picard.util

Class LiftOverIntervalList

java.lang.Object

picard.cmdline.CommandLineProgram

picard.util.LiftOverIntervalList

public class LiftOverIntervalList
extends CommandLineProgram

Author:

alecw@broadinstitute.org

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	CHAIN
java.io.File	INPUT
double	MIN_LIFTOVER_PCT
java.io.File	OUTPUT
java.io.File	SEQUENCE_DICTIONARY

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
LiftOverIntervalList()

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[] argv)

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(doc="Interval list to be lifted over.",
        shortName="I")
public java.io.File INPUT

OUTPUT

@Option(doc="Where to write lifted-over interval list.",
        shortName="O")
public java.io.File OUTPUT

SEQUENCE_DICTIONARY

@Option(doc="Sequence dictionary to write into the output interval list.",
        shortName="SD")
public java.io.File SEQUENCE_DICTIONARY

CHAIN

@Option(doc="Chain file that guides LiftOver.")
public java.io.File CHAIN

MIN_LIFTOVER_PCT

@Option(doc="Minimum percentage of bases in each input interval that must map to output interval.")
public double MIN_LIFTOVER_PCT

Constructor Detail

LiftOverIntervalList

public LiftOverIntervalList()

Method Detail

main

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

doWork

protected int doWork()

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.