Package org.snpeff.snpEffect.commandLine

Class SnpEffCmdEff

java.lang.Object

org.snpeff.SnpEff

org.snpeff.snpEffect.commandLine.SnpEffCmdEff

All Implemented Interfaces:

CommandLine, VcfAnnotator

public class SnpEffCmdEff
extends SnpEff
implements VcfAnnotator

Command line program: Predict variant effects

Author:

Pablo Cingolani

Nested Class Summary

Nested classes/interfaces inherited from class org.snpeff.SnpEff

SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat

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
static java.lang.String	TEMPLATES_DIR

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

Constructor Summary

Constructors

Constructor	Description
SnpEffCmdEff()

Method Summary

Modifier and Type	Method	Description
boolean	addHeaders(VcfFileIterator vcfFile)	Add annotation headers to VCF file
boolean	annotate(java.lang.String inputFile, java.lang.String outputFile)	Annotate: Calculate the effect of variants and show results
boolean	annotate(VcfEntry vcfEntry)	Annotate a VCF entry
boolean	annotateFinish(VcfFileIterator vcfFile)	Finish annotations and create reports
protected void	annotateInit(java.lang.String outputFile)	Calculate the effect of variants and show results
boolean	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 arguments
java.util.HashMap<java.lang.String,java.lang.String>	reportValues()	Additional values to be reported
boolean	run()	Run according to command line options
java.util.List<VcfEntry>	run(boolean createList)	Run according to command line options
void	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, 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

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.snpeff.snpEffect.commandLine.CommandLine

getArgs

Methods inherited from interface org.snpeff.snpEffect.VcfAnnotator

setConfig, setDebug, setVerbose

Field Detail

TEMPLATES_DIR

public static final java.lang.String TEMPLATES_DIR

See Also:

Constant Field Values

SUMMARY_TEMPLATE

public static final java.lang.String SUMMARY_TEMPLATE

See Also:

Constant Field Values

SUMMARY_CSV_TEMPLATE

public static final java.lang.String SUMMARY_CSV_TEMPLATE

See Also:

Constant Field Values

SUMMARY_GENES_TEMPLATE

public static final java.lang.String SUMMARY_GENES_TEMPLATE

See Also:

Constant Field Values

DEFAULT_SUMMARY_HTML_FILE

public static final java.lang.String DEFAULT_SUMMARY_HTML_FILE

See Also:

Constant Field Values

DEFAULT_SUMMARY_CSV_FILE

public static final java.lang.String DEFAULT_SUMMARY_CSV_FILE

See Also:

Constant Field Values

DEFAULT_SUMMARY_GENES_FILE

public static final java.lang.String DEFAULT_SUMMARY_GENES_FILE

See Also:

Constant Field Values

SHOW_EVERY

public static final int SHOW_EVERY

See Also:

Constant Field Values

Constructor Detail

SnpEffCmdEff

public SnpEffCmdEff()

Method Detail

addHeaders

public boolean addHeaders(VcfFileIterator vcfFile)

Description copied from interface: VcfAnnotator

Add annotation headers to VCF file

Specified by:

addHeaders in interface VcfAnnotator

Returns:

true if OK, false on error

annotate

public boolean annotate(java.lang.String inputFile,
                        java.lang.String outputFile)

Annotate: Calculate the effect of variants and show results

annotate

public boolean annotate(VcfEntry vcfEntry)

Annotate a VCF entry

Specified by:

annotate in interface VcfAnnotator

Returns:

true if the entry was annotated

annotateFinish

public boolean annotateFinish(VcfFileIterator vcfFile)

Finish annotations and create reports

Specified by:

annotateFinish in interface VcfAnnotator

Returns:

true if OK, false on error

annotateInit

protected void annotateInit(java.lang.String outputFile)

Calculate the effect of variants and show results

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 interface VcfAnnotator

Returns:

true if OK, false on error

getChangeEffectResutStats

public VariantEffectStats getChangeEffectResutStats()

getTotalErrs

public int getTotalErrs()

getvariantStats

public VariantStats getvariantStats()

parseArgs

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

Parse command line arguments

Specified by:

parseArgs in interface CommandLine

Overrides:

parseArgs in class SnpEff

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 class SnpEff

run

public boolean run()

Run according to command line options

Specified by:

run in interface CommandLine

Overrides:

run in class SnpEff

run

public java.util.List<VcfEntry> run(boolean createList)

Run according to command line options

setFormatVersion

public void setFormatVersion(EffFormatVersion formatVersion)

usage

public void usage(java.lang.String message)

Show 'usage;' message and exit with an error code '-1'

Specified by:

usage in interface CommandLine

Overrides:

usage in class SnpEff

Parameters:

message -