Package org.snpsift
Class SnpSiftCmdPhastCons
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdPhastCons
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- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdPhastCons extends SnpSift
Annotate using PhastCons score files- Author:
- pcingola
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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
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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
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Constructor Summary
Constructors Constructor Description SnpSiftCmdPhastCons()
SnpSiftCmdPhastCons(java.lang.String[] args)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
init()
Initialize default valuesvoid
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Runjava.util.List<org.snpeff.vcf.VcfEntry>
run(boolean createList)
Run annotationsvoid
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
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Field Detail
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START_FIELD
public static final java.lang.String START_FIELD
- See Also:
- Constant Field Values
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FIXED_STEP_FIELD
public static final java.lang.String FIXED_STEP_FIELD
- See Also:
- Constant Field Values
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VCF_INFO_PHASTCONS_FIELD
public static final java.lang.String VCF_INFO_PHASTCONS_FIELD
- See Also:
- Constant Field Values
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SHOW_EVERY
public static final int SHOW_EVERY
- See Also:
- Constant Field Values
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Method Detail
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init
public void init()
Description copied from class:SnpSift
Initialize default values
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parseArgs
public void parseArgs(java.lang.String[] args)
Description copied from class:SnpSift
Parse command line arguments
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run
public boolean run()
Run
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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:
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