picard.sam.markduplicates

Class MarkDuplicates

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram

picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram

picard.sam.markduplicates.MarkDuplicates

public class MarkDuplicates
extends AbstractMarkDuplicatesCommandLineProgram

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

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	MAX_FILE_HANDLES_FOR_READ_ENDS_MAP
int	MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP If more than this many sequences in SAM file, don't spill to disk because there will not be enough file handles.
double	SORTING_COLLECTION_SIZE_RATIO

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

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
MarkDuplicates()

Method Summary

Methods

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

MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP

@Option(shortName="MAX_SEQS",
        doc="This option is obsolete. ReadEnds will always be spilled to disk.")
public int MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP

If more than this many sequences in SAM file, don't spill to disk because there will not be enough file handles.

MAX_FILE_HANDLES_FOR_READ_ENDS_MAP

@Option(shortName="MAX_FILE_HANDLES",
        doc="Maximum number of file handles to keep open when spilling read ends to disk. Set this number a little lower than the per-process maximum number of file that may be open. This number can be found by executing the \'ulimit -n\' command on a Unix system.")
public int MAX_FILE_HANDLES_FOR_READ_ENDS_MAP

SORTING_COLLECTION_SIZE_RATIO

@Option(doc="This number, plus the maximum RAM available to the JVM, determine the memory footprint used by some of the sorting collections.  If you are running out of memory, try reducing this number.")
public double SORTING_COLLECTION_SIZE_RATIO

Constructor Detail

MarkDuplicates

public MarkDuplicates()

Method Detail

main

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

Stock main method.

doWork

protected int doWork()

Main work method. Reads the BAM file once and collects sorted information about the 5' ends of both ends of each read (or just one end in the case of pairs). Then makes a pass through those determining duplicates before re-reading the input file and writing it out with duplication flags set correctly.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.