateFinder(java.lang.String readNameRegex, int opticalDuplicatePixelDistance, htsjdk.samtools.util.Log log)

Method Summary

Modifier and Type	Method and Description
boolean[]	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.
void	setBigDuplicateSetSize(int bigDuplicateSetSize) Sets the size of a set that is big enough to log progress about.

Methods inherited from class picard.sam.util.ReadNameParser

addLocationInformation, getLastThreeFields, rapidParseInt

Methods inherited from class java.lang.Object

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

Field Detail

opticalDuplicatePixelDistance

public int opticalDuplicatePixelDistance

DEFAULT_OPTICAL_DUPLICATE_DISTANCE

public static final int DEFAULT_OPTICAL_DUPLICATE_DISTANCE

See Also:

Constant Field Values

DEFAULT_BIG_DUPLICATE_SET_SIZE

public static final int DEFAULT_BIG_DUPLICATE_SET_SIZE

See Also:

Constant Field Values

Constructor Detail

OpticalDuplicateFinder

public OpticalDuplicateFinder()

Uses the default duplicate distance and the default read name regex ReadNameParser.DEFAULT_READ_NAME_REGEX.

OpticalDuplicateFinder

public OpticalDuplicateFinder(java.lang.String readNameRegex,
                              int opticalDuplicatePixelDistance,
                              htsjdk.samtools.util.Log log)

Parameters:

readNameRegex - see ReadNameParser.DEFAULT_READ_NAME_REGEX.

opticalDuplicatePixelDistance - the optical duplicate pixel distance

log - the log to which to write messages.

Method Detail

setBigDuplicateSetSize

public void setBigDuplicateSetSize(int bigDuplicateSetSize)

Sets the size of a set that is big enough to log progress about. Defaults to

Parameters:

bigDuplicateSetSize - the size of a set that is big enough to log progress about

findOpticalDuplicates

public boolean[] 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. Within each cluster of optical duplicates that is found, one read remains un-flagged for optical duplication and the rest are flagged as optical duplicates. The set of reads that are considered optical duplicates are indicated by returning "true" at the same index in the resulting boolean[] as the read appeared in the input list of physical locations.

Parameters:

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

keeper - a single PhysicalLocation that is the one being kept as non-duplicate, and thus should never be annotated as an optical duplicate. May in some cases be null, or a PhysicalLocation not contained within the list!

Returns:

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