Package org.snpsift

Class SnpSiftCmdPrivate

java.lang.Object

org.snpsift.SnpSift

org.snpsift.SnpSiftCmdPrivate

All Implemented Interfaces:

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

public class SnpSiftCmdPrivate
extends SnpSift

Annotate if a variant is 'private'. I.e. only represented within a family (or group)

Author:

pcingola

Field Summary

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

Method Summary

Modifier and Type	Method	Description
boolean	annotate(org.snpeff.vcf.VcfEntry ve)	Parse a single VCF entry
boolean	annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile)
void	parseArgs(java.lang.String[] args)	Parse command line arguments
boolean	run()	Run annotations
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, annotateFinish, 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 java.lang.Object

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

Constructor Detail

SnpSiftCmdPrivate

public SnpSiftCmdPrivate()

SnpSiftCmdPrivate

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

Method Detail

annotate

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

Parse a single VCF entry

Specified by:

annotate in interface org.snpeff.snpEffect.VcfAnnotator

Overrides:

annotate in class SnpSift

annotateInit

public boolean annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile)

Specified by:

annotateInit in interface org.snpeff.snpEffect.VcfAnnotator

Overrides:

annotateInit 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 annotations

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. Create a list of VcfEntries if 'createList' is true (use for test cases)

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