ConvertHaplotypeDatabaseToVcf (picard 3.4.0 API)

java.lang.Object

picard.cmdline.CommandLineProgram

picard.fingerprint.ConvertHaplotypeDatabaseToVcf

public class ConvertHaplotypeDatabaseToVcf extends CommandLineProgram

Field Summary

Fields

Modifier and Type

Field

Description

File

INPUT

File

OUTPUT

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

ConvertHaplotypeDatabaseToVcf()
Method Summary

Modifier and Type

Method

Description

protected int

doWork()

Do the work after command line has been parsed.

protected boolean

requiresReference()

Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, 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 converted to VCF.", shortName="I") public File INPUT
- OUTPUT
  
  @Argument(doc="Where to write converted haplotype database VCF.", shortName="O") public File OUTPUT
Constructor Details
- ConvertHaplotypeDatabaseToVcf
  
  public ConvertHaplotypeDatabaseToVcf()
Method Details
- requiresReference
  
  protected boolean requiresReference()
  
  Overrides:
  
  requiresReference in class CommandLineProgram
- 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.