picard.util

Class ScatterIntervalsByNs

java.lang.Object

picard.cmdline.CommandLineProgram

picard.util.ScatterIntervalsByNs

public class ScatterIntervalsByNs
extends CommandLineProgram

A CLP for breaking up a reference into intervals of Ns and ACGTs bases. Used for creating a broken-up interval list for calling WGS.

Field Summary

Fields

Modifier and Type	Field and Description
int	MAX_TO_MERGE
java.io.File	OUTPUT
picard.util.ScatterIntervalsByNs.OutputType	OUTPUT_TYPE
java.io.File	REFERENCE

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
ScatterIntervalsByNs()

Method Summary

Methods

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.
static void	main(java.lang.String[] args)
static htsjdk.samtools.util.IntervalList	segregateReference(htsjdk.samtools.reference.ReferenceSequenceFile refFile, int maxNmerToMerge) **************************************************************** Generate an interval list that alternates between Ns and ACGTs * ****************************************************************

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, 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

REFERENCE

@Option(shortName="R",
        doc="Reference sequence to use.")
public java.io.File REFERENCE

OUTPUT

@Option(shortName="O",
        doc="Output file for interval list.")
public java.io.File OUTPUT

OUTPUT_TYPE

@Option(shortName="OT",
        doc="Type of intervals to output.",
        optional=true)
public picard.util.ScatterIntervalsByNs.OutputType OUTPUT_TYPE

MAX_TO_MERGE

@Option(shortName="N",
        doc="Maximal number of contiguous N bases to tolerate, thereby continuing the current ACGT interval.",
        optional=true)
public int MAX_TO_MERGE

Constructor Detail

ScatterIntervalsByNs

public ScatterIntervalsByNs()

Method Detail

main

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

doWork

protected int doWork()

Description copied from class: CommandLineProgram

Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.

segregateReference

public static htsjdk.samtools.util.IntervalList segregateReference(htsjdk.samtools.reference.ReferenceSequenceFile refFile,
                                                   int maxNmerToMerge)

**************************************************************** Generate an interval list that alternates between Ns and ACGTs * ****************************************************************