picard.sam.markduplicates

Class MarkDuplicatesWithMateCigar

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram

picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram

picard.sam.markduplicates.MarkDuplicatesWithMateCigar

public class MarkDuplicatesWithMateCigar
extends AbstractMarkDuplicatesCommandLineProgram

An even better duplication marking algorithm that handles all cases including clipped and gapped alignments.

This tool differs with MarkDuplicates as it may break ties differently. Furthermore, as it is a one-pass algorithm, it cannot know the program records contained in the file that should be chained in advance. Therefore it will only be able to examine the header to attempt to infer those program group records that have no associated previous program group record. If a read is encountered without a program record, or not one as previously defined, it will not be updated.

This tool will also not work with alignments that have large gaps or skips, such as those from RNA-seq data. This is due to the need to buffer small genomic windows to ensure integrity of the duplicate marking, while large skips (ex. skipping introns) in the alignment records would force making that window very large, thus exhausting memory.

Author:

Nils Homer

Nested Class Summary

Nested classes/interfaces inherited from class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram

AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator

Field Summary

Fields

Modifier and Type	Field and Description
int	BLOCK_SIZE
int	MINIMUM_DISTANCE

Fields inherited from class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram

ASSUME_SORT_ORDER, ASSUME_SORTED, COMMENT, DUPLICATE_SCORING_STRATEGY, INPUT, METRICS_FILE, OUTPUT, pgIdsSeen, PROGRAM_GROUP_COMMAND_LINE, PROGRAM_GROUP_NAME, PROGRAM_GROUP_VERSION, PROGRAM_RECORD_ID, REMOVE_DUPLICATES

Fields inherited from class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram

LOG, OPTICAL_DUPLICATE_PIXEL_DISTANCE, opticalDuplicateFinder, 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
MarkDuplicatesWithMateCigar()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Main work method.
static void	main(java.lang.String[] args) Stock main method.

Methods inherited from class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram

finalizeAndWriteMetrics, getChainedPgIds, openInputs, trackOpticalDuplicates

Methods inherited from class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram

customCommandLineValidation, setupOpticalDuplicateFinder

Methods inherited from class picard.cmdline.CommandLineProgram

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

MINIMUM_DISTANCE

@Option(doc="The minimum distance to buffer records to account for clipping on the 5\' end of the records.Set this number to -1 to use twice the first read\'s read length (or 100, whichever is smaller).",
        optional=true)
public int MINIMUM_DISTANCE

BLOCK_SIZE

@Option(doc="The block size for use in the coordinate-sorted record buffer.",
        optional=true)
public int BLOCK_SIZE

Constructor Detail

MarkDuplicatesWithMateCigar

public MarkDuplicatesWithMateCigar()

Method Detail

main

public static void main(java.lang.String[] args)

Stock main method.

doWork

protected int doWork()

Main work method.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.