picard.util

Class IntervalListToBed

java.lang.Object

picard.cmdline.CommandLineProgram

picard.util.IntervalListToBed

public class IntervalListToBed
extends CommandLineProgram

Trivially simple command line program to convert an IntervalList file to a BED file.

Author:

Tim Fennell

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	INPUT
java.io.File	OUTPUT
int	SCORE
boolean	SORT

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
IntervalListToBed()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.

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="Input IntervalList file.")
public java.io.File INPUT

OUTPUT

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

SCORE

@Option(doc="The score, between 0-1000, to output for each interval in the BED file.")
public int SCORE

SORT

@Option(doc="If true, sort the interval list prior to outputting as BED file.")
public boolean SORT

Constructor Detail

IntervalListToBed

public IntervalListToBed()

Method Detail

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.