picard.sam.markduplicates.util

Class AbstractOpticalDuplicateFinderCommandLineProgram

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram

Direct Known Subclasses:

AbstractMarkDuplicatesCommandLineProgram, EstimateLibraryComplexity

public abstract class AbstractOpticalDuplicateFinderCommandLineProgram
extends CommandLineProgram

Abstract class that holds parameters and methods common to classes that optical duplicate detection. We put them here so that the explanation about how read names are parsed is in once place

Field Summary

Fields

Modifier and Type	Field and Description
protected static htsjdk.samtools.util.Log	LOG
int	OPTICAL_DUPLICATE_PIXEL_DISTANCE
protected OpticalDuplicateFinder	opticalDuplicateFinder
java.lang.String	READ_NAME_REGEX

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
AbstractOpticalDuplicateFinderCommandLineProgram()

Method Summary

Methods

Modifier and Type	Method and Description
protected java.lang.String[]	customCommandLineValidation() Put any custom command-line validation in an override of this method.
void	setupOpticalDuplicateFinder()

Methods inherited from class picard.cmdline.CommandLineProgram

doWork, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

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

Field Detail

LOG

protected static htsjdk.samtools.util.Log LOG

READ_NAME_REGEX

@Option(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.",
        optional=true)
public java.lang.String READ_NAME_REGEX

OPTICAL_DUPLICATE_PIXEL_DISTANCE

@Option(doc="The maximum offset between two duplicte 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.")
public int OPTICAL_DUPLICATE_PIXEL_DISTANCE

opticalDuplicateFinder

protected OpticalDuplicateFinder opticalDuplicateFinder

Constructor Detail

AbstractOpticalDuplicateFinderCommandLineProgram

public AbstractOpticalDuplicateFinderCommandLineProgram()

Method Detail

setupOpticalDuplicateFinder

public void setupOpticalDuplicateFinder()

customCommandLineValidation

protected java.lang.String[] customCommandLineValidation()

Description copied from class: CommandLineProgram

Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.

Overrides:

customCommandLineValidation in class CommandLineProgram

Returns:

null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.