Package org.broadinstitute.hellbender.cmdline.argumentcollections

Class OpticalDuplicatesArgumentCollection

java.lang.Object

org.broadinstitute.hellbender.cmdline.argumentcollections.OpticalDuplicatesArgumentCollection

All Implemented Interfaces:

Serializable

public final class OpticalDuplicatesArgumentCollection
extends Object
implements Serializable

An argument collection for use with tools that mark optical duplicates.

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
int	OPTICAL_DUPLICATE_PIXEL_DISTANCE
static final String	OPTICAL_DUPLICATE_PIXEL_DISTANCE_LONG_NAME
String	READ_NAME_REGEX
static final String	READ_NAME_REGEX_LONG_NAME

Constructor Summary

Constructors

Constructor	Description
OpticalDuplicatesArgumentCollection()

Method Summary

Methods inherited from class java.lang.Object

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

Field Details

READ_NAME_REGEX_LONG_NAME

public static final String READ_NAME_REGEX_LONG_NAME

See Also:

• Constant Field Values

OPTICAL_DUPLICATE_PIXEL_DISTANCE_LONG_NAME

public static final String OPTICAL_DUPLICATE_PIXEL_DISTANCE_LONG_NAME

See Also:

• Constant Field Values

READ_NAME_REGEX

@Argument(doc="Regular expression that can be used to parse read names in the incoming SAM file. Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. Set this option to null to disable optical duplicate detection. The regular expression should contain three capture groups for the three variables, in order. It must match the entire read name. Note that if the default regex is specified, a regex match is not actually done, but instead the read name  is split on colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements are assumed to be tile, x and y values.",
          fullName="read-name-regex",
          optional=true)
public String READ_NAME_REGEX

OPTICAL_DUPLICATE_PIXEL_DISTANCE

@Argument(doc="The maximum offset between two duplicate clusters in order to consider them optical duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal.",
          fullName="optical-duplicate-pixel-distance",
          optional=true)
public int OPTICAL_DUPLICATE_PIXEL_DISTANCE

Constructor Details

OpticalDuplicatesArgumentCollection

public OpticalDuplicatesArgumentCollection()