picard.util

Class BedToIntervalList

java.lang.Object

picard.cmdline.CommandLineProgram

picard.util.BedToIntervalList

public class BedToIntervalList
extends CommandLineProgram

Author:

nhomer

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	INPUT
java.io.File	OUTPUT
java.io.File	SEQUENCE_DICTIONARY
boolean	SORT
boolean	UNIQUE

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
BedToIntervalList()

Method Summary

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)

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

INPUT

@Option(shortName="I",
        doc="The input BED file")
public java.io.File INPUT

SEQUENCE_DICTIONARY

@Option(shortName="SD",
        doc="The sequence dictionary")
public java.io.File SEQUENCE_DICTIONARY

OUTPUT

@Option(shortName="O",
        doc="The output Picard Interval List")
public java.io.File OUTPUT

SORT

@Option(doc="If true, sort the output interval list before writing it.")
public boolean SORT

UNIQUE

@Option(doc="If true, unique the output interval list by merging overlapping regions, before writing it (implies sort=true).")
public boolean UNIQUE

Constructor Detail

BedToIntervalList

public BedToIntervalList()

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.