Package org.snpsift.fileIterator
Class DbNsfp
java.lang.Object
org.snpsift.fileIterator.DbNsfp
- All Implemented Interfaces:
DbMarker<org.snpeff.interval.Variant,
DbNsfpEntry>
DbNSFP database:
Reference https://sites.google.com/site/jpopgen/dbNSFP
- Author:
- pcingola, lletourn (original author)
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String
protected int
protected int
static final String
static final String
static final String
static final String
static final String
static final int
static final int
protected boolean
protected String[]
protected String
protected org.snpeff.interval.Genome
static final String
protected List
<DbNsfpEntry> protected org.snpeff.interval.Marker
protected int
protected boolean[]
static final String
protected int
protected int
static final String
static final String
static final char
static final char
protected htsjdk.tribble.readers.TabixReader
protected org.snpeff.vcf.VcfInfoType[]
protected boolean
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
close()
Close database, free resourcesprotected boolean
Guess field types: Read many lines and guess the data type for each columnvoid
Force missing types as stringint
org.snpeff.interval.Chromosome
getChromosome
(String chromoName) Find chromosome 'chromoName'.int
int
int
getFieldName
(int idx) String[]
int
int
int
org.snpeff.vcf.VcfInfoType[]
getTypes()
protected org.snpeff.vcf.VcfInfoType
guessDataType
(String value) Guess value typeprotected boolean
Guess data types from fileboolean
Do we have a column 'colName'?protected boolean
Initialize tabix readerprotected boolean
match
(org.snpeff.interval.Variant var, DbNsfpEntry dbEntry) Does database entry 'DbNsfpEntry' match 'variant'?void
open()
Open database (load index in memory if required)query
(org.snpeff.interval.Variant variant) Query tabix file to get dbNsfp entries (or cached entries from latest results)protected void
saveDataTypesCache
(String cacheFileName) Save data types to cache filevoid
setDebug
(boolean debug) void
setVerbose
(boolean verbose)
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Field Details
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DATA_TYPES_CACHE_EXT
- See Also:
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DATA_TYPES_MIN_LINES
public static final int DATA_TYPES_MIN_LINES- See Also:
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DATA_TYPES_MAX_LINES
public static final int DATA_TYPES_MAX_LINES- See Also:
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HEADER_PREFIX
- See Also:
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COLUMN_SEPARATOR
- See Also:
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SUBFIELD_SEPARATOR_CHAR
public static final char SUBFIELD_SEPARATOR_CHAR- See Also:
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SUBFIELD_SEPARATOR
- See Also:
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SUBFIELD_SEPARATOR_CHAR_2
public static final char SUBFIELD_SEPARATOR_CHAR_2- See Also:
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SUBFIELD_SEPARATOR_2
- See Also:
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COLUMN_CHR_NAME
- See Also:
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COLUMN_POS_NAME_v2
- See Also:
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COLUMN_POS_NAME_v3
- See Also:
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ALT_NAME
- See Also:
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REF_NAME
- See Also:
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fileName
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debug
protected boolean debug -
multipleValues
protected boolean[] multipleValues -
verbose
protected boolean verbose -
chromosomeIdx
protected int chromosomeIdx -
startIdx
protected int startIdx -
altIdx
protected int altIdx -
refIdx
protected int refIdx -
maxChrPosRefAltIdx
protected int maxChrPosRefAltIdx -
fieldNames
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types
protected org.snpeff.vcf.VcfInfoType[] types -
genome
protected org.snpeff.interval.Genome genome -
names2index
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tabixReader
protected htsjdk.tribble.readers.TabixReader tabixReader -
latestResults
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latestResultsInterval
protected org.snpeff.interval.Marker latestResultsInterval
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Constructor Details
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DbNsfp
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Method Details
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close
public void close()Description copied from interface:DbMarker
Close database, free resources- Specified by:
close
in interfaceDbMarker<org.snpeff.interval.Variant,
DbNsfpEntry>
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dataTypes
protected boolean dataTypes()Guess field types: Read many lines and guess the data type for each column -
forceMissingTypesAsString
public void forceMissingTypesAsString()Force missing types as string -
getAltIdx
public int getAltIdx() -
getChrPosRefAltIdx
public int getChrPosRefAltIdx() -
getChromosome
Find chromosome 'chromoName'. If it does not exists and 'createChromos' is true, the chromosome is created -
getChromosomeIdx
public int getChromosomeIdx() -
getFieldCount
public int getFieldCount() -
getFieldName
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getFieldNames
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getFieldNamesSorted
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getIndex
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getNames2index
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getRefIdx
public int getRefIdx() -
getStartIdx
public int getStartIdx() -
getTypes
public org.snpeff.vcf.VcfInfoType[] getTypes() -
guessDataType
Guess value type -
guessDataTypes
protected boolean guessDataTypes()Guess data types from file -
hasField
Do we have a column 'colName'? -
initTabix
Initialize tabix reader -
match
Does database entry 'DbNsfpEntry' match 'variant'? -
open
public void open()Description copied from interface:DbMarker
Open database (load index in memory if required)- Specified by:
open
in interfaceDbMarker<org.snpeff.interval.Variant,
DbNsfpEntry>
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query
Query tabix file to get dbNsfp entries (or cached entries from latest results)- Specified by:
query
in interfaceDbMarker<org.snpeff.interval.Variant,
DbNsfpEntry> - Parameters:
variant
- : Variant to query in DnNSFP- Returns:
- A list of result
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saveDataTypesCache
Save data types to cache file -
setDebug
public void setDebug(boolean debug) - Specified by:
setDebug
in interfaceDbMarker<org.snpeff.interval.Variant,
DbNsfpEntry>
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setVerbose
public void setVerbose(boolean verbose) - Specified by:
setVerbose
in interfaceDbMarker<org.snpeff.interval.Variant,
DbNsfpEntry>
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