Package org.snpeff.snpEffect

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()

    • 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)

    • 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