SnpSiftCmdPedShow (SnpSift 5.4 API)

java.lang.Object

org.snpsift.SnpSift

org.snpsift.SnpSiftCmdPedShow

All Implemented Interfaces:: org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator

public class SnpSiftCmdPedShow extends SnpSift

Draws a pedigree using SVG according to a VCF file

Author:: pablocingolani

Field Summary

Fields inherited from class SnpSift
args, BUILD, command, config, configFile, dataDir, dbFileName, dbTabix, dbType, debug, download, EMPTY_ARGS, errCount, genomeVersion, help, log, needsConfig, needsDb, needsGenome, numWorkers, output, quiet, REVISION, saveOutput, shiftArgs, SHOW_EVERY_VCFLINES, showVcfHeader, showVersion, SOFTWARE_NAME, suppressOutput, vcfHeaderAddProgramVersion, vcfHeaderProcessed, vcfInputFile, verbose, VERSION, VERSION_MAJOR, VERSION_NO_NAME, VERSION_SHORT
Constructor Summary

Constructors

Constructor

Description

SnpSiftCmdPedShow()

SnpSiftCmdPedShow(String[] args)
Method Summary

Modifier and Type

Method

Description

void

parseArgs(String[] args)

Parse command line arguments

boolean

run()

Run: Main method

void

usage(String msg)

Show usage message

Methods inherited from class SnpSift
addHeaders, annotate, annotateFinish, annotateInit, cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, headers, init, isOpt, loadConfig, main, openVcfInputFile, processVcfHeader, setCommand, setCommand, setConfig, setConfigFile, setDbFileName, setDebug, setQuiet, setSaveOutput, setShowVcfHeader, setShowVersion, setSuppressOutput, setVcfHeaderAddProgramVersion, setVerbose, showCmd, showVersion, unSanitize, usageGenericAndDb

Methods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- SnpSiftCmdPedShow
  
  public SnpSiftCmdPedShow()
- SnpSiftCmdPedShow
  
  public SnpSiftCmdPedShow(String[] args)
Method Details
- parseArgs
  
  public void parseArgs(String[] args)
  
  Description copied from class: SnpSift
  
  Parse command line arguments
  
  Specified by:
  
  parseArgs in interface org.snpeff.snpEffect.commandLine.CommandLine
  
  Overrides:
  
  parseArgs in class SnpSift
- run
  
  public boolean run()
  
  Run: Main method
  
  Specified by:
  
  run in interface org.snpeff.snpEffect.commandLine.CommandLine
  
  Overrides:
  
  run in class SnpSift
  
  Parameters:
  
  tfamFile -
  
  vcfFileName -
  
  outputDir -
  
  chrPos -
- usage
  
  public void usage(String msg)
  
  Description copied from class: SnpSift
  
  Show usage message
  
  Specified by:
  
  usage in interface org.snpeff.snpEffect.commandLine.CommandLine
  
  Overrides:
  
  usage in class SnpSift