Package org.snpsift

Class SnpSiftCmdPhastCons

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 java.lang.String	FIXED_STEP_FIELD
static int	SHOW_EVERY
static java.lang.String	START_FIELD
static java.lang.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(java.lang.String[] args)

Method Summary

Modifier and Type	Method	Description
void	init()	Initialize default values
void	parseArgs(java.lang.String[] args)	Parse command line arguments
boolean	run()	Run
java.util.List<org.snpeff.vcf.VcfEntry>	run(boolean createList)	Run annotations
void	usage(java.lang.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 Detail

START_FIELD

public static final java.lang.String START_FIELD

See Also:

Constant Field Values

FIXED_STEP_FIELD

public static final java.lang.String FIXED_STEP_FIELD

See Also:

Constant Field Values

VCF_INFO_PHASTCONS_FIELD

public static final java.lang.String VCF_INFO_PHASTCONS_FIELD

See Also:

Constant Field Values

SHOW_EVERY

public static final int SHOW_EVERY

See Also:

Constant Field Values

Constructor Detail

SnpSiftCmdPhastCons

public SnpSiftCmdPhastCons()

SnpSiftCmdPhastCons

public SnpSiftCmdPhastCons(java.lang.String[] args)

Method Detail

init

public void init()

Description copied from class: SnpSift

Initialize default values

Overrides:

init in class SnpSift

parseArgs

public void parseArgs(java.lang.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 java.util.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(java.lang.String msg)

Show usage message

Specified by:

usage in interface org.snpeff.snpEffect.commandLine.CommandLine

Overrides:

usage in class SnpSift

Parameters:

msg -