LiftOverHaplotypeMap (picard 3.4.0 API)

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

Description

File

CHAIN

File

INPUT

static final int

LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS

File

OUTPUT

File

SEQUENCE_DICTIONARY

Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
Constructor Summary

Constructors

Constructor

Description

LiftOverHaplotypeMap()
Method Summary

Modifier and Type

Method

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 Details
- INPUT
  
  @Argument(doc="Haplotype database to be lifted over.", shortName="I") public File INPUT
- OUTPUT
  
  @Argument(doc="Where to write lifted-over haplotype database.", shortName="O") public 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 File SEQUENCE_DICTIONARY
- CHAIN
  
  @Argument(doc="Chain file that guides LiftOver. (UCSC format)") public 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 Details
- LiftOverHaplotypeMap
  
  public LiftOverHaplotypeMap()
Method Details
- 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.