picard.fingerprint

Class LiftOverHaplotypeMap

java.lang.Object

picard.cmdline.CommandLineProgram

picard.fingerprint.LiftOverHaplotypeMap

public class LiftOverHaplotypeMap
extends CommandLineProgram

Liftover SNPs in HaplotypeMaps from one reference to another

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	CHAIN
java.io.File	INPUT
static int	LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS
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_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
LiftOverHaplotypeMap()

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

checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

INPUT

@Argument(doc="Haplotype database to be lifted over.",
          shortName="I")
public java.io.File INPUT

OUTPUT

@Argument(doc="Where to write lifted-over haplotype database.",
          shortName="O")
public java.io.File OUTPUT

SEQUENCE_DICTIONARY

@Argument(doc="Sequence dictionary to write into the output haplotype database. (Any file from which a dictionary is extractable.)",
          shortName="SD")
public java.io.File SEQUENCE_DICTIONARY

CHAIN

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

LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS

public static final int LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS

See Also:

Constant Field Values

Constructor Detail

LiftOverHaplotypeMap

public LiftOverHaplotypeMap()

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.