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
Annotate using PhastCons score files
- Author:
- pcingola
-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String
static final int
static final String
static final String
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 -
Method Summary
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
-
Field Details
-
START_FIELD
- See Also:
-
FIXED_STEP_FIELD
- See Also:
-
VCF_INFO_PHASTCONS_FIELD
- See Also:
-
SHOW_EVERY
public static final int SHOW_EVERY- See Also:
-
-
Constructor Details
-
SnpSiftCmdPhastCons
public SnpSiftCmdPhastCons() -
SnpSiftCmdPhastCons
-
-
Method Details
-
init
public void init()Description copied from class:SnpSift
Initialize default values -
parseArgs
Description copied from class:SnpSift
Parse command line arguments -
run
public boolean run()Run -
run
Run annotations- Parameters:
createList
- : If true, create a list of VcfEntries (used for test cases)- Returns:
-
usage
Show usage message
-