Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdEff
- java.lang.Object
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- org.snpeff.SnpEff
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- org.snpeff.snpEffect.commandLine.SnpEffCmdEff
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- All Implemented Interfaces:
CommandLine
,VcfAnnotator
public class SnpEffCmdEff extends SnpEff implements VcfAnnotator
Command line program: Predict variant effects- Author:
- Pablo Cingolani
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Nested Class Summary
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Nested classes/interfaces inherited from class org.snpeff.SnpEff
SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
DEFAULT_SUMMARY_CSV_FILE
static java.lang.String
DEFAULT_SUMMARY_GENES_FILE
static java.lang.String
DEFAULT_SUMMARY_HTML_FILE
static int
SHOW_EVERY
static java.lang.String
SUMMARY_CSV_TEMPLATE
static java.lang.String
SUMMARY_GENES_TEMPLATE
static java.lang.String
SUMMARY_TEMPLATE
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Fields inherited from class org.snpeff.SnpEff
args, BUILD, BUILD_DATE, canonical, canonicalFile, command, COMMAND_LINE_WIDTH, config, configFile, configOverride, customIntervalFiles, dataDir, debug, DEFAULT_COMMAND, download, expandIub, genome, genomeVer, help, hgvs, hgvsForce, hgvsOld, hgvsOneLetterAa, hgvsShift, hgvsTrId, interaction, log, maxTranscriptSupportLevel, motif, multiThreaded, nextProt, nextProtKeepAllTrs, noGenome, numWorkers, onlyProtein, onlyRegulation, onlyTranscriptsFile, output, quiet, regulationTracks, REVISION, saveOutput, shiftArgs, snpEffCmd, SOFTWARE_NAME, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, spliceSiteSize, strict, suppressOutput, treatAllAsProteinCoding, upDownStreamLength, verbose, VERSION, VERSION_AUTHOR, VERSION_BUILD, VERSION_MAJOR, VERSION_SHORT
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Constructor Summary
Constructors Constructor Description SnpEffCmdEff()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
addHeaders(VcfFileIterator vcfFile)
Add annotation headers to VCF fileboolean
annotate(java.lang.String inputFile, java.lang.String outputFile)
Annotate: Calculate the effect of variants and show resultsboolean
annotate(VcfEntry vcfEntry)
Annotate a VCF entryboolean
annotateFinish(VcfFileIterator vcfFile)
Finish annotations and create reportsprotected void
annotateInit(java.lang.String outputFile)
Calculate the effect of variants and show resultsboolean
annotateInit(VcfFileIterator vcfFile)
Initialize annotator: This method is called after vcfFile is opened, but before the header is output.VariantEffectStats
getChangeEffectResutStats()
int
getTotalErrs()
VariantStats
getvariantStats()
void
parseArgs(java.lang.String[] args)
Parse command line argumentsjava.util.HashMap<java.lang.String,java.lang.String>
reportValues()
Additional values to be reportedboolean
run()
Run according to command line optionsjava.util.List<VcfEntry>
run(boolean createList)
Run according to command line optionsvoid
setFormatVersion(EffFormatVersion formatVersion)
void
usage(java.lang.String message)
Show 'usage;' message and exit with an error code '-1'-
Methods inherited from class org.snpeff.SnpEff
addRegulationTrack, canonical, cmd, commandLineStr, error, fatalError, getArgs, getConfig, getConfigFile, getOutput, isOpt, load, loadConfig, loadCustomFile, loadDb, loadMarkers, main, run, setCanonical, setConfig, setConfigFile, setDebug, setGenomeVer, setLog, setNextProt, setNextProtKeepAllTrs, setShiftHgvs, setSpliceSiteSize, setSupressOutput, setUpDownStreamLength, setVerbose, usageDb, usageGeneric, usageGenericAndDb, warning
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.snpeff.snpEffect.commandLine.CommandLine
getArgs
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Methods inherited from interface org.snpeff.snpEffect.VcfAnnotator
setConfig, setDebug, setVerbose
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Field Detail
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SUMMARY_TEMPLATE
public static final java.lang.String SUMMARY_TEMPLATE
- See Also:
- Constant Field Values
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SUMMARY_CSV_TEMPLATE
public static final java.lang.String SUMMARY_CSV_TEMPLATE
- See Also:
- Constant Field Values
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SUMMARY_GENES_TEMPLATE
public static final java.lang.String SUMMARY_GENES_TEMPLATE
- See Also:
- Constant Field Values
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DEFAULT_SUMMARY_HTML_FILE
public static final java.lang.String DEFAULT_SUMMARY_HTML_FILE
- See Also:
- Constant Field Values
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DEFAULT_SUMMARY_CSV_FILE
public static final java.lang.String DEFAULT_SUMMARY_CSV_FILE
- See Also:
- Constant Field Values
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DEFAULT_SUMMARY_GENES_FILE
public static final java.lang.String DEFAULT_SUMMARY_GENES_FILE
- 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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addHeaders
public boolean addHeaders(VcfFileIterator vcfFile)
Description copied from interface:VcfAnnotator
Add annotation headers to VCF file- Specified by:
addHeaders
in interfaceVcfAnnotator
- Returns:
- true if OK, false on error
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annotate
public boolean annotate(java.lang.String inputFile, java.lang.String outputFile)
Annotate: Calculate the effect of variants and show results
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annotate
public boolean annotate(VcfEntry vcfEntry)
Annotate a VCF entry- Specified by:
annotate
in interfaceVcfAnnotator
- Returns:
- true if the entry was annotated
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annotateFinish
public boolean annotateFinish(VcfFileIterator vcfFile)
Finish annotations and create reports- Specified by:
annotateFinish
in interfaceVcfAnnotator
- Returns:
- true if OK, false on error
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annotateInit
protected void annotateInit(java.lang.String outputFile)
Calculate the effect of variants and show results
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annotateInit
public boolean annotateInit(VcfFileIterator vcfFile)
Description copied from interface:VcfAnnotator
Initialize annotator: This method is called after vcfFile is opened, but before the header is output. The first vcfEntry might have (and often has) already been read from the file.- Specified by:
annotateInit
in interfaceVcfAnnotator
- Returns:
- true if OK, false on error
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getChangeEffectResutStats
public VariantEffectStats getChangeEffectResutStats()
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getTotalErrs
public int getTotalErrs()
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getvariantStats
public VariantStats getvariantStats()
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parseArgs
public void parseArgs(java.lang.String[] args)
Parse command line arguments- Specified by:
parseArgs
in interfaceCommandLine
- Overrides:
parseArgs
in classSnpEff
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reportValues
public java.util.HashMap<java.lang.String,java.lang.String> reportValues()
Description copied from class:SnpEff
Additional values to be reported- Overrides:
reportValues
in classSnpEff
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run
public boolean run()
Run according to command line options- Specified by:
run
in interfaceCommandLine
- Overrides:
run
in classSnpEff
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run
public java.util.List<VcfEntry> run(boolean createList)
Run according to command line options
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setFormatVersion
public void setFormatVersion(EffFormatVersion formatVersion)
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usage
public void usage(java.lang.String message)
Show 'usage;' message and exit with an error code '-1'- Specified by:
usage
in interfaceCommandLine
- Overrides:
usage
in classSnpEff
- Parameters:
message
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