Package org.snpeff

Class SnpEff

java.lang.Object
org.snpeff.SnpEff
All Implemented Interfaces:
CommandLine
Direct Known Subclasses:
SnpEffCmdAcat, SnpEffCmdBuild, SnpEffCmdBuildNextProt, SnpEffCmdCds, SnpEffCmdClosest, SnpEffCmdCount, SnpEffCmdDatabases, SnpEffCmdDownload, SnpEffCmdDump, SnpEffCmdEff, SnpEffCmdGenes2Bed, SnpEffCmdGsa, SnpEffCmdLen, SnpEffCmdPdb, SnpEffCmdProtein, SnpEffCmdSeq, SnpEffCmdShow, SnpEffCmdSpliceAnalysis, SnpEffCmdTranslocationsReport

public class SnpEff extends Object implements CommandLine
SnpEff's main command line program
Author:
pcingola
  • Field Details

    • DEFAULT_COMMAND

      public static final String DEFAULT_COMMAND
      See Also:
    • COMMAND_LINE_WIDTH

      public static final int COMMAND_LINE_WIDTH
      See Also:
    • SOFTWARE_NAME

      public static final String SOFTWARE_NAME
      See Also:
    • REVISION

      public static final String REVISION
      See Also:
    • BUILD

      public static final String BUILD
      See Also:
    • BUILD_DATE

      public static final String BUILD_DATE
      See Also:
    • VERSION_MAJOR

      public static final String VERSION_MAJOR
      See Also:
    • VERSION_SHORT

      public static final String VERSION_SHORT
      See Also:
    • VERSION_BUILD

      public static final String VERSION_BUILD
      See Also:
    • VERSION_AUTHOR

      public static final String VERSION_AUTHOR
      See Also:
    • VERSION

      public static final String VERSION
      See Also:
    • command

      protected String command
    • args

      protected String[] args
    • shiftArgs

      protected String[] shiftArgs
    • canonical

      protected boolean canonical
    • debug

      protected boolean debug
    • download

      protected boolean download
    • expandIub

      protected boolean expandIub
    • help

      protected boolean help
    • hgvs

      protected boolean hgvs
    • hgvsForce

      protected boolean hgvsForce
    • hgvsOneLetterAa

      protected boolean hgvsOneLetterAa
    • hgvsOld

      protected boolean hgvsOld
    • hgvsShift

      protected boolean hgvsShift
    • hgvsTrId

      protected boolean hgvsTrId
    • interaction

      protected boolean interaction
    • log

      protected boolean log
    • motif

      protected boolean motif
    • multiThreaded

      protected boolean multiThreaded
    • nextProt

      protected boolean nextProt
    • nextProtKeepAllTrs

      protected boolean nextProtKeepAllTrs
    • noGenome

      protected boolean noGenome
    • onlyProtein

      protected boolean onlyProtein
    • onlyRegulation

      protected boolean onlyRegulation
    • quiet

      protected boolean quiet
    • strict

      protected boolean strict
    • saveOutput

      protected boolean saveOutput
    • suppressOutput

      protected boolean suppressOutput
    • verbose

      protected boolean verbose
    • treatAllAsProteinCoding

      protected Boolean treatAllAsProteinCoding
    • numWorkers

      protected int numWorkers
    • spliceSiteSize

      protected int spliceSiteSize
    • spliceRegionExonSize

      protected int spliceRegionExonSize
    • spliceRegionIntronMin

      protected int spliceRegionIntronMin
    • spliceRegionIntronMax

      protected int spliceRegionIntronMax
    • upDownStreamLength

      protected int upDownStreamLength
    • configFile

      protected String configFile
    • dataDir

      protected String dataDir
    • genomeVer

      protected String genomeVer
    • onlyTranscriptsFile

      protected String onlyTranscriptsFile
    • canonicalFile

      protected String canonicalFile
    • maxTranscriptSupportLevel

      protected TranscriptSupportLevel maxTranscriptSupportLevel
    • output

      protected StringBuilder output
    • config

      protected Config config
    • genome

      protected Genome genome
    • snpEffCmd

      protected SnpEff snpEffCmd
    • customIntervalFiles

      protected ArrayList<String> customIntervalFiles
    • filterIntervalFiles

      protected ArrayList<String> filterIntervalFiles
    • regulationTracks

      protected HashSet<String> regulationTracks
    • configOverride

      protected Map<String,String> configOverride
  • Constructor Details

    • SnpEff

      public SnpEff()
    • SnpEff

      public SnpEff(String[] args)
  • Method Details

    • main

      public static void main(String[] args)
      Main
    • addRegulationTrack

      public void addRegulationTrack(String cellType)
    • canonical

      protected void canonical()
      Filter canonical transcripts
    • cmd

      public SnpEff cmd()
      Create an appropriate SnpEffCmd* object
    • commandLineStr

      protected String commandLineStr(boolean splitLines)
      Command line argument list (try to fit it into COMMAND_LINE_WIDTH)
    • getArgs

      public String[] getArgs()
      Specified by:
      getArgs in interface CommandLine
    • getConfig

      public Config getConfig()
    • getConfigFile

      public String getConfigFile()
    • getOutput

      public String getOutput()
    • isOpt

      protected boolean isOpt(String arg)
      Is this a command line option (e.g. "-tfam" is a command line option, but "-" means STDIN)
    • load

      public void load()
    • loadConfig

      protected void loadConfig()
      Read config file
    • loadCustomFile

      protected int loadCustomFile(String fileName)
      Read a custom interval file
    • loadDb

      public void loadDb()
      Load database
    • loadMarkers

      protected Markers loadMarkers(String fileName)
      Read markers file Supported formats: BED, TXT, BigBed, GFF
    • parseArgs

      public void parseArgs(String[] args)
      Parse command line arguments
      Specified by:
      parseArgs in interface CommandLine
    • reportValues

      public HashMap<String,String> reportValues()
      Additional values to be reported
    • run

      public boolean run()
      Run according to command line options
      Specified by:
      run in interface CommandLine
    • run

      protected boolean run(SnpEff snpEff, String[] args, StringBuilder err)
      Run a SnpEff (usually a sub-class)
    • setCanonical

      public void setCanonical(boolean canonical)
    • setConfig

      public void setConfig(Config config)
    • setConfigFile

      public void setConfigFile(String configFile)
    • setDebug

      public void setDebug(boolean debug)
    • setGenomeVer

      public void setGenomeVer(String genomeVer)
    • setLog

      public void setLog(boolean log)
    • setNextProt

      public void setNextProt(boolean nextProt)
    • setNextProtKeepAllTrs

      public void setNextProtKeepAllTrs(boolean nextProtKeepAllTrs)
    • setShiftHgvs

      public void setShiftHgvs(boolean shiftHgvs)
    • setSpliceSiteSize

      public void setSpliceSiteSize(int spliceSiteSize)
    • setSupressOutput

      public void setSupressOutput(boolean suppressOutput)
    • setUpDownStreamLength

      public void setUpDownStreamLength(int upDownStreamLength)
    • setVerbose

      public void setVerbose(boolean verbose)
    • usage

      public void usage(String message)
      Show 'usage' message and exit with an error code '-1'
      Specified by:
      usage in interface CommandLine
    • usageDb

      protected void usageDb()
      Show database load and build options
    • usageGeneric

      protected void usageGeneric()
      Show generic options
    • usageGenericAndDb

      protected void usageGenericAndDb()