Package org.snpsift

Class SnpSiftCmdVarType

java.lang.Object

org.snpsift.SnpSift

org.snpsift.SnpSiftCmdVarType

All Implemented Interfaces:

org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator

public class SnpSiftCmdVarType
extends SnpSift

Annotate a VCF file with variant type

Author:

pablocingolani

Field Summary

Fields

Modifier and Type	Field	Description
static int	SHOW
static int	SHOW_LINES
static java.lang.String	VARTYPE

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
SnpSiftCmdVarType()
SnpSiftCmdVarType(java.lang.String[] args)

Method Summary

Modifier and Type	Method	Description
boolean	annotate(org.snpeff.vcf.VcfEntry vcfEntry)	Annotate one entry
protected java.util.List<org.snpeff.vcf.VcfHeaderEntry>	headers()	Headers to add
void	parseArgs(java.lang.String[] args)	Parse command line arguments
boolean	run()	Annotate entries
void	usage(java.lang.String msg)	Show usage message

Methods inherited from class org.snpsift.SnpSift

addHeaders, annotateFinish, annotateInit, cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, 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 java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

SHOW

public static final int SHOW

See Also:

Constant Field Values

SHOW_LINES

public static final int SHOW_LINES

See Also:

Constant Field Values

VARTYPE

public static final java.lang.String VARTYPE

See Also:

Constant Field Values

Constructor Detail

SnpSiftCmdVarType

public SnpSiftCmdVarType()

SnpSiftCmdVarType

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

Method Detail

annotate

public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry)

Annotate one entry

Specified by:

annotate in interface org.snpeff.snpEffect.VcfAnnotator

Overrides:

annotate in class SnpSift

headers

protected java.util.List<org.snpeff.vcf.VcfHeaderEntry> headers()

Description copied from class: SnpSift

Headers to add

Overrides:

headers in class SnpSift

parseArgs

public void parseArgs(java.lang.String[] args)

Parse command line arguments

Specified by:

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

Overrides:

parseArgs in class SnpSift

run

public boolean run()

Annotate entries

Specified by:

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

Overrides:

run in class SnpSift

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 -