java.lang.Object

org.snpsift.SnpSift

org.snpsift.SnpSiftCmdPhastCons

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

public class SnpSiftCmdPhastCons extends SnpSift

Annotate using PhastCons score files

Author:: pcingola

Field Summary

Fields

Modifier and Type

Field

Description

static final String

FIXED_STEP_FIELD

static final int

SHOW_EVERY

static final String

START_FIELD

static final String

VCF_INFO_PHASTCONS_FIELD

Fields inherited from class org.snpsift.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

SnpSiftCmdPhastCons()

SnpSiftCmdPhastCons(String[] args)
Method Summary

Modifier and Type

Method

Description

void

init()

Initialize default values

void

parseArgs(String[] args)

Parse command line arguments

boolean

run()

Run

List<org.snpeff.vcf.VcfEntry>

run(boolean createList)

Run annotations

void

usage(String msg)

Show usage message

Methods inherited from class org.snpsift.SnpSift
addHeaders, annotate, annotateFinish, annotateInit, cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, headers, 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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- START_FIELD
  
  public static final String START_FIELD
  See Also:
  
  Constant Field Values
- FIXED_STEP_FIELD
  
  public static final String FIXED_STEP_FIELD
  See Also:
  
  Constant Field Values
- VCF_INFO_PHASTCONS_FIELD
  
  public static final String VCF_INFO_PHASTCONS_FIELD
  See Also:
  
  Constant Field Values
- SHOW_EVERY
  
  public static final int SHOW_EVERY
  See Also:
  
  Constant Field Values
Constructor Details
- SnpSiftCmdPhastCons
  
  public SnpSiftCmdPhastCons()
- SnpSiftCmdPhastCons
  
  public SnpSiftCmdPhastCons(String[] args)
Method Details
- init
  
  public void init()
  
  Description copied from class: SnpSift
  
  Initialize default values
  
  Overrides:
  
  init in class SnpSift
- 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
  
  Specified by:
  
  run in interface org.snpeff.snpEffect.commandLine.CommandLine
  
  Overrides:
  
  run in class SnpSift
- run
  
  public List<org.snpeff.vcf.VcfEntry> run(boolean createList)
  
  Run annotations
  
  Parameters:
  
  createList - : If true, create a list of VcfEntries (used for test cases)
  
  Returns:
- usage
  
  public void usage(String msg)
  
  Show usage message
  
  Specified by:
  
  usage in interface org.snpeff.snpEffect.commandLine.CommandLine
  
  Overrides:
  
  usage in class SnpSift
  
  Parameters:
  
  msg -

Class SnpSiftCmdPhastCons

Field Summary

Fields inherited from class org.snpsift.SnpSift

Constructor Summary

Method Summary

Methods inherited from class org.snpsift.SnpSift

Methods inherited from class java.lang.Object

Field Details

START_FIELD

FIXED_STEP_FIELD

VCF_INFO_PHASTCONS_FIELD

SHOW_EVERY

Constructor Details

SnpSiftCmdPhastCons

SnpSiftCmdPhastCons

Method Details

init

parseArgs

run

run

usage