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()