Package org.snpeff.snpEffect
Class Config
- java.lang.Object
-
- org.snpeff.snpEffect.Config
-
- All Implemented Interfaces:
java.io.Serializable
,java.lang.Iterable<java.lang.String>
public class Config extends java.lang.Object implements java.io.Serializable, java.lang.Iterable<java.lang.String>
- See Also:
- Serialized Form
-
-
Field Summary
Fields Modifier and Type Field Description static java.lang.String[]
COMPATIBLE_WITH_5_1
static java.util.Map<java.lang.String,java.lang.String[]>
DATABASE_COMPATIBLE_VERSIONS
static java.lang.String
DEFAULT_CONFIG_FILE
static java.lang.String
DEFAULT_COORDINATES
static java.lang.String
DEFAULT_DATA_DIR
static java.lang.String
ETC_CONFIG_FILE
static java.lang.String
GENOMES_DIR
static java.lang.String
KEY_BUNDLE_SUFIX
static java.lang.String
KEY_CODON_PREFIX
static java.lang.String
KEY_CODONTABLE_SUFIX
static java.lang.String
KEY_COORDINATES
static java.lang.String
KEY_DATA_DIR
static java.lang.String
KEY_DATABASE_LOCAL
static java.lang.String
KEY_DATABASE_REPOSITORY
static java.lang.String
KEY_DATABASE_REPOSITORY_KEY
static java.lang.String
KEY_DBNSFP_FIELDS
static java.lang.String
KEY_GENOME_SUFIX
static java.lang.String
KEY_LOF_DELETE_PROTEIN_CODING_BASES
static java.lang.String
KEY_LOF_IGNORE_PROTEIN_CODING_AFTER
static java.lang.String
KEY_LOF_IGNORE_PROTEIN_CODING_BEFORE
static java.lang.String
KEY_REFERENCE_SUFIX
static java.lang.String
KEY_VERSIONS_URL
static java.lang.String
PREFERRED_CONFIG_FILE
-
Constructor Summary
Constructors Constructor Description Config(java.lang.String genomeVersion)
Create a config (uses DEFAULT_CONFIG_FILE)Config(java.lang.String genomeVersion, java.lang.String configFileName)
Create a configuration from 'configFileName'Config(java.lang.String genomeVersion, java.lang.String configFileName, java.lang.String dataDir, java.util.Map<java.lang.String,java.lang.String> override)
Create a configuration from 'configFileName'Config(java.lang.String genomeVersion, java.lang.String configFileName, java.lang.String dataDir, java.util.Map<java.lang.String,java.lang.String> override, boolean verbose)
Config(Genome genome)
This constructor is used in test cases
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static java.lang.String
defaultConfigFile()
If Debian-preferred config file is available, give it.java.util.List<java.net.URL>
downloadUrl(java.lang.String genomeVer)
Get a list of URLs that can be used to download a database Use compatible versions from 'getDatabaseCompatibilityVersions()'java.net.URL
downloadUrl(java.lang.String genomeVer, java.lang.String version)
Build the URL for downloading a database filestatic Config
get()
java.lang.String
getBaseFileNameGenes()
Genes file path (no extension)java.lang.String
getBaseFileNameMotif()
java.lang.String
getBaseFileNameRegulation()
Regulation file (GFF format)java.lang.String
getBaseFileNameSequence()
java.lang.String
getBundleName(java.lang.String genomeVer)
Is this genome packed in a bundle?java.lang.String
getConfigFileName()
java.lang.String
getCoordinates()
java.util.List<java.lang.String>
getDatabaseCompatibilityVersions()
Return a list of databases that are compatible with this SnpEff version numberjava.lang.String
getDatabaseLocal(java.lang.String dbName)
Database local file for a specific database, such as 'dbSnp', 'ClinVar', etc.java.lang.String
getDatabaseLocalKey(java.lang.String dbName)
java.lang.String
getDatabaseRepository()
java.lang.String
getDatabaseRepository(java.lang.String dbName)
Database repository for a specific database, such as 'dbSnp', 'ClinVar', etc.java.net.URL
getDatabaseRepositoryUrl(java.lang.String dbName)
java.lang.String
getDbNsfpFields()
java.lang.String
getDirData()
Main data directoryjava.lang.String
getDirDataGenomeVersion()
Data dir for a specific genome version (i.e.java.lang.String
getDirMain()
Main dirjava.lang.String
getDirRegulationBed()
Directory where regulation 'BED' files aredouble
getDouble(java.lang.String propertyName, double defaultValue)
Get a property as a doublejava.util.List<java.lang.String>
getFileListGenomeFasta()
Filenames for reference sequence (fasta files)java.lang.String
getFileNameCds()
java.lang.String
getFileNameGenomeFasta()
Filename for reference sequence (fasta file) Scans the list of files 'getFileListGenomeFasta()' and finds the first file that existsjava.lang.String
getFileNameProteins()
java.lang.String
getFileNameSequence()
java.lang.String
getFileNameSequence(java.lang.String chr)
java.lang.String
getFileSnpEffectPredictor()
Genome
getGenome()
Genome
getGenome(java.lang.String genomeId)
java.lang.String
getGenomeVersion()
double
getLofDeleteProteinCodingBases()
double
getLofIgnoreProteinCodingAfter()
double
getLofIgnoreProteinCodingBefore()
long
getLong(java.lang.String propertyName, long defaultValue)
Get a property as a longjava.lang.String
getName(java.lang.String genomeVersion)
java.lang.String
getReference(java.lang.String genomeVersion)
SnpEffectPredictor
getSnpEffectPredictor()
java.lang.String
getString(java.lang.String propertyName)
Get a property as a stringjava.lang.String
getString(java.lang.String propertyName, java.lang.String defaultValue)
Get a property as a stringjava.lang.String
getVersionsUrl()
boolean
isDebug()
boolean
isErrorChromoHit()
boolean
isErrorOnMissingChromo()
boolean
isExpandIub()
boolean
isHgvs()
boolean
isHgvs1LetterAA()
boolean
isHgvsOld()
boolean
isHgvsShift()
boolean
isHgvsTrId()
boolean
isOnlyRegulation()
boolean
isQuiet()
boolean
isTreatAllAsProteinCoding()
boolean
isVerbose()
java.util.Iterator<java.lang.String>
iterator()
java.util.List<java.lang.String>
keys()
SnpEffectPredictor
loadSnpEffectPredictor()
Load a snpEff predictor WARNING: 'genome' object get replaced upon loading a snpEffectPredictor (this is a dangerous side effect)static Config
reset()
void
setDebug(boolean debug)
void
setErrorChromoHit(boolean errorChromoHit)
void
setErrorOnMissingChromo(boolean errorOnMissingChromo)
void
setExpandIub(boolean expandIub)
void
setHgvsOld(boolean hgvsDnaOld)
void
setHgvsOneLetterAA(boolean hgvsOneLetterAa)
void
setHgvsShift(boolean hgvsShift)
void
setHgvsTrId(boolean hgvsTrId)
void
setOnlyRegulation(boolean onlyRegulation)
void
setQuiet(boolean quiet)
void
setSnpEffectPredictor(SnpEffectPredictor snpEffectPredictor)
void
setString(java.lang.String propertyName, java.lang.String value)
void
setTreatAllAsProteinCoding(boolean treatAllAsProteinCoding)
void
setUseHgvs(boolean useHgvs)
void
setVerbose(boolean verbose)
java.lang.String
toString()
-
-
-
Field Detail
-
DEFAULT_CONFIG_FILE
public static final java.lang.String DEFAULT_CONFIG_FILE
- See Also:
- Constant Field Values
-
ETC_CONFIG_FILE
public static final java.lang.String ETC_CONFIG_FILE
- See Also:
- Constant Field Values
-
PREFERRED_CONFIG_FILE
public static final java.lang.String PREFERRED_CONFIG_FILE
-
DEFAULT_DATA_DIR
public static final java.lang.String DEFAULT_DATA_DIR
- See Also:
- Constant Field Values
-
KEY_BUNDLE_SUFIX
public static final java.lang.String KEY_BUNDLE_SUFIX
- See Also:
- Constant Field Values
-
KEY_CODON_PREFIX
public static final java.lang.String KEY_CODON_PREFIX
- See Also:
- Constant Field Values
-
KEY_CODONTABLE_SUFIX
public static final java.lang.String KEY_CODONTABLE_SUFIX
- See Also:
- Constant Field Values
-
KEY_COORDINATES
public static final java.lang.String KEY_COORDINATES
- See Also:
- Constant Field Values
-
KEY_DATA_DIR
public static final java.lang.String KEY_DATA_DIR
- See Also:
- Constant Field Values
-
KEY_DATABASE_LOCAL
public static final java.lang.String KEY_DATABASE_LOCAL
- See Also:
- Constant Field Values
-
KEY_DATABASE_REPOSITORY
public static final java.lang.String KEY_DATABASE_REPOSITORY
- See Also:
- Constant Field Values
-
KEY_DATABASE_REPOSITORY_KEY
public static final java.lang.String KEY_DATABASE_REPOSITORY_KEY
- See Also:
- Constant Field Values
-
KEY_DBNSFP_FIELDS
public static final java.lang.String KEY_DBNSFP_FIELDS
- See Also:
- Constant Field Values
-
KEY_GENOME_SUFIX
public static final java.lang.String KEY_GENOME_SUFIX
- See Also:
- Constant Field Values
-
KEY_LOF_IGNORE_PROTEIN_CODING_AFTER
public static final java.lang.String KEY_LOF_IGNORE_PROTEIN_CODING_AFTER
- See Also:
- Constant Field Values
-
KEY_LOF_IGNORE_PROTEIN_CODING_BEFORE
public static final java.lang.String KEY_LOF_IGNORE_PROTEIN_CODING_BEFORE
- See Also:
- Constant Field Values
-
KEY_LOF_DELETE_PROTEIN_CODING_BASES
public static final java.lang.String KEY_LOF_DELETE_PROTEIN_CODING_BASES
- See Also:
- Constant Field Values
-
KEY_REFERENCE_SUFIX
public static final java.lang.String KEY_REFERENCE_SUFIX
- See Also:
- Constant Field Values
-
KEY_VERSIONS_URL
public static final java.lang.String KEY_VERSIONS_URL
- See Also:
- Constant Field Values
-
COMPATIBLE_WITH_5_1
public static final java.lang.String[] COMPATIBLE_WITH_5_1
-
DATABASE_COMPATIBLE_VERSIONS
public static final java.util.Map<java.lang.String,java.lang.String[]> DATABASE_COMPATIBLE_VERSIONS
-
GENOMES_DIR
public static java.lang.String GENOMES_DIR
-
DEFAULT_COORDINATES
public static java.lang.String DEFAULT_COORDINATES
-
-
Constructor Detail
-
Config
public Config(Genome genome)
This constructor is used in test cases
-
Config
public Config(java.lang.String genomeVersion)
Create a config (uses DEFAULT_CONFIG_FILE)
-
Config
public Config(java.lang.String genomeVersion, java.lang.String configFileName)
Create a configuration from 'configFileName'
-
Config
public Config(java.lang.String genomeVersion, java.lang.String configFileName, java.lang.String dataDir, java.util.Map<java.lang.String,java.lang.String> override)
Create a configuration from 'configFileName'
-
Config
public Config(java.lang.String genomeVersion, java.lang.String configFileName, java.lang.String dataDir, java.util.Map<java.lang.String,java.lang.String> override, boolean verbose)
-
-
Method Detail
-
get
public static Config get()
-
reset
public static Config reset()
-
defaultConfigFile
public static java.lang.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 java.util.List<java.net.URL> downloadUrl(java.lang.String genomeVer)
Get a list of URLs that can be used to download a database Use compatible versions from 'getDatabaseCompatibilityVersions()'
-
downloadUrl
public java.net.URL downloadUrl(java.lang.String genomeVer, java.lang.String version)
Build the URL for downloading a database fileFormat : 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 java.lang.String getBaseFileNameGenes()
Genes file path (no extension)
-
getBaseFileNameMotif
public java.lang.String getBaseFileNameMotif()
-
getBaseFileNameRegulation
public java.lang.String getBaseFileNameRegulation()
Regulation file (GFF format)
-
getBaseFileNameSequence
public java.lang.String getBaseFileNameSequence()
-
getBundleName
public java.lang.String getBundleName(java.lang.String genomeVer)
Is this genome packed in a bundle?
-
getConfigFileName
public java.lang.String getConfigFileName()
-
getCoordinates
public java.lang.String getCoordinates()
-
getDatabaseCompatibilityVersions
public java.util.List<java.lang.String> getDatabaseCompatibilityVersions()
Return a list of databases that are compatible with this SnpEff version number
-
getDatabaseLocal
public java.lang.String getDatabaseLocal(java.lang.String dbName)
Database local file for a specific database, such as 'dbSnp', 'ClinVar', etc.
-
getDatabaseLocalKey
public java.lang.String getDatabaseLocalKey(java.lang.String dbName)
-
getDatabaseRepository
public java.lang.String getDatabaseRepository()
-
getDatabaseRepository
public java.lang.String getDatabaseRepository(java.lang.String dbName)
Database repository for a specific database, such as 'dbSnp', 'ClinVar', etc.
-
getDatabaseRepositoryUrl
public java.net.URL getDatabaseRepositoryUrl(java.lang.String dbName)
-
getDbNsfpFields
public java.lang.String getDbNsfpFields()
-
getDirData
public java.lang.String getDirData()
Main data directory
-
getDirDataGenomeVersion
public java.lang.String getDirDataGenomeVersion()
Data dir for a specific genome version (i.e. where the database is)
-
getDirMain
public java.lang.String getDirMain()
Main dir
-
getDirRegulationBed
public java.lang.String getDirRegulationBed()
Directory where regulation 'BED' files are
-
getDouble
public double getDouble(java.lang.String propertyName, double defaultValue)
Get a property as a double
-
getFileListGenomeFasta
public java.util.List<java.lang.String> getFileListGenomeFasta()
Filenames for reference sequence (fasta files)
-
getFileNameCds
public java.lang.String getFileNameCds()
-
getFileNameGenomeFasta
public java.lang.String getFileNameGenomeFasta()
Filename for reference sequence (fasta file) Scans the list of files 'getFileListGenomeFasta()' and finds the first file that exists
-
getFileNameProteins
public java.lang.String getFileNameProteins()
-
getFileNameSequence
public java.lang.String getFileNameSequence()
-
getFileNameSequence
public java.lang.String getFileNameSequence(java.lang.String chr)
-
getFileSnpEffectPredictor
public java.lang.String getFileSnpEffectPredictor()
-
getGenome
public Genome getGenome()
-
getGenome
public Genome getGenome(java.lang.String genomeId)
-
getGenomeVersion
public java.lang.String getGenomeVersion()
-
getLofDeleteProteinCodingBases
public double getLofDeleteProteinCodingBases()
-
getLofIgnoreProteinCodingAfter
public double getLofIgnoreProteinCodingAfter()
-
getLofIgnoreProteinCodingBefore
public double getLofIgnoreProteinCodingBefore()
-
getLong
public long getLong(java.lang.String propertyName, long defaultValue)
Get a property as a long
-
getName
public java.lang.String getName(java.lang.String genomeVersion)
-
getReference
public java.lang.String getReference(java.lang.String genomeVersion)
-
getSnpEffectPredictor
public SnpEffectPredictor getSnpEffectPredictor()
-
setSnpEffectPredictor
public void setSnpEffectPredictor(SnpEffectPredictor snpEffectPredictor)
-
getString
public java.lang.String getString(java.lang.String propertyName)
Get a property as a string
-
getString
public java.lang.String getString(java.lang.String propertyName, java.lang.String defaultValue)
Get a property as a string
-
getVersionsUrl
public java.lang.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 java.util.Iterator<java.lang.String> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<java.lang.String>
-
keys
public java.util.List<java.lang.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(java.lang.String propertyName, java.lang.String value)
-
setUseHgvs
public void setUseHgvs(boolean useHgvs)
-
toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
-
-