Class Config

java.lang.Object
org.snpeff.snpEffect.Config
All Implemented Interfaces:
Serializable, Iterable<String>

public class Config extends Object implements Serializable, Iterable<String>
See Also:
  • Field Details

  • Constructor Details

    • Config

      public Config(Genome genome)
      This constructor is used in test cases
    • Config

      public Config(String genomeVersion)
      Create a config (uses DEFAULT_CONFIG_FILE)
    • Config

      public Config(String genomeVersion, String configFileName)
      Create a configuration from 'configFileName'
    • Config

      public Config(String genomeVersion, String configFileName, String dataDir, Map<String,String> override)
      Create a configuration from 'configFileName'
    • Config

      public Config(String genomeVersion, String configFileName, String dataDir, Map<String,String> override, boolean verbose)
  • Method Details

    • get

      public static Config get()
    • reset

      public static Config reset()
    • defaultConfigFile

      public static String defaultConfigFile()
      If Debian-preferred config file is available, give it. else, if the config file in /etc/snpeff is available, give it. Else, default to DEFAULT_CONFIG_FILE.
    • downloadUrl

      public List<URL> downloadUrl(String genomeVer)
      Get a list of URLs that can be used to download a database Use compatible versions from 'getDatabaseCompatibilityVersions()'
    • downloadUrl

      public URL downloadUrl(String genomeVer, String version)
      Build the URL for downloading a database file

      Format : DatabaseRepository / v VERSION / snpEff_v VERSION _ genomeVersion .zip Example : http://downloads.sourceforge.net/project/snpeff/databases/v2_0_3/snpEff_v2_0_3_EF3.64.zip

    • getBaseFileNameGenes

      public String getBaseFileNameGenes()
      Genes file path (no extension)
    • getBaseFileNameMotif

      public String getBaseFileNameMotif()
    • getBaseFileNameRegulation

      public String getBaseFileNameRegulation()
      Regulation file (GFF format)
    • getBaseFileNameSequence

      public String getBaseFileNameSequence()
    • getBundleName

      public String getBundleName(String genomeVer)
      Is this genome packed in a bundle?
    • getConfigFileName

      public String getConfigFileName()
    • getConfigFileCanonicaPath

      public String getConfigFileCanonicaPath()
    • getCoordinates

      public String getCoordinates()
    • getDatabaseCompatibilityVersions

      public List<String> getDatabaseCompatibilityVersions()
      Return a list of databases that are compatible with this SnpEff version number
    • getDatabaseLocal

      public String getDatabaseLocal(String dbName)
      Database local file for a specific database, such as 'dbSnp', 'ClinVar', etc.
    • getDatabaseLocalKey

      public String getDatabaseLocalKey(String dbName)
    • getDatabaseRepository

      public String getDatabaseRepository()
    • getDatabaseRepository

      public String getDatabaseRepository(String dbName)
      Database repository for a specific database, such as 'dbSnp', 'ClinVar', etc.
    • getDatabaseRepositoryUrl

      public URL getDatabaseRepositoryUrl(String dbName)
    • getDbNsfpFields

      public String getDbNsfpFields()
    • getDirData

      public String getDirData()
      Main data directory
    • getDirDataGenomeVersion

      public String getDirDataGenomeVersion()
      Data dir for a specific genome version (i.e. where the database is)
    • getDirMain

      public String getDirMain()
      Main dir
    • getDirRegulationBed

      public String getDirRegulationBed()
      Directory where regulation 'BED' files are
    • getDouble

      public double getDouble(String propertyName, double defaultValue)
      Get a property as a double
    • getFileListGenomeFasta

      public List<String> getFileListGenomeFasta()
      Filenames for reference sequence (fasta files)
    • getFileNameCds

      public String getFileNameCds()
    • getFileNameGenomeFasta

      public String getFileNameGenomeFasta()
      Filename for reference sequence (fasta file) Scans the list of files 'getFileListGenomeFasta()' and finds the first file that exists
    • getFileNameProteins

      public String getFileNameProteins()
    • getFileNameSequence

      public String getFileNameSequence()
    • getFileNameSequence

      public String getFileNameSequence(String chr)
    • getFileSnpEffectPredictor

      public String getFileSnpEffectPredictor()
    • getGenome

      public Genome getGenome()
    • getGenome

      public Genome getGenome(String genomeId)
    • getGenomeVersion

      public String getGenomeVersion()
    • getLofDeleteProteinCodingBases

      public double getLofDeleteProteinCodingBases()
    • getLofIgnoreProteinCodingAfter

      public double getLofIgnoreProteinCodingAfter()
    • getLofIgnoreProteinCodingBefore

      public double getLofIgnoreProteinCodingBefore()
    • getLong

      public long getLong(String propertyName, long defaultValue)
      Get a property as a long
    • getName

      public String getName(String genomeVersion)
    • getProperty

      public String getProperty(String property)
    • propertyToStringArray

      public String[] propertyToStringArray(String attr)
      Parse a comma separated property as a string array
    • getReference

      public String getReference(String genomeVersion)
    • getSnpEffectPredictor

      public SnpEffectPredictor getSnpEffectPredictor()
    • setSnpEffectPredictor

      public void setSnpEffectPredictor(SnpEffectPredictor snpEffectPredictor)
    • getString

      public String getString(String propertyName)
      Get a property as a string
    • getString

      public String getString(String propertyName, String defaultValue)
      Get a property as a string
    • getVersionsUrl

      public String getVersionsUrl()
    • isDebug

      public boolean isDebug()
    • setDebug

      public void setDebug(boolean debug)
    • isErrorChromoHit

      public boolean isErrorChromoHit()
    • setErrorChromoHit

      public void setErrorChromoHit(boolean errorChromoHit)
    • isErrorOnMissingChromo

      public boolean isErrorOnMissingChromo()
    • setErrorOnMissingChromo

      public void setErrorOnMissingChromo(boolean errorOnMissingChromo)
    • isExpandIub

      public boolean isExpandIub()
    • setExpandIub

      public void setExpandIub(boolean expandIub)
    • isHgvs

      public boolean isHgvs()
    • isHgvs1LetterAA

      public boolean isHgvs1LetterAA()
    • isHgvsOld

      public boolean isHgvsOld()
    • setHgvsOld

      public void setHgvsOld(boolean hgvsDnaOld)
    • isHgvsShift

      public boolean isHgvsShift()
    • setHgvsShift

      public void setHgvsShift(boolean hgvsShift)
    • isHgvsTrId

      public boolean isHgvsTrId()
    • setHgvsTrId

      public void setHgvsTrId(boolean hgvsTrId)
    • isOnlyRegulation

      public boolean isOnlyRegulation()
    • setOnlyRegulation

      public void setOnlyRegulation(boolean onlyRegulation)
    • isQuiet

      public boolean isQuiet()
    • setQuiet

      public void setQuiet(boolean quiet)
    • isTreatAllAsProteinCoding

      public boolean isTreatAllAsProteinCoding()
    • setTreatAllAsProteinCoding

      public void setTreatAllAsProteinCoding(boolean treatAllAsProteinCoding)
    • isVerbose

      public boolean isVerbose()
    • setVerbose

      public void setVerbose(boolean verbose)
    • iterator

      public Iterator<String> iterator()
      Specified by:
      iterator in interface Iterable<String>
    • keys

      public List<String> keys()
    • loadSnpEffectPredictor

      public SnpEffectPredictor loadSnpEffectPredictor()
      Load a snpEff predictor WARNING: 'genome' object get replaced upon loading a snpEffectPredictor (this is a dangerous side effect)
    • setHgvsOneLetterAA

      public void setHgvsOneLetterAA(boolean hgvsOneLetterAa)
    • setString

      public void setString(String propertyName, String value)
    • setUseHgvs

      public void setUseHgvs(boolean useHgvs)
    • toString

      public String toString()
      Overrides:
      toString in class Object