Index
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form
A
- ACGT - Static variable in class org.snpsift.util.RandomUtil
- action(RuleContext, int, int) - Method in class org.snpsift.antlr.SnpSiftLexer
- add(int, int, long) - Method in class org.snpsift.annotate.VcfIndexDataChromo
-
Add [start, end] => filePos
- add(String) - Method in class org.snpsift.annotate.mem.arrays.StringArrayBase
-
Add a string to the array WARNING: Typically you use either 'add' or 'set', but not both
- add(String) - Method in class org.snpsift.SnpSiftCmdAnnotateMem
-
Add a database file
- add(String, String) - Method in class org.snpsift.fileIterator.DbNsfpEntry
-
Add a value
- add(Marker) - Method in class org.snpsift.annotate.VcfIndexTree
- add(Markers) - Method in class org.snpsift.annotate.VcfIndexTree
- add(VariantVcfEntry) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
-
Add a VCF entry to the database
- add(VcfEntry, long) - Method in class org.snpsift.annotate.VcfIndex
-
Add an interval parse from 'line'
- add(VcfHeaderInfo) - Method in class org.snpsift.annotate.mem.Fields
- add(DataFrameRow) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
-
Add a row to the data frame
- addChild(Individual) - Method in class org.snpsift.pedigree.Individual
- addEffect(String) - Method in class org.snpsift.caseControl.VariantCounter
- addEnum(String) - Method in class org.snpsift.annotate.mem.arrays.EnumArray
-
Add an enum, return the ordinal
- addHeaders(VcfFileIterator) - Method in class org.snpsift.SnpSift
-
Add VCF headers
- addHeaders(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdDbNsfp
-
Add some lines to header before showing it
- addSet(String) - Method in class org.snpsift.SnpSiftCmdFilter
-
Read a file as a string set
- addSet(String) - Method in class org.snpsift.SnpSiftCmdFilterGt
-
Read a file as a string set
- ALT - Static variable in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
- ALT_NAME - Static variable in class org.snpsift.fileIterator.DbNsfp
- altIdx - Variable in class org.snpsift.fileIterator.DbNsfp
- And - Class in org.snpsift.lang.expression
-
And expression
- And(Expression, Expression) - Constructor for class org.snpsift.lang.expression.And
- annotate(Variant, Map<String, String>) - Method in class org.snpsift.SnpSiftCmdDbNsfp
-
Annotate a VCF entry
- annotate(VcfEntry) - Method in class org.snpsift.annotate.AnnotateVcfDb
-
Annotate a VCF entry
- annotate(VcfEntry) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
-
This method is used to annotate a VCF entry The annotations are added to the INFO field of the VCF entry
- annotate(VcfEntry) - Method in class org.snpsift.SnpSift
- annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdAnnotate
- annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdAnnotateMem
- annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdCaseControl
-
Annotate VCF entry
- annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdDbNsfp
- annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdFilter
- annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdGeneSets
-
Annotate one entry
- annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdGwasCatalog
- annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdPrivate
-
Parse a single VCF entry
- annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdVarType
-
Annotate one entry
- annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdVcfOperator
- annotate(VcfEntry, String[]) - Method in class org.snpsift.annotate.mem.database.VariantDataFrame
-
Annotate a VCF entry with the fields in this VariantDataFrame
- annotateDb - Variable in class org.snpsift.SnpSiftCmdAnnotate
- annotateEmpty - Variable in class org.snpsift.annotate.AnnotateVcfDb
- annotateEmpty - Variable in class org.snpsift.SnpSiftCmdAnnotate
- annotateEmpty - Variable in class org.snpsift.SnpSiftCmdDbNsfp
- annotateExists(VcfEntry) - Method in class org.snpsift.annotate.AnnotateVcfDb
-
Add 'exists' flag to INFO fields
- annotateFinish() - Method in class org.snpsift.SnpSiftCmdAnnotateMem
- annotateFinish(VcfFileIterator) - Method in class org.snpsift.SnpSift
- annotateFinish(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdDbNsfp
- annotateFinish(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdGwasCatalog
- annotateIds(VcfEntry, Set<String>) - Method in class org.snpsift.annotate.AnnotateVcfDb
-
Add ID information.
- annotateInfo(VcfEntry, Map<String, String>) - Method in class org.snpsift.annotate.AnnotateVcfDb
-
Add INFO fields.
- annotateInit(VcfFileIterator) - Method in class org.snpsift.SnpSift
- annotateInit(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdAnnotate
-
Initialize database for annotation process
- annotateInit(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdAnnotateMem
-
Initialize database for annotation process
- annotateInit(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdDbNsfp
-
Initialize annotation process
- annotateInit(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdFilter
- annotateInit(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdGeneSets
- annotateInit(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdGwasCatalog
- annotateInit(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdPrivate
- annotateMissing - Variable in class org.snpsift.SnpSiftCmdDbNsfp
- AnnotateVcfDb - Class in org.snpsift.annotate
-
Annotate using a VCF "database"
- AnnotateVcfDb() - Constructor for class org.snpsift.annotate.AnnotateVcfDb
- AnnotateVcfDbMem - Class in org.snpsift.annotate
-
Annotate using a VCF "database" Note: Reads and loads the whole VCF file into memory
- AnnotateVcfDbMem(String) - Constructor for class org.snpsift.annotate.AnnotateVcfDbMem
- AnnotateVcfDbSorted - Class in org.snpsift.annotate
-
Annotate using a VCF "database" Note: Assumes that the VCF database file is sorted.
- AnnotateVcfDbSorted(String, int) - Constructor for class org.snpsift.annotate.AnnotateVcfDbSorted
- AnnotateVcfDbTabix - Class in org.snpsift.annotate
-
Annotate using a tabix indexed VCF "database"
- AnnotateVcfDbTabix(String) - Constructor for class org.snpsift.annotate.AnnotateVcfDbTabix
- applyOp(List<Double>) - Method in class org.snpsift.SnpSiftCmdVcfOperator
- args - Variable in class org.snpsift.SnpSift
- asBool() - Method in class org.snpsift.lang.Value
- asFloat() - Method in class org.snpsift.lang.Value
- asInt() - Method in class org.snpsift.lang.Value
- assignOrder() - Method in class org.snpsift.pedigree.PedigreeDraw
-
Assign order
- asString() - Method in class org.snpsift.lang.Value
B
- benchmarkSortedVariantsVcfIterator(String) - Method in class org.snpsift.annotate.mem.Zzz
- benchmarkVcfIterator(String) - Method in class org.snpsift.annotate.mem.Zzz
- BOOL_LITERAL - Static variable in class org.snpsift.antlr.SnpSiftLexer
- BOOL_LITERAL - Static variable in class org.snpsift.antlr.SnpSiftParser
- BOOL_LITERAL() - Method in class org.snpsift.antlr.SnpSiftParser.LiteralBoolContext
- BoolArray - Class in org.snpsift.annotate.mem.arrays
-
A "memory efficient" boolean array Is is implemented as an array of bytes, where each bit is a boolean value.
- BoolArray(int) - Constructor for class org.snpsift.annotate.mem.arrays.BoolArray
- build() - Method in class org.snpsift.annotate.VcfIndexTree
- BUILD - Static variable in class org.snpsift.SnpSift
- bytes - Variable in class org.snpsift.annotate.mem.arrays.BoolArray
C
- calcDepth() - Method in class org.snpsift.pedigree.Individual
-
Depth in the graph.
- calcDepth() - Method in class org.snpsift.pedigree.PedigreeDraw
-
Max depth in this pedigree
- canBeFloat() - Method in class org.snpsift.lang.Value
- canBeInt() - Method in class org.snpsift.lang.Value
- canCompare(Value) - Method in class org.snpsift.lang.Value
-
Can these values be compared?
- capacity() - Method in class org.snpsift.annotate.mem.arrays.PosIndex
- caseControl - Variable in class org.snpsift.SnpSiftCmdCaseControl
- CaseControl - Static variable in class org.snpsift.caseControl.SnpSiftCmdCaseControlSummary
- channelNames - Static variable in class org.snpsift.antlr.SnpSiftLexer
- check() - Method in class org.snpsift.annotate.mem.arrays.PosIndex
-
Check that all positions are in non-decreasing order.
- check() - Method in class org.snpsift.annotate.mem.database.VariantDataFrame
-
This is used after creating the data to verify there are no issues with the dataFrames and indeces
- check() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
- check() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
-
Check data consistency
- checkFields(String[], boolean) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
-
Check that all `fieldNames` are available in `fields`
- checkFieldsToAdd() - Method in class org.snpsift.SnpSiftCmdDbNsfp
-
Check that all fields to add are available
- CHR1_NUM_ENTRIES - Static variable in class org.snpsift.annotate.mem.Zzz
- chrId - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- chromosomeIdx - Variable in class org.snpsift.fileIterator.DbNsfp
- chrPos - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- chrPrepend - Variable in class org.snpsift.annotate.DbVcfTabix
- chrPrev - Variable in class org.snpsift.annotate.AnnotateVcfDb
- chrPrev - Variable in class org.snpsift.SnpSiftCmdAnnotate
- ci95 - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- circle(int, int, int, String, int, String) - Method in class org.snpsift.pedigree.PedigreeDraw
- clear(int) - Method in class org.snpsift.annotate.mem.arrays.BoolArray
-
Clear null data
- cloneShallow() - Method in class org.snpsift.fileIterator.DbNsfpEntry
- close() - Method in class org.snpsift.annotate.AnnotateVcfDb
- close() - Method in interface org.snpsift.annotate.DbMarker
-
Close database, free resources
- close() - Method in class org.snpsift.annotate.DbVcf
- close() - Method in class org.snpsift.annotate.DbVcfMem
- close() - Method in class org.snpsift.annotate.DbVcfSorted
- close() - Method in class org.snpsift.annotate.DbVcfTabix
- close() - Method in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
- close() - Method in class org.snpsift.annotate.VcfIndex
-
Close file and free memory
- close() - Method in class org.snpsift.fileIterator.DbNsfp
- cmd() - Method in class org.snpsift.SnpSift
-
Run: Executes the appropriate class
- cnv - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- COLLAPSE_MAX_NUM_ENTRIES - Static variable in class org.snpsift.annotate.VcfIndexTree
- collapseRepeatedValues - Variable in class org.snpsift.SnpSiftCmdDbNsfp
- colorAffected() - Method in class org.snpsift.pedigree.PedigreeDraw
-
Color individuals by affected status
- COLUMN_CHR_NAME - Static variable in class org.snpsift.fileIterator.DbNsfp
- COLUMN_POS_NAME_v2 - Static variable in class org.snpsift.fileIterator.DbNsfp
- COLUMN_POS_NAME_v3 - Static variable in class org.snpsift.fileIterator.DbNsfp
- COLUMN_SEPARATOR - Static variable in class org.snpsift.fileIterator.DbNsfp
- columnNames() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
- command - Variable in class org.snpsift.SnpSift
- commandLineStr() - Method in class org.snpsift.SnpSift
-
Show command line
- COMMENT_HASH - Static variable in class org.snpsift.antlr.SnpSiftLexer
- COMMENT_HASH - Static variable in class org.snpsift.antlr.SnpSiftParser
- COMMENT_SL - Static variable in class org.snpsift.antlr.SnpSiftLexer
- COMMENT_SL - Static variable in class org.snpsift.antlr.SnpSiftParser
- compareTo(Value) - Method in class org.snpsift.lang.Value
- compareTo(Individual) - Method in class org.snpsift.pedigree.Individual
- compilationUnit() - Method in class org.snpsift.antlr.SnpSiftParser
- CompilationUnitContext(ParserRuleContext, int) - Constructor for class org.snpsift.antlr.SnpSiftParser.CompilationUnitContext
- compile(String) - Method in class org.snpsift.lang.LangFactory
-
Create an AST from a program (using ANTLR lexer invalid input: '&' parser) Returns null if error Use 'alreadyIncluded' to keep track of from 'include' statements
- config - Variable in class org.snpsift.SnpSift
- CONFIG_DBNSFP_DB_NAME - Variable in class org.snpsift.SnpSiftCmdDbNsfp
- CONFIG_GWAS_DB_NAME - Variable in class org.snpsift.SnpSiftCmdGwasCatalog
- configFile - Variable in class org.snpsift.SnpSift
- contains(int) - Method in class org.snpsift.annotate.mem.arrays.PosIndex
- context - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- copyFrom(SnpSiftParser.ExpressionContext) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionContext
- count - Variable in class org.snpsift.SnpSiftCmdDbNsfp
- count(String) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
-
Count the number of variants in a VCF file
- count(String, Boolean, VariantEffect.FunctionalClass, String, int) - Method in class org.snpsift.caseControl.Summary
- count(VcfFileIterator) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
- count(VcfEntry) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
-
Count the number of variants in a VCF file
- count(VcfEntry) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
-
Count the number of variants in a VCF file
- countAnnotated - Variable in class org.snpsift.SnpSiftCmdDbNsfp
- countBadRef - Variable in class org.snpsift.SnpSiftCmdAnnotate
- countByCategory - Variable in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
- CountHet - Class in org.snpsift.lang.function
-
Count number of heterozygous samples
- CountHet() - Constructor for class org.snpsift.lang.function.CountHet
- CountHom - Class in org.snpsift.lang.function
-
Count number of homozygous samples
- CountHom() - Constructor for class org.snpsift.lang.function.CountHom
- countNonZeroGenotypes() - Method in class org.snpsift.caseControl.VariantCounter
- CountRef - Class in org.snpsift.lang.function
-
Count number of refernces samples
- CountRef() - Constructor for class org.snpsift.lang.function.CountRef
- CountVariant - Class in org.snpsift.lang.function
-
Count number of ALT samples
- CountVariant() - Constructor for class org.snpsift.lang.function.CountVariant
- countVariants - Variable in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
- countVariants - Variable in class org.snpsift.SnpSiftCmdDbNsfp
- countVariants(String) - Static method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
-
Count variants in a string of VCF lines (i.e.
- countVcfEntries - Variable in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
- covariance() - Method in class org.snpsift.SnpSiftCmdCovarianceMatrix
-
Calculate covariance matrix
- create() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
-
Create a database from a VCF file
- create() - Method in class org.snpsift.SnpSiftCmdAnnotateMem
-
Create all databases
- create(String) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
-
Create a database from a VCF file content (as a string) This is used for testing
- createColumn(VcfHeaderInfo) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
-
Create a column of a given type
- createColumns() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
-
Create columns based on fields
- currentDbEntry - Variable in class org.snpsift.SnpSiftCmdDbNsfp
- currentIndex - Variable in class org.snpsift.annotate.mem.arrays.StringArrayBase
D
- data - Variable in class org.snpsift.annotate.mem.arrays.EnumArray
- data - Variable in class org.snpsift.annotate.mem.arrays.StringArray
- DATA_TYPES_CACHE_EXT - Static variable in class org.snpsift.fileIterator.DbNsfp
- DATA_TYPES_MAX_LINES - Static variable in class org.snpsift.fileIterator.DbNsfp
- DATA_TYPES_MIN_LINES - Static variable in class org.snpsift.fileIterator.DbNsfp
- databaseDownload() - Method in class org.snpsift.SnpSift
-
Download a database
- databaseFind() - Method in class org.snpsift.SnpSift
-
Find database file name.
- dataDir - Variable in class org.snpsift.SnpSift
- DataFrame - Class in org.snpsift.annotate.mem.dataFrame
-
A set of DataColumns, indexed by position This is used to store data for a chromosome
- DataFrame(VariantTypeCounter, VariantCategory, boolean, boolean) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrame
- DataFrameColumn<T> - Class in org.snpsift.annotate.mem.dataFrame.dataFrameColumn
-
A wrapper for a data column of primitive type T A Data Column is a column of a specific data tyle (String, Float, Long, etc.) that is stored using primitive types for memory efficiency.
- DataFrameColumn(String, int) - Constructor for class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
- DataFrameColumnBool - Class in org.snpsift.annotate.mem.dataFrame.dataFrameColumn
-
A column of boolean values, that can also be null The bollean values are stored in a BoolArray
- DataFrameColumnBool(String, int) - Constructor for class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnBool
- DataFrameColumnChar - Class in org.snpsift.annotate.mem.dataFrame.dataFrameColumn
- DataFrameColumnChar(String, int) - Constructor for class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnChar
- DataFrameColumnDouble - Class in org.snpsift.annotate.mem.dataFrame.dataFrameColumn
- DataFrameColumnDouble(String, int) - Constructor for class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnDouble
- DataFrameColumnInt - Class in org.snpsift.annotate.mem.dataFrame.dataFrameColumn
- DataFrameColumnInt(String, int) - Constructor for class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnInt
- DataFrameColumnLong - Class in org.snpsift.annotate.mem.dataFrame.dataFrameColumn
- DataFrameColumnLong(String, int) - Constructor for class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnLong
- DataFrameColumnString - Class in org.snpsift.annotate.mem.dataFrame.dataFrameColumn
- DataFrameColumnString(String, int, int) - Constructor for class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnString
-
Constructor
- DataFrameDel - Class in org.snpsift.annotate.mem.dataFrame
- DataFrameDel(VariantTypeCounter, VariantCategory) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameDel
- DataFrameIns - Class in org.snpsift.annotate.mem.dataFrame
- DataFrameIns(VariantTypeCounter, VariantCategory) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameIns
- DataFrameMixed - Class in org.snpsift.annotate.mem.dataFrame
- DataFrameMixed(VariantTypeCounter, VariantCategory) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameMixed
- DataFrameMnp - Class in org.snpsift.annotate.mem.dataFrame
- DataFrameMnp(VariantTypeCounter, VariantCategory) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameMnp
- DataFrameOther - Class in org.snpsift.annotate.mem.dataFrame
- DataFrameOther(VariantTypeCounter, VariantCategory) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameOther
- DataFrameRow - Class in org.snpsift.annotate.mem.dataFrame
-
A DataFrame 'row'.
- DataFrameRow(DataFrame, int, String, String) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameRow
- DataFrameRow(DataFrame, int, String, String, int) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameRow
- DataFrameSnp - Class in org.snpsift.annotate.mem.dataFrame
-
A set of DataColumns specific SNP 'alt' (e.g.
- DataFrameSnp(VariantTypeCounter, VariantCategory) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameSnp
- dataTypes() - Method in class org.snpsift.fileIterator.DbNsfp
-
Guess field types: Read many lines and guess the data type for each column
- date - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- dateAddedtoCatalog - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- dbDirFromVcfFileName(String) - Static method in class org.snpsift.annotate.mem.database.VariantDatabase
-
Get the database directory name from a "VCF database" file name buy just appending ".snpsift.vardb"
- dbFileName - Variable in class org.snpsift.annotate.DbVcf
- dbFileName - Variable in class org.snpsift.SnpSift
- DbMarker<Q,
R> - Interface in org.snpsift.annotate -
Use a file as a 'marker' database.
- dbNsfp - Variable in class org.snpsift.SnpSiftCmdDbNsfp
- DbNsfp - Class in org.snpsift.fileIterator
-
DbNSFP database: Reference https://sites.google.com/site/jpopgen/dbNSFP
- DbNsfp(String) - Constructor for class org.snpsift.fileIterator.DbNsfp
- DBNSFP_VCF_INFO_PREFIX - Static variable in class org.snpsift.SnpSiftCmdDbNsfp
- DbNsfpEntry - Class in org.snpsift.fileIterator
-
DbNSFP database entry: Reference https://sites.google.com/site/jpopgen/dbNSFP Added lazy parsing of key/value pairs
- DbNsfpEntry(DbNsfp, String) - Constructor for class org.snpsift.fileIterator.DbNsfpEntry
- dbTabix - Variable in class org.snpsift.SnpSift
- dbType - Variable in class org.snpsift.SnpSift
- dbVcf - Variable in class org.snpsift.annotate.AnnotateVcfDb
- DbVcf - Class in org.snpsift.annotate
-
Use a VCF file as a database for annotations A VCF database consists of a VCF file and an index.
- DbVcf(String) - Constructor for class org.snpsift.annotate.DbVcf
- DbVcfMem - Class in org.snpsift.annotate
-
Loads a VCF file into memory.
- DbVcfMem(String) - Constructor for class org.snpsift.annotate.DbVcfMem
- DbVcfSorted - Class in org.snpsift.annotate
-
Use an uncompressed sorted VCF file as a database for annotations Note: Assumes that the VCF database file is sorted and uncompressed.
- DbVcfSorted(String) - Constructor for class org.snpsift.annotate.DbVcfSorted
- DbVcfTabix - Class in org.snpsift.annotate
-
Use a bgzip-compressed, tabix indexed VCF file as a database for annotations
- DbVcfTabix(String) - Constructor for class org.snpsift.annotate.DbVcfTabix
- debug - Variable in class org.snpsift.annotate.AnnotateVcfDb
- debug - Variable in class org.snpsift.annotate.DbVcf
- debug - Variable in class org.snpsift.fileIterator.DbNsfp
- debug - Static variable in class org.snpsift.hwe.VcfHwe
- debug - Static variable in class org.snpsift.lang.expression.Expression
- debug - Static variable in class org.snpsift.lang.LangFactory
- debug - Static variable in class org.snpsift.lang.Value
- debug - Static variable in class org.snpsift.pedigree.PedigreeDraw
- debug - Variable in class org.snpsift.SnpSift
- debug - Static variable in class org.snpsift.VcfLd
- DEFAULT_FIELDS_NAMES_TO_ADD - Static variable in class org.snpsift.SnpSiftCmdDbNsfp
- DEFAULT_MAX_BLOCK_SIZE - Static variable in class org.snpsift.annotate.VcfIndexTree
- DEL - Enum constant in enum class org.snpsift.annotate.mem.VariantCategory
- diamond(int, int, int, int, String, int, String) - Method in class org.snpsift.pedigree.PedigreeDraw
-
Draw a diamond (unknown sex)
- discoverInfoFields() - Method in class org.snpsift.annotate.AnnotateVcfDb
- discoverInfoFields(VcfEntry) - Method in class org.snpsift.annotate.AnnotateVcfDb
-
If 'ALL' info fields are being used, we can try to discover new fields that have not already been added to the annotation list (e.g.
- Div - Class in org.snpsift.lang.expression
-
And expression
- Div(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Div
- DO_NOT_USE - Enum constant in enum class org.snpsift.SnpSiftCmdVcf2Tped.UseMissing
- download - Variable in class org.snpsift.SnpSift
- downstreamGeneDistance - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- downstreamGeneId - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- drawSvg() - Method in class org.snpsift.pedigree.PedigreeDraw
-
Draw the full pedigree as an SVG graph
- drawSvgByFamily(String, String) - Method in class org.snpsift.pedigree.PedigreeDraw
-
Draw each family
E
- EFFECT - Enum constant in enum class org.snpsift.lang.expression.FieldIterator.IteratorType
- elapsedSec() - Method in class org.snpsift.util.ShowProgress
- EMPTY_ARGS - Static variable in class org.snpsift.SnpSift
- enterCompilationUnit(SnpSiftParser.CompilationUnitContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by
SnpSiftParser.compilationUnit()
. - enterCompilationUnit(SnpSiftParser.CompilationUnitContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by
SnpSiftParser.compilationUnit()
. - enterEveryRule(ParserRuleContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
- enterExpressionComp(SnpSiftParser.ExpressionCompContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by the
expressionComp
labeled alternative inSnpSiftParser.expression()
. - enterExpressionComp(SnpSiftParser.ExpressionCompContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by the
expressionComp
labeled alternative inSnpSiftParser.expression()
. - enterExpressionCond(SnpSiftParser.ExpressionCondContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by the
expressionCond
labeled alternative inSnpSiftParser.expression()
. - enterExpressionCond(SnpSiftParser.ExpressionCondContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by the
expressionCond
labeled alternative inSnpSiftParser.expression()
. - enterExpressionExists(SnpSiftParser.ExpressionExistsContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by the
expressionExists
labeled alternative inSnpSiftParser.expression()
. - enterExpressionExists(SnpSiftParser.ExpressionExistsContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by the
expressionExists
labeled alternative inSnpSiftParser.expression()
. - enterExpressionLogic(SnpSiftParser.ExpressionLogicContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by the
expressionLogic
labeled alternative inSnpSiftParser.expression()
. - enterExpressionLogic(SnpSiftParser.ExpressionLogicContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by the
expressionLogic
labeled alternative inSnpSiftParser.expression()
. - enterExpressionParen(SnpSiftParser.ExpressionParenContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by the
expressionParen
labeled alternative inSnpSiftParser.expression()
. - enterExpressionParen(SnpSiftParser.ExpressionParenContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by the
expressionParen
labeled alternative inSnpSiftParser.expression()
. - enterExpressionPlus(SnpSiftParser.ExpressionPlusContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by the
expressionPlus
labeled alternative inSnpSiftParser.expression()
. - enterExpressionPlus(SnpSiftParser.ExpressionPlusContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by the
expressionPlus
labeled alternative inSnpSiftParser.expression()
. - enterExpressionSet(SnpSiftParser.ExpressionSetContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by the
expressionSet
labeled alternative inSnpSiftParser.expression()
. - enterExpressionSet(SnpSiftParser.ExpressionSetContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by the
expressionSet
labeled alternative inSnpSiftParser.expression()
. - enterExpressionTimes(SnpSiftParser.ExpressionTimesContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by the
expressionTimes
labeled alternative inSnpSiftParser.expression()
. - enterExpressionTimes(SnpSiftParser.ExpressionTimesContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by the
expressionTimes
labeled alternative inSnpSiftParser.expression()
. - enterExpressionUnary(SnpSiftParser.ExpressionUnaryContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by the
expressionUnary
labeled alternative inSnpSiftParser.expression()
. - enterExpressionUnary(SnpSiftParser.ExpressionUnaryContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by the
expressionUnary
labeled alternative inSnpSiftParser.expression()
. - enterFunctionCall(SnpSiftParser.FunctionCallContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by the
functionCall
labeled alternative inSnpSiftParser.expression()
. - enterFunctionCall(SnpSiftParser.FunctionCallContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by the
functionCall
labeled alternative inSnpSiftParser.expression()
. - enterLiteralBool(SnpSiftParser.LiteralBoolContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by the
literalBool
labeled alternative inSnpSiftParser.expression()
. - enterLiteralBool(SnpSiftParser.LiteralBoolContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by the
literalBool
labeled alternative inSnpSiftParser.expression()
. - enterLiteralFloat(SnpSiftParser.LiteralFloatContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by the
literalFloat
labeled alternative inSnpSiftParser.expression()
. - enterLiteralFloat(SnpSiftParser.LiteralFloatContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by the
literalFloat
labeled alternative inSnpSiftParser.expression()
. - enterLiteralIndex(SnpSiftParser.LiteralIndexContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by the
literalIndex
labeled alternative inSnpSiftParser.expression()
. - enterLiteralIndex(SnpSiftParser.LiteralIndexContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by the
literalIndex
labeled alternative inSnpSiftParser.expression()
. - enterLiteralInt(SnpSiftParser.LiteralIntContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by the
literalInt
labeled alternative inSnpSiftParser.expression()
. - enterLiteralInt(SnpSiftParser.LiteralIntContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by the
literalInt
labeled alternative inSnpSiftParser.expression()
. - enterLiteralString(SnpSiftParser.LiteralStringContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by the
literalString
labeled alternative inSnpSiftParser.expression()
. - enterLiteralString(SnpSiftParser.LiteralStringContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by the
literalString
labeled alternative inSnpSiftParser.expression()
. - enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.CompilationUnitContext
- enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionCompContext
- enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionCondContext
- enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionExistsContext
- enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionLogicContext
- enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionParenContext
- enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionPlusContext
- enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionSetContext
- enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionTimesContext
- enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionUnaryContext
- enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.FunctionCallContext
- enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.LiteralBoolContext
- enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.LiteralFloatContext
- enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.LiteralIndexContext
- enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.LiteralIntContext
- enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.LiteralStringContext
- enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.VarReferenceContext
- enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.VarReferenceListContext
- enterRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.VarReferenceListSubContext
- enterVarReference(SnpSiftParser.VarReferenceContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by the
varReference
labeled alternative inSnpSiftParser.expression()
. - enterVarReference(SnpSiftParser.VarReferenceContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by the
varReference
labeled alternative inSnpSiftParser.expression()
. - enterVarReferenceList(SnpSiftParser.VarReferenceListContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by the
varReferenceList
labeled alternative inSnpSiftParser.expression()
. - enterVarReferenceList(SnpSiftParser.VarReferenceListContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by the
varReferenceList
labeled alternative inSnpSiftParser.expression()
. - enterVarReferenceListSub(SnpSiftParser.VarReferenceListSubContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Enter a parse tree produced by the
varReferenceListSub
labeled alternative inSnpSiftParser.expression()
. - enterVarReferenceListSub(SnpSiftParser.VarReferenceListSubContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Enter a parse tree produced by the
varReferenceListSub
labeled alternative inSnpSiftParser.expression()
. - enum2ord - Variable in class org.snpsift.annotate.mem.arrays.EnumArray
- EnumArray - Class in org.snpsift.annotate.mem.arrays
-
Implement a memory efficient array of enums It only stores bytes (i.e.
- EnumArray(int) - Constructor for class org.snpsift.annotate.mem.arrays.EnumArray
-
Constructor
- EnumArray(String[]) - Constructor for class org.snpsift.annotate.mem.arrays.EnumArray
-
Constructor for using an array of strings
- EOF() - Method in class org.snpsift.antlr.SnpSiftParser.CompilationUnitContext
- eq(int, int, String, String) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
-
Does the entry at possition 'idx' match the given (pos, ref, alt) values?
- eq(int, int, String, String) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameSnp
-
Does the entry at possition 'idx' match the given (pos, ref, alt) values?
- Eq - Class in org.snpsift.lang.expression
-
Equal
- Eq(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Eq
- equals(Object) - Method in class org.snpsift.lang.Value
- errCount - Variable in class org.snpsift.annotate.AnnotateVcfDb
- errCount - Variable in class org.snpsift.SnpSift
- error(Throwable, String) - Method in class org.snpsift.SnpSift
-
Show an error (if not 'quiet' mode)
- error(Throwable, String) - Method in class org.snpsift.SnpSiftCmdTsTv
-
Show an error (if not 'quiet' mode)
- eval(VcfEntry) - Method in class org.snpsift.lang.expression.And
- eval(VcfEntry) - Method in class org.snpsift.lang.expression.Expression
-
Evaluate expression using VcfEntry
- eval(VcfEntry) - Method in class org.snpsift.lang.expression.ExpressionBinary
- eval(VcfEntry) - Method in class org.snpsift.lang.expression.ExpressionUnary
- eval(VcfEntry) - Method in class org.snpsift.lang.expression.Field
- eval(VcfEntry) - Method in class org.snpsift.lang.expression.FieldConstantFloat
- eval(VcfEntry) - Method in class org.snpsift.lang.expression.Literal
- eval(VcfEntry) - Method in class org.snpsift.lang.expression.Or
- eval(VcfEntry) - Method in class org.snpsift.lang.function.CountHet
- eval(VcfEntry) - Method in class org.snpsift.lang.function.CountHom
- eval(VcfEntry) - Method in class org.snpsift.lang.function.CountRef
- eval(VcfEntry) - Method in class org.snpsift.lang.function.CountVariant
- eval(VcfEntry) - Method in class org.snpsift.lang.function.In
- eval(VcfEntry) - Method in class org.snpsift.lang.function.IsHet
- eval(VcfEntry) - Method in class org.snpsift.lang.function.IsHom
- eval(VcfEntry) - Method in class org.snpsift.lang.function.IsRef
- eval(VcfEntry) - Method in class org.snpsift.lang.function.IsVariant
- eval(VcfGenotype) - Method in class org.snpsift.lang.expression.Expression
-
Evaluate expression using genotype
- eval(VcfGenotype) - Method in class org.snpsift.lang.expression.ExpressionBinary
- eval(VcfGenotype) - Method in class org.snpsift.lang.expression.ExpressionUnary
- eval(VcfGenotype) - Method in class org.snpsift.lang.expression.Field
- eval(VcfGenotype) - Method in class org.snpsift.lang.expression.Literal
- eval(VcfGenotype) - Method in class org.snpsift.lang.function.CountHet
- eval(VcfGenotype) - Method in class org.snpsift.lang.function.CountHom
- eval(VcfGenotype) - Method in class org.snpsift.lang.function.CountRef
- eval(VcfGenotype) - Method in class org.snpsift.lang.function.CountVariant
- eval(VcfGenotype) - Method in class org.snpsift.lang.function.In
- eval(VcfGenotype) - Method in class org.snpsift.lang.function.IsHet
- eval(VcfGenotype) - Method in class org.snpsift.lang.function.IsHom
- eval(VcfGenotype) - Method in class org.snpsift.lang.function.IsRef
- eval(VcfGenotype) - Method in class org.snpsift.lang.function.IsVariant
- evalGenotype(VcfEntry) - Method in class org.snpsift.lang.expression.FieldGenotype
-
Evaluate expressions and return VcfGenotype
- evalGenotype(VcfEntry) - Method in class org.snpsift.lang.function.FunctionBoolGenotype
-
Evaluate index expression and obtein genotype
- evalIndex(VcfEntry) - Method in class org.snpsift.lang.expression.FieldSub
-
Evaluate index expression
- evalIndex(VcfEntry, Expression) - Method in class org.snpsift.lang.expression.FieldSub
-
Evaluate index expression (VCF entry)
- evalIndex(VcfGenotype) - Method in class org.snpsift.lang.expression.FieldSub
-
Evaluate index expression (VCF genotype)
- evalIndex(VcfGenotype, Expression) - Method in class org.snpsift.lang.expression.FieldSub
-
Evaluate index expression (VCF genotype)
- evalOp(Value) - Method in class org.snpsift.lang.expression.Exists
- evalOp(Value) - Method in class org.snpsift.lang.expression.ExpressionUnary
- evalOp(Value) - Method in class org.snpsift.lang.expression.Not
- evalOp(Value, Value) - Method in class org.snpsift.lang.expression.And
- evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Div
- evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Eq
- evalOp(Value, Value) - Method in class org.snpsift.lang.expression.ExpressionBinary
- evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Ge
- evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Gt
- evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Has
- evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Le
- evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Lt
- evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Match
- evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Minus
- evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Mod
- evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Or
- evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Plus
- evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Times
- evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Xor
- exceptionIfNotFound - Variable in class org.snpsift.lang.expression.Field
- Exists - Class in org.snpsift.lang.expression
-
Exists operator (true if a field exists)
- Exists(Expression) - Constructor for class org.snpsift.lang.expression.Exists
- existsInfoField - Variable in class org.snpsift.annotate.AnnotateVcfDb
- existsInfoField - Variable in class org.snpsift.SnpSiftCmdAnnotate
- exitCompilationUnit(SnpSiftParser.CompilationUnitContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by
SnpSiftParser.compilationUnit()
. - exitCompilationUnit(SnpSiftParser.CompilationUnitContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by
SnpSiftParser.compilationUnit()
. - exitEveryRule(ParserRuleContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
- exitExpressionComp(SnpSiftParser.ExpressionCompContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by the
expressionComp
labeled alternative inSnpSiftParser.expression()
. - exitExpressionComp(SnpSiftParser.ExpressionCompContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by the
expressionComp
labeled alternative inSnpSiftParser.expression()
. - exitExpressionCond(SnpSiftParser.ExpressionCondContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by the
expressionCond
labeled alternative inSnpSiftParser.expression()
. - exitExpressionCond(SnpSiftParser.ExpressionCondContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by the
expressionCond
labeled alternative inSnpSiftParser.expression()
. - exitExpressionExists(SnpSiftParser.ExpressionExistsContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by the
expressionExists
labeled alternative inSnpSiftParser.expression()
. - exitExpressionExists(SnpSiftParser.ExpressionExistsContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by the
expressionExists
labeled alternative inSnpSiftParser.expression()
. - exitExpressionLogic(SnpSiftParser.ExpressionLogicContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by the
expressionLogic
labeled alternative inSnpSiftParser.expression()
. - exitExpressionLogic(SnpSiftParser.ExpressionLogicContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by the
expressionLogic
labeled alternative inSnpSiftParser.expression()
. - exitExpressionParen(SnpSiftParser.ExpressionParenContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by the
expressionParen
labeled alternative inSnpSiftParser.expression()
. - exitExpressionParen(SnpSiftParser.ExpressionParenContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by the
expressionParen
labeled alternative inSnpSiftParser.expression()
. - exitExpressionPlus(SnpSiftParser.ExpressionPlusContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by the
expressionPlus
labeled alternative inSnpSiftParser.expression()
. - exitExpressionPlus(SnpSiftParser.ExpressionPlusContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by the
expressionPlus
labeled alternative inSnpSiftParser.expression()
. - exitExpressionSet(SnpSiftParser.ExpressionSetContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by the
expressionSet
labeled alternative inSnpSiftParser.expression()
. - exitExpressionSet(SnpSiftParser.ExpressionSetContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by the
expressionSet
labeled alternative inSnpSiftParser.expression()
. - exitExpressionTimes(SnpSiftParser.ExpressionTimesContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by the
expressionTimes
labeled alternative inSnpSiftParser.expression()
. - exitExpressionTimes(SnpSiftParser.ExpressionTimesContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by the
expressionTimes
labeled alternative inSnpSiftParser.expression()
. - exitExpressionUnary(SnpSiftParser.ExpressionUnaryContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by the
expressionUnary
labeled alternative inSnpSiftParser.expression()
. - exitExpressionUnary(SnpSiftParser.ExpressionUnaryContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by the
expressionUnary
labeled alternative inSnpSiftParser.expression()
. - exitFunctionCall(SnpSiftParser.FunctionCallContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by the
functionCall
labeled alternative inSnpSiftParser.expression()
. - exitFunctionCall(SnpSiftParser.FunctionCallContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by the
functionCall
labeled alternative inSnpSiftParser.expression()
. - exitLiteralBool(SnpSiftParser.LiteralBoolContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by the
literalBool
labeled alternative inSnpSiftParser.expression()
. - exitLiteralBool(SnpSiftParser.LiteralBoolContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by the
literalBool
labeled alternative inSnpSiftParser.expression()
. - exitLiteralFloat(SnpSiftParser.LiteralFloatContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by the
literalFloat
labeled alternative inSnpSiftParser.expression()
. - exitLiteralFloat(SnpSiftParser.LiteralFloatContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by the
literalFloat
labeled alternative inSnpSiftParser.expression()
. - exitLiteralIndex(SnpSiftParser.LiteralIndexContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by the
literalIndex
labeled alternative inSnpSiftParser.expression()
. - exitLiteralIndex(SnpSiftParser.LiteralIndexContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by the
literalIndex
labeled alternative inSnpSiftParser.expression()
. - exitLiteralInt(SnpSiftParser.LiteralIntContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by the
literalInt
labeled alternative inSnpSiftParser.expression()
. - exitLiteralInt(SnpSiftParser.LiteralIntContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by the
literalInt
labeled alternative inSnpSiftParser.expression()
. - exitLiteralString(SnpSiftParser.LiteralStringContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by the
literalString
labeled alternative inSnpSiftParser.expression()
. - exitLiteralString(SnpSiftParser.LiteralStringContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by the
literalString
labeled alternative inSnpSiftParser.expression()
. - exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.CompilationUnitContext
- exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionCompContext
- exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionCondContext
- exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionExistsContext
- exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionLogicContext
- exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionParenContext
- exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionPlusContext
- exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionSetContext
- exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionTimesContext
- exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionUnaryContext
- exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.FunctionCallContext
- exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.LiteralBoolContext
- exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.LiteralFloatContext
- exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.LiteralIndexContext
- exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.LiteralIntContext
- exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.LiteralStringContext
- exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.VarReferenceContext
- exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.VarReferenceListContext
- exitRule(ParseTreeListener) - Method in class org.snpsift.antlr.SnpSiftParser.VarReferenceListSubContext
- exitVarReference(SnpSiftParser.VarReferenceContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by the
varReference
labeled alternative inSnpSiftParser.expression()
. - exitVarReference(SnpSiftParser.VarReferenceContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by the
varReference
labeled alternative inSnpSiftParser.expression()
. - exitVarReferenceList(SnpSiftParser.VarReferenceListContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by the
varReferenceList
labeled alternative inSnpSiftParser.expression()
. - exitVarReferenceList(SnpSiftParser.VarReferenceListContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by the
varReferenceList
labeled alternative inSnpSiftParser.expression()
. - exitVarReferenceListSub(SnpSiftParser.VarReferenceListSubContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
-
Exit a parse tree produced by the
varReferenceListSub
labeled alternative inSnpSiftParser.expression()
. - exitVarReferenceListSub(SnpSiftParser.VarReferenceListSubContext) - Method in interface org.snpsift.antlr.SnpSiftListener
-
Exit a parse tree produced by the
varReferenceListSub
labeled alternative inSnpSiftParser.expression()
. - expr - Variable in class org.snpsift.lang.expression.ExpressionUnary
- expression() - Method in class org.snpsift.antlr.SnpSiftParser.CompilationUnitContext
- expression() - Method in class org.snpsift.antlr.SnpSiftParser
- expression() - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionCompContext
- expression() - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionCondContext
- expression() - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionExistsContext
- expression() - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionLogicContext
- expression() - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionParenContext
- expression() - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionPlusContext
- expression() - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionSetContext
- expression() - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionTimesContext
- expression() - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionUnaryContext
- expression() - Method in class org.snpsift.antlr.SnpSiftParser.FunctionCallContext
- expression() - Method in class org.snpsift.antlr.SnpSiftParser.VarReferenceListContext
- expression() - Method in class org.snpsift.antlr.SnpSiftParser.VarReferenceListSubContext
- expression(int) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionCompContext
- expression(int) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionCondContext
- expression(int) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionLogicContext
- expression(int) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionPlusContext
- expression(int) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionSetContext
- expression(int) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionTimesContext
- expression(int) - Method in class org.snpsift.antlr.SnpSiftParser.FunctionCallContext
- expression(int) - Method in class org.snpsift.antlr.SnpSiftParser.VarReferenceListContext
- expression(int) - Method in class org.snpsift.antlr.SnpSiftParser.VarReferenceListSubContext
- Expression - Class in org.snpsift.lang.expression
-
A generic expresion Expressions have values (VcfInfoType)
- Expression() - Constructor for class org.snpsift.lang.expression.Expression
- Expression(String) - Constructor for class org.snpsift.lang.expression.Expression
- ExpressionBinary - Class in org.snpsift.lang.expression
-
Binary condition
- ExpressionBinary(Expression, Expression, String) - Constructor for class org.snpsift.lang.expression.ExpressionBinary
- ExpressionCompContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.ExpressionCompContext
- ExpressionCondContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.ExpressionCondContext
- ExpressionContext() - Constructor for class org.snpsift.antlr.SnpSiftParser.ExpressionContext
- ExpressionContext(ParserRuleContext, int) - Constructor for class org.snpsift.antlr.SnpSiftParser.ExpressionContext
- ExpressionExistsContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.ExpressionExistsContext
- expressionFactory(ParseTree) - Method in class org.snpsift.lang.LangFactory
-
Create 'Expressions' from Tree
- ExpressionLogicContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.ExpressionLogicContext
- ExpressionParenContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.ExpressionParenContext
- ExpressionPlusContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.ExpressionPlusContext
- ExpressionSetContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.ExpressionSetContext
- expressionSetFactory(ParseTree) - Method in class org.snpsift.lang.LangFactory
-
Create FunctionBoolSet from AST
- ExpressionTimesContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.ExpressionTimesContext
- ExpressionUnary - Class in org.snpsift.lang.expression
-
An expression that can be negated
- ExpressionUnary(Expression, String) - Constructor for class org.snpsift.lang.expression.ExpressionUnary
- ExpressionUnaryContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.ExpressionUnaryContext
- exts - Static variable in class org.snpsift.SnpSiftCmdSplit
F
- factory(String) - Static method in class org.snpsift.lang.expression.FieldConstant
-
Create fields from constant names
- FALSE - Static variable in class org.snpsift.lang.Value
- FastaSample - Class in org.snpsift.util
-
Get a region from a fasta file
- FastaSample() - Constructor for class org.snpsift.util.FastaSample
- female(Individual) - Method in class org.snpsift.pedigree.PedigreeDraw
- Field - Class in org.snpsift.lang.expression
-
A field: E.g.: 'DP', 'CHROM'
- Field(String) - Constructor for class org.snpsift.lang.expression.Field
- FieldConstant - Class in org.snpsift.lang.expression
-
A 'constant' field: e.g.
- FieldConstant(String) - Constructor for class org.snpsift.lang.expression.FieldConstant
- FieldConstant.FieldConstantNames - Enum Class in org.snpsift.lang.expression
- FieldConstantFloat - Class in org.snpsift.lang.expression
-
A 'constant' field: e.g.
- FieldConstantFloat(String, double) - Constructor for class org.snpsift.lang.expression.FieldConstantFloat
- FieldEff - Class in org.snpsift.lang.expression
-
An 'EFF' field form SnpEff: E.g.: 'EFF[2].GENE'
- FieldEff(String, Expression, EffFormatVersion, String) - Constructor for class org.snpsift.lang.expression.FieldEff
-
Constructor
- fieldFactory(ParseTree) - Method in class org.snpsift.lang.LangFactory
-
Create 'Expression' from Tree
- FieldGenotype - Class in org.snpsift.lang.expression
-
A field: E.g.: 'GEN[2].GT'
- FieldGenotype(String, Expression) - Constructor for class org.snpsift.lang.expression.FieldGenotype
- FieldGenotypeSub - Class in org.snpsift.lang.expression
-
A field: E.g.: 'GEN[2].PL[3]'
- FieldGenotypeSub(String, Expression, Expression) - Constructor for class org.snpsift.lang.expression.FieldGenotypeSub
- fieldHeaderNotFound(VcfEntry) - Method in class org.snpsift.lang.expression.Field
- FieldIterator - Class in org.snpsift.lang.expression
-
Iterates on fields / sub-fields It's a singleton
- FieldIterator() - Constructor for class org.snpsift.lang.expression.FieldIterator
- FieldIterator.IteratorType - Enum Class in org.snpsift.lang.expression
- FieldLof - Class in org.snpsift.lang.expression
-
A LOF field form SnpEff: E.g.: 'LOF[2].GENE'
- FieldLof(String, Expression) - Constructor for class org.snpsift.lang.expression.FieldLof
- fieldNames - Variable in class org.snpsift.fileIterator.DbNsfp
- FieldNmd - Class in org.snpsift.lang.expression
-
A NMD field form SnpEff: E.g.: 'NMD[2].GENE'
- FieldNmd(String, Expression) - Constructor for class org.snpsift.lang.expression.FieldNmd
- fieldNotFound(VcfEntry) - Method in class org.snpsift.lang.expression.Field
- fields - Variable in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
- fields - Variable in class org.snpsift.SnpSiftCmdVcfOperator
- Fields - Class in org.snpsift.annotate.mem
- Fields() - Constructor for class org.snpsift.annotate.mem.Fields
- FIELDS_EXT - Static variable in class org.snpsift.annotate.mem.database.VariantDatabase
- fieldsDescription - Variable in class org.snpsift.SnpSiftCmdDbNsfp
- fieldsNamesToAdd - Variable in class org.snpsift.SnpSiftCmdDbNsfp
- fieldsString - Variable in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
- fieldsToAdd - Variable in class org.snpsift.SnpSiftCmdDbNsfp
- fieldsType - Variable in class org.snpsift.SnpSiftCmdDbNsfp
- FieldSub - Class in org.snpsift.lang.expression
-
A field that has sub fields (e.g.
- FieldSub(String, Expression) - Constructor for class org.snpsift.lang.expression.FieldSub
- fileIdx - Variable in class org.snpsift.annotate.MarkerFile
- fileName - Variable in class org.snpsift.fileIterator.DbNsfp
- fileSize(int, int) - Method in class org.snpsift.annotate.VcfIndexDataChromo
-
File size between startIdx and endIdx inclusive
- fill() - Method in class org.snpsift.annotate.mem.arrays.BoolArray
- filter(String, String, boolean) - Method in class org.snpsift.SnpSiftCmdFilter
-
Filter a file
- filter(String, String, boolean) - Method in class org.snpsift.SnpSiftCmdFilterGt
-
Filter a file
- filter(VcfEntry) - Method in class org.snpsift.SnpSiftCmdFilterChrPos
-
Filter this line?
- find(int, String, String) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
-
Get data from a column index by searching by position, reference and alternative alleles.
- find(Variant) - Method in class org.snpsift.annotate.AnnotateVcfDb
- find(VcfEntry) - Method in class org.snpsift.annotate.AnnotateVcfDb
-
Find matching entries in the database
- findDbExists(QueryResult) - Method in class org.snpsift.annotate.AnnotateVcfDb
-
Should we annotate using 'exists' field?
- findDbId(Set<String>, QueryResult) - Method in class org.snpsift.annotate.AnnotateVcfDb
-
Find an ID for this variant and add them to idSet
- findDbInfo(String, QueryResult) - Method in class org.snpsift.annotate.AnnotateVcfDb
-
Find all non-empty INFO fields 'infoFieldName' in results
- findDbInfo(Map<String, String>, QueryResult) - Method in class org.snpsift.annotate.AnnotateVcfDb
-
Find INFO fields for this VCF entry
- findDbInfoAlt(String, QueryResult) - Method in class org.snpsift.annotate.AnnotateVcfDb
-
Find the first non-empty INFO field 'infoFieldName' in results Note: ALT must match
- findDbInfoRef(Map<String, String>, Set<VcfEntry>) - Method in class org.snpsift.annotate.AnnotateVcfDb
-
Fill values for INFO fields requiring 'REF' value
- findSpouses(Individual) - Method in class org.snpsift.pedigree.PedigreeDraw
- firstAuthor - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- FIXED_STEP_FIELD - Static variable in class org.snpsift.SnpSiftCmdPhastCons
- FLOAT_LITERAL - Static variable in class org.snpsift.antlr.SnpSiftLexer
- FLOAT_LITERAL - Static variable in class org.snpsift.antlr.SnpSiftParser
- FLOAT_LITERAL() - Method in class org.snpsift.antlr.SnpSiftParser.LiteralFloatContext
- forceMissingTypesAsString() - Method in class org.snpsift.fileIterator.DbNsfp
-
Force missing types as string
- formatBytes(long) - Static method in class org.snpsift.util.FormatUtil
-
Format bytes as a human readable string
- FormatUtil - Class in org.snpsift.util
- FormatUtil() - Constructor for class org.snpsift.util.FormatUtil
- formatVersion - Static variable in class org.snpsift.caseControl.SnpSiftCmdCaseControlSummary
- Function - Class in org.snpsift.lang.function
-
A function that returns an expression (i.e.
- Function(String) - Constructor for class org.snpsift.lang.function.Function
- FunctionBoolGenotype - Class in org.snpsift.lang.function
-
A function that returns a bool type (i.e.
- FunctionBoolGenotype(String, Expression) - Constructor for class org.snpsift.lang.function.FunctionBoolGenotype
- functionBoolGenotypeFactory(ParseTree) - Method in class org.snpsift.lang.LangFactory
-
Create FunctionBoolGenotype from AST
- FunctionCallContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.FunctionCallContext
- functionFactory(ParseTree) - Method in class org.snpsift.lang.LangFactory
-
Create function
- functionVcfEntryFactory(ParseTree) - Method in class org.snpsift.lang.LangFactory
-
Create Functions from tree Note: These functions that are calculated on the whole VcfEntry.
G
- Ge - Class in org.snpsift.lang.expression
-
Greater equal
- Ge(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Ge
- genome - Variable in class org.snpsift.fileIterator.DbNsfp
- genomeVersion - Variable in class org.snpsift.SnpSift
- GENOTYPE - Enum constant in enum class org.snpsift.lang.expression.FieldIterator.IteratorType
- GENOTYPE_VAR - Enum constant in enum class org.snpsift.lang.expression.FieldIterator.IteratorType
- get() - Static method in class org.snpsift.lang.expression.FieldIterator
- get(int) - Method in class org.snpsift.annotate.mem.arrays.EnumArray
-
Get the string at array index 'i'
- get(int) - Method in class org.snpsift.annotate.mem.arrays.PosIndex
-
Get position at index 'i'
- get(int) - Method in class org.snpsift.annotate.mem.arrays.StringArray
-
Get the string at array index 'i'
- get(int) - Method in class org.snpsift.annotate.mem.arrays.StringArrayBase
-
Get the string at array index 'i'
- get(int) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
-
Get value at index i, considering null data
- get(String) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
-
Get the database for a chromosome
- get(String) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
- get(String) - Method in class org.snpsift.annotate.mem.Fields
- get(String) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
- get(String) - Method in class org.snpsift.gwasCatalog.GwasCatalog
- get(String) - Method in class org.snpsift.pedigree.PedigreeDraw
- get(String, int) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
-
Get data from a column by searching by position, reference and alternative alleles.
- get(String, int) - Method in class org.snpsift.gwasCatalog.GwasCatalog
-
Get all entries at a given chromosome invalid input: '&' position Note: Position is zero based.
- get(FieldIterator.IteratorType) - Method in class org.snpsift.lang.expression.FieldIterator
-
Set 'max' parameter for an iterator
- getAffected() - Method in class org.snpsift.pedigree.Individual
- getAlt() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
- getAlt() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameSnp
- getAltIdx() - Method in class org.snpsift.fileIterator.DbNsfp
- getArgs() - Method in class org.snpsift.SnpSift
- getArgs() - Method in class org.snpsift.SnpSiftCmdVcfOperator
- getATN() - Method in class org.snpsift.antlr.SnpSiftLexer
- getATN() - Method in class org.snpsift.antlr.SnpSiftParser
- getByRs(String) - Method in class org.snpsift.gwasCatalog.GwasCatalog
-
Get an entry based on 'RS' number
- getChannelNames() - Method in class org.snpsift.antlr.SnpSiftLexer
- getChilds() - Method in class org.snpsift.pedigree.Individual
- getChilds(Individual) - Method in class org.snpsift.pedigree.Individual
-
Get only childs from this spouse
- getChromosome() - Method in class org.snpsift.annotate.VcfIndexDataChromo
- getChromosome() - Method in class org.snpsift.annotate.VcfIndexTree
- getChromosome(String) - Method in class org.snpsift.fileIterator.DbNsfp
-
Find chromosome 'chromoName'.
- getChromosomeIdx() - Method in class org.snpsift.fileIterator.DbNsfp
- getChrPosRefAltIdx() - Method in class org.snpsift.fileIterator.DbNsfp
- getColor() - Method in class org.snpsift.pedigree.Individual
- getColumn(String) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
-
Get a column
- getConcordance() - Method in class org.snpsift.SnpSiftCmdConcordance
- getConcordanceBySample() - Method in class org.snpsift.SnpSiftCmdConcordance
- getConfig() - Method in class org.snpsift.SnpSift
- getConfigFile() - Method in class org.snpsift.SnpSift
- getCount(VariantCategory) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
- getCountByCategory() - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
- getCountEntries() - Method in class org.snpsift.SnpSiftCmdConcordance
- getD() - Method in class org.snpsift.VcfLd
- getData() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnString
-
Get the data, used for testing
- getData(int) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
- getData(int) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnBool
- getData(int) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnChar
- getData(int) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnDouble
- getData(int) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnInt
- getData(int) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnLong
- getData(int) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnString
- getDatabaseVcfFileName() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
- getDataFrameByCategory(VariantCategory) - Method in class org.snpsift.annotate.mem.database.VariantDataFrame
- getDataFrameByVariantType(Variant) - Method in class org.snpsift.annotate.mem.database.VariantDataFrame
-
Select the appropirate data set for a variant
- getDataFrameValue(String) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
-
Get data single column value from the data frame
- getDataFrameValues() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
-
Return all data for this row from the data frame
- getDbDir() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
- getDepth() - Method in class org.snpsift.pedigree.Individual
- getDmax() - Method in class org.snpsift.VcfLd
- getDmin() - Method in class org.snpsift.VcfLd
- getDprime() - Method in class org.snpsift.VcfLd
- getEnd(int) - Method in class org.snpsift.annotate.VcfIndexDataChromo
- getFamilyId() - Method in class org.snpsift.pedigree.Individual
- getFather() - Method in class org.snpsift.pedigree.Individual
- getFieldCount() - Method in class org.snpsift.fileIterator.DbNsfp
- getFieldFloat(VcfEntry) - Method in class org.snpsift.lang.expression.FieldConstantFloat
- getFieldName(int) - Method in class org.snpsift.fileIterator.DbNsfp
- getFieldNames() - Method in class org.snpsift.fileIterator.DbNsfp
- getFieldNamesSorted() - Method in class org.snpsift.fileIterator.DbNsfp
- getFields() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
- getFields() - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
- getFields() - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
- getFieldString(VcfEntry) - Method in class org.snpsift.lang.expression.FieldEff
-
Get a field from VcfEntry
- getFieldString(VcfEntry) - Method in class org.snpsift.lang.expression.FieldGenotype
-
Get a field from VcfEntry
- getFieldString(VcfEntry) - Method in class org.snpsift.lang.expression.FieldGenotypeSub
-
Get a field from VcfEntry
- getFieldString(VcfEntry) - Method in class org.snpsift.lang.expression.FieldLof
-
Get a field from VcfEntry
- getFieldString(VcfEntry) - Method in class org.snpsift.lang.expression.FieldSub
-
Get a field from VcfEntry
- getFieldString(VcfGenotype) - Method in class org.snpsift.lang.expression.Field
- getFieldString(VcfGenotype) - Method in class org.snpsift.lang.expression.FieldGenotype
-
Get a field (as a Float) from VcfEntry
- getFieldString(VcfGenotype) - Method in class org.snpsift.lang.expression.FieldGenotypeSub
-
Get a field from VcfGenotype
- getFieldString(VcfGenotype) - Method in class org.snpsift.lang.expression.FieldSub
-
Get a field from VcfEntry
- getFieldsType() - Method in class org.snpsift.SnpSiftCmdDbNsfp
- getFileIdx() - Method in class org.snpsift.annotate.MarkerFile
- getFileNames() - Method in class org.snpsift.SnpSiftCmdSplit
-
Names of files created when splitting
- getFilePosEnd(int) - Method in class org.snpsift.annotate.VcfIndexDataChromo
- getFilePosStart(int) - Method in class org.snpsift.annotate.VcfIndexDataChromo
- getGenome() - Method in class org.snpsift.annotate.VcfIndex
- getGenotype(int) - Method in class org.snpsift.caseControl.VariantCounter
- getGrammarFileName() - Method in class org.snpsift.antlr.SnpSiftLexer
- getGrammarFileName() - Method in class org.snpsift.antlr.SnpSiftParser
- getId() - Method in class org.snpsift.pedigree.Individual
- getIdx() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
- getIndex(String) - Method in class org.snpsift.fileIterator.DbNsfp
- getIndividuals() - Method in class org.snpsift.pedigree.PedigreeDraw
- getIntervals() - Method in class org.snpsift.annotate.VcfIndexTree
- getLabel() - Method in class org.snpsift.pedigree.Individual
- getModeNames() - Method in class org.snpsift.antlr.SnpSiftLexer
- getMother() - Method in class org.snpsift.pedigree.Individual
- getName() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
- getName() - Method in class org.snpsift.lang.expression.Field
- getName() - Method in class org.snpsift.lang.expression.FieldEff
- getName() - Method in class org.snpsift.lang.expression.FieldLof
- getNames() - Method in class org.snpsift.annotate.mem.Fields
- getNames2index() - Method in class org.snpsift.fileIterator.DbNsfp
- getOffset() - Method in class org.snpsift.annotate.mem.arrays.StringArray
- getOrCreate(String) - Method in class org.snpsift.annotate.VcfIndex
-
Get IntervalFileChromo by chromosome name.
- getOrd(int) - Method in class org.snpsift.annotate.mem.arrays.EnumArray
-
Get the ordinal at array index 'i'
- getOrder() - Method in class org.snpsift.pedigree.Individual
- getOutput() - Method in class org.snpsift.SnpSift
- getOutput() - Method in class org.snpsift.SnpSiftCmdGt
- getpA() - Method in class org.snpsift.VcfLd
- getpB() - Method in class org.snpsift.VcfLd
- getPos() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
- getPosition() - Method in class org.snpsift.pedigree.Individual
- getQa() - Method in class org.snpsift.VcfLd
- getQb() - Method in class org.snpsift.VcfLd
- getRef() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
- getRefIdx() - Method in class org.snpsift.fileIterator.DbNsfp
- getReturnType(VcfEntry) - Method in class org.snpsift.lang.expression.FieldEff
- getReturnType(VcfEntry) - Method in class org.snpsift.lang.expression.FieldLof
- getReturnType(VcfGenotype) - Method in class org.snpsift.lang.expression.Field
- getRow(int, String, String) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
-
Get a 'row' from the data frame.
- getrSquare() - Method in class org.snpsift.VcfLd
- getRuleIndex() - Method in class org.snpsift.antlr.SnpSiftParser.CompilationUnitContext
- getRuleIndex() - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionContext
- getRuleNames() - Method in class org.snpsift.antlr.SnpSiftLexer
- getRuleNames() - Method in class org.snpsift.antlr.SnpSiftParser
- getSampleNum(VcfEntry, String) - Method in class org.snpsift.lang.expression.Field
- getSerializedATN() - Method in class org.snpsift.antlr.SnpSiftLexer
- getSerializedATN() - Method in class org.snpsift.antlr.SnpSiftParser
- getSex() - Method in class org.snpsift.pedigree.Individual
- getSize(VariantCategory, String) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
-
Get total size (in bytes) of a field (only string fields)
- getSizesByField() - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
- getSizeX() - Method in class org.snpsift.pedigree.PedigreeDraw
- getSizeY() - Method in class org.snpsift.pedigree.PedigreeDraw
- getStart(int) - Method in class org.snpsift.annotate.VcfIndexDataChromo
- getStartIdx() - Method in class org.snpsift.fileIterator.DbNsfp
- getTokenNames() - Method in class org.snpsift.antlr.SnpSiftLexer
-
Deprecated.
- getTokenNames() - Method in class org.snpsift.antlr.SnpSiftParser
-
Deprecated.
- getTraitCode() - Method in class org.snpsift.gwasCatalog.GwasCatalogEntry
-
Trait as a 'code' (only alpha-num chars)
- getTree(String) - Method in class org.snpsift.annotate.VcfIndex
- getType() - Method in enum class org.snpsift.lang.expression.FieldConstant.FieldConstantNames
- getType() - Method in class org.snpsift.lang.expression.FieldIterator
- getTypes() - Method in class org.snpsift.fileIterator.DbNsfp
- getValues() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
- getValues(VcfEntry) - Method in class org.snpsift.SnpSiftCmdVcfOperator
- getValues(VcfEntry, String) - Method in class org.snpsift.SnpSiftCmdVcfOperator
-
Parse an INFO field (can be multiple valued) and return a list of Double
- getVariantTypeCounters() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
- getVcf() - Method in class org.snpsift.annotate.VcfIndex
- getVcfHeader() - Method in class org.snpsift.annotate.DbVcf
- getVcfIndexChromo(String) - Method in class org.snpsift.annotate.VcfIndex
- getVcfInfo(String) - Method in class org.snpsift.fileIterator.DbNsfpEntry
-
Get data in a VCF INFO field compatible format
- getVocabulary() - Method in class org.snpsift.antlr.SnpSiftLexer
- getVocabulary() - Method in class org.snpsift.antlr.SnpSiftParser
- groups - Variable in class org.snpsift.SnpSiftCmdCaseControl
- Gt - Class in org.snpsift.lang.expression
-
Greater equal
- Gt(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Gt
- gtFieldNotFound(VcfGenotype) - Method in class org.snpsift.lang.expression.Field
- guessDataType(String) - Method in class org.snpsift.fileIterator.DbNsfp
-
Guess value type
- guessDataTypes() - Method in class org.snpsift.fileIterator.DbNsfp
-
Guess data types from file
- GWAS_CATALOG - Variable in class org.snpsift.SnpSiftCmdGwasCatalog
- GwasCatalog - Class in org.snpsift.gwasCatalog
-
GWAS catalog table.
- GwasCatalog(String) - Constructor for class org.snpsift.gwasCatalog.GwasCatalog
- GwasCatalogEntry - Class in org.snpsift.gwasCatalog
-
Entry from a GWAS-catalog References: http://www.genome.gov/gwastudies/#download http://www.genome.gov/Pages/About/OD/OPG/GWAS%20Catalog/Tab_delimited_column_descriptions_09_27.pdf
- GwasCatalogEntry() - Constructor for class org.snpsift.gwasCatalog.GwasCatalogEntry
- GwasCatalogFileIterator - Class in org.snpsift.gwasCatalog
-
Iterate on each line of a GWAS catalog (TXT, tab separated format)
- GwasCatalogFileIterator(String) - Constructor for class org.snpsift.gwasCatalog.GwasCatalogFileIterator
H
- Has - Class in org.snpsift.lang.expression
-
Equal
- Has(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Has
- hasEntry(int, String, String) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
-
Get data from a column by searching by position, reference and alternative alleles.
- hasField(String) - Method in class org.snpsift.fileIterator.DbNsfp
-
Do we have a column 'colName'?
- hashCode() - Method in class org.snpsift.lang.Value
- hasNext() - Method in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
- hasNext() - Method in class org.snpsift.lang.expression.FieldIterator
-
Is there a 'next'
- hasOrder() - Method in class org.snpsift.pedigree.Individual
- hasPosition() - Method in class org.snpsift.pedigree.Individual
- hasValues(String) - Method in class org.snpsift.fileIterator.DbNsfpEntry
-
Do we have values for this allele
- hasVcfInfoPerAlleleRef - Variable in class org.snpsift.annotate.AnnotateVcfDb
- HEADER_PREFIX - Static variable in class org.snpsift.fileIterator.DbNsfp
- headers() - Method in class org.snpsift.hwe.SnpSiftCmdHwe
- headers() - Method in class org.snpsift.SnpSift
-
Headers to add
- headers() - Method in class org.snpsift.SnpSiftCmdAnnotate
-
Build headers to add
- headers() - Method in class org.snpsift.SnpSiftCmdAnnotateMem
-
Build headers to add
- headers() - Method in class org.snpsift.SnpSiftCmdCaseControl
-
Lines to be added to VCF header
- headers() - Method in class org.snpsift.SnpSiftCmdFilter
- headers() - Method in class org.snpsift.SnpSiftCmdFilterGt
- headers() - Method in class org.snpsift.SnpSiftCmdGeneSets
- headers() - Method in class org.snpsift.SnpSiftCmdGt
- headers() - Method in class org.snpsift.SnpSiftCmdGwasCatalog
- headers() - Method in class org.snpsift.SnpSiftCmdVarType
- headers() - Method in class org.snpsift.SnpSiftCmdVcfOperator
- help - Variable in class org.snpsift.SnpSift
- hwe(VcfEntry, boolean) - Method in class org.snpsift.hwe.VcfHwe
-
Calculate Hardy-Weimberg equilibrium and add data to vcfEntry (INFO fields)
- hweLogPn12(int, int, int) - Method in class org.snpsift.hwe.VcfHwe
-
Calculate exact log of "P[ n12 | n1, n2]" References: "Principles of population genetics", Hartl invalid input: '&' Clark, page 58 (formula 2.5) "A Note on Exact test of Hardy Weinbeg Equilibrium", G.
- hweP(int, int, int) - Method in class org.snpsift.hwe.VcfHwe
-
Calculate goodness of fit for n1, n2 combination.
- hwePchi2(int, int, int) - Method in class org.snpsift.hwe.VcfHwe
-
Calculate goodness of fit using Chi square approximation
- hwePn12(int, int, int) - Method in class org.snpsift.hwe.VcfHwe
-
Calculate exact probability of "P[ n12 | n1, n2]" References: "Principles of population genetics", Hartl invalid input: '&' Clark, page 58 (formula 2.5) "A Note on Exact test of Hardy Weinbeg Equilibrium", G.
I
- ID - Static variable in class org.snpsift.antlr.SnpSiftLexer
- ID - Static variable in class org.snpsift.antlr.SnpSiftParser
- ID() - Method in class org.snpsift.antlr.SnpSiftParser.FunctionCallContext
- ID() - Method in class org.snpsift.antlr.SnpSiftParser.VarReferenceContext
- idx - Variable in class org.snpsift.antlr.SnpSiftParser.LiteralIndexContext
- In - Class in org.snpsift.lang.function
-
Is an expression in a set?
- In(ArrayList<HashSet<String>>, Expression, Expression) - Constructor for class org.snpsift.lang.function.In
- incGenotype(int) - Method in class org.snpsift.caseControl.VariantCounter
- incGenotype(int, int) - Method in class org.snpsift.caseControl.VariantCounter
- index() - Method in class org.snpsift.annotate.VcfIndex
-
Load or create index
- INDEX_EXT - Static variable in class org.snpsift.annotate.VcfIndex
- INDEX_FORMAT_VERSION - Static variable in class org.snpsift.annotate.VcfIndex
- index2offset - Variable in class org.snpsift.annotate.mem.arrays.StringArray
- indexOf(int) - Method in class org.snpsift.annotate.mem.arrays.PosIndex
-
Find the index of a position using binary search
- indexOfSlow(int) - Method in class org.snpsift.annotate.mem.arrays.PosIndex
-
Find the index of a position using a (slow) linear search Used for testing
- indexStr(int) - Method in class org.snpsift.lang.expression.Field
-
Convert and index to a string
- Individual - Class in org.snpsift.pedigree
-
An individual in the pedigree Individuals are like TfamEntries but have drawing info (coordinates, color, etc.)
- Individual(TfamEntry) - Constructor for class org.snpsift.pedigree.Individual
- Inf - Enum constant in enum class org.snpsift.lang.expression.FieldConstant.FieldConstantNames
- INFO_GENE_SETS - Static variable in class org.snpsift.SnpSiftCmdGeneSets
- infoFields - Variable in class org.snpsift.annotate.AnnotateVcfDb
- infoFields - Variable in class org.snpsift.SnpSiftCmdAnnotate
- infoFields - Variable in class org.snpsift.SnpSiftCmdVcfOperator
- init() - Method in class org.snpsift.lang.expression.FieldLof
- init() - Method in class org.snpsift.lang.expression.FieldNmd
- init() - Method in class org.snpsift.SnpSift
-
Initialize default values
- init() - Method in class org.snpsift.SnpSiftCmdAnnotate
-
Initialize default values
- init() - Method in class org.snpsift.SnpSiftCmdAnnotateMem
-
Initialize
- init() - Method in class org.snpsift.SnpSiftCmdCaseControl
- init() - Method in class org.snpsift.SnpSiftCmdConcordance
- init() - Method in class org.snpsift.SnpSiftCmdDbNsfp
-
Initialize default values
- init() - Method in class org.snpsift.SnpSiftCmdExtractFields
- init() - Method in class org.snpsift.SnpSiftCmdFilter
-
Initialize default values
- init() - Method in class org.snpsift.SnpSiftCmdFilterGt
-
Initialize default values
- init() - Method in class org.snpsift.SnpSiftCmdGwasCatalog
-
Initialize default values
- init() - Method in class org.snpsift.SnpSiftCmdIntervals
-
Initialize default values
- init() - Method in class org.snpsift.SnpSiftCmdIntervalsIndex
- init() - Method in class org.snpsift.SnpSiftCmdJoin
- init() - Method in class org.snpsift.SnpSiftCmdPhastCons
- init() - Method in class org.snpsift.SnpSiftCmdVcf2Tped
-
Default parameters
- INITIAL_CAPACITY - Static variable in class org.snpsift.annotate.VcfIndexDataChromo
- INITIAL_CAPACITY - Static variable in class org.snpsift.annotate.VcfIndexTree
- initialSampleSize - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- initialValue() - Method in class org.snpsift.SnpSiftCmdVcfOperator
- initTabix(String) - Method in class org.snpsift.annotate.DbVcfTabix
-
Initialize tabix reader
- initTabix(String) - Method in class org.snpsift.fileIterator.DbNsfp
-
Initialize tabix reader
- INS - Enum constant in enum class org.snpsift.annotate.mem.VariantCategory
- INT_LITERAL - Static variable in class org.snpsift.antlr.SnpSiftLexer
- INT_LITERAL - Static variable in class org.snpsift.antlr.SnpSiftParser
- INT_LITERAL() - Method in class org.snpsift.antlr.SnpSiftParser.LiteralIntContext
- intergenic - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- intersects(int, int) - Method in class org.snpsift.annotate.VcfIndexDataChromo
-
Does interval at position 'idx' intersect positions 'pos'?
- intersects(int, Marker) - Method in class org.snpsift.annotate.VcfIndexDataChromo
-
Does interval at position 'idx' intersect 'marker'?
- inverseFieldSelection - Variable in class org.snpsift.SnpSiftCmdDbNsfp
- is(int) - Method in class org.snpsift.annotate.mem.arrays.BoolArray
-
Is the data value is index i set?
- isBool() - Method in class org.snpsift.lang.Value
- isConstantField(String) - Static method in class org.snpsift.lang.expression.FieldConstant
-
Is this string a constant's name?
- isDescendant(Individual) - Method in class org.snpsift.pedigree.Individual
-
Is 'this' descendant from 'ind' (e.g.
- isEmpty() - Method in class org.snpsift.annotate.VcfIndexTree
- isFemale() - Method in class org.snpsift.pedigree.Individual
- isFloat() - Method in class org.snpsift.lang.Value
- IsHet - Class in org.snpsift.lang.function
-
Is 'genotypeNum' heterozygous?
- IsHet(Expression) - Constructor for class org.snpsift.lang.function.IsHet
- IsHom - Class in org.snpsift.lang.function
-
Is 'genotypeNum' homozygous?
- IsHom(Expression) - Constructor for class org.snpsift.lang.function.IsHom
- isInSync() - Method in class org.snpsift.annotate.VcfIndexTree
- isInt() - Method in class org.snpsift.lang.Value
- isMale() - Method in class org.snpsift.pedigree.Individual
- isNull() - Method in class org.snpsift.lang.Value
- isNull(int) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
-
Is the data at index i null?
- isNUllData - Variable in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
- isOpt(String) - Method in class org.snpsift.SnpSift
-
Is this a command line option (e.g.
- IsRef - Class in org.snpsift.lang.function
-
Is 'genotypeNum' reference?
- IsRef(Expression) - Constructor for class org.snpsift.lang.function.IsRef
- isRoot() - Method in class org.snpsift.pedigree.Individual
-
Is this a root node?
- isSampleName(VcfEntry, String) - Method in class org.snpsift.lang.expression.Field
- isString() - Method in class org.snpsift.lang.Value
- isSub() - Method in class org.snpsift.lang.expression.Field
- isSub() - Method in class org.snpsift.lang.expression.FieldGenotype
- isSub() - Method in class org.snpsift.lang.expression.FieldGenotypeSub
- isSub() - Method in class org.snpsift.lang.expression.FieldSub
- IsVariant - Class in org.snpsift.lang.function
-
Is 'genotypeNum' reference?
- IsVariant(Expression) - Constructor for class org.snpsift.lang.function.IsVariant
- iterator() - Method in class org.snpsift.annotate.mem.arrays.StringArrayBase
- iterator() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
- iterator() - Method in class org.snpsift.annotate.mem.Fields
- iterator() - Method in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
- iterator() - Method in class org.snpsift.annotate.VcfIndexTree
- iterator() - Method in class org.snpsift.gwasCatalog.GwasCatalog
J
- join(boolean) - Method in class org.snpsift.SnpSiftCmdSplit
-
Join files
- journal - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
K
- key(String, int) - Method in class org.snpsift.gwasCatalog.GwasCatalog
-
Create a 'key' string
- key(GwasCatalogEntry) - Method in class org.snpsift.gwasCatalog.GwasCatalog
-
Create a 'key' string
L
- label(Point, String) - Method in class org.snpsift.pedigree.PedigreeDraw
- LangFactory - Class in org.snpsift.lang
-
Creates objects from an AST
- LangFactory() - Constructor for class org.snpsift.lang.LangFactory
- LangFactory(ArrayList<HashSet<String>>, EffFormatVersion, boolean) - Constructor for class org.snpsift.lang.LangFactory
- latestResults - Variable in class org.snpsift.fileIterator.DbNsfp
- latestResultsInterval - Variable in class org.snpsift.fileIterator.DbNsfp
- latestVcfEntry - Variable in class org.snpsift.SnpSiftCmdConcordance
- ld() - Method in class org.snpsift.VcfLd
-
Calculate linkage disequilibrium parameters
- ld(VcfEntry, VcfEntry) - Method in class org.snpsift.VcfLd
-
Calculate linkage disequilibrium parameter
- Le - Class in org.snpsift.lang.expression
-
Less or equal than
- Le(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Le
- left - Variable in class org.snpsift.lang.expression.ExpressionBinary
- length() - Method in class org.snpsift.annotate.mem.arrays.StringArrayBase
-
Number of ellements in the array
- line(Point, Point) - Method in class org.snpsift.pedigree.PedigreeDraw
- line(Point, Point, String) - Method in class org.snpsift.pedigree.PedigreeDraw
- line(Individual, Individual, Individual) - Method in class org.snpsift.pedigree.PedigreeDraw
-
Line between Mother-Father and Child
- lineDashed(Point, Point, String) - Method in class org.snpsift.pedigree.PedigreeDraw
- lines2SortedVariantsVcfIterator(String) - Static method in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
-
Create a VcfFileIterator from a string containig VCF lines
- link - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- Literal - Class in org.snpsift.lang.expression
- Literal(long) - Constructor for class org.snpsift.lang.expression.Literal
- Literal(Boolean) - Constructor for class org.snpsift.lang.expression.Literal
- Literal(Double) - Constructor for class org.snpsift.lang.expression.Literal
- Literal(String) - Constructor for class org.snpsift.lang.expression.Literal
- LiteralBoolContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.LiteralBoolContext
- LiteralFloatContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.LiteralFloatContext
- LiteralIndexContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.LiteralIndexContext
- LiteralIntContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.LiteralIntContext
- LiteralStringContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.LiteralStringContext
- load() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
- load(DataInputStream) - Method in class org.snpsift.annotate.VcfIndexTree
-
Read data from input stream
- load(String) - Static method in class org.snpsift.annotate.mem.Fields
- load(String) - Static method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
-
Load from file
- load(String) - Method in class org.snpsift.gwasCatalog.GwasCatalog
-
Load data from file
- load(String, boolean) - Static method in class org.snpsift.annotate.mem.database.VariantDataFrame
- load(String, Genome) - Method in class org.snpsift.annotate.VcfIndexTree
- loadConfig() - Method in class org.snpsift.SnpSift
-
Read config file
- loadIndex(String) - Method in class org.snpsift.annotate.VcfIndex
-
Load index form a file
- loadIntervals() - Method in class org.snpsift.SnpSiftCmdIntervalsIndex
-
Load all BED files
- loadVcfFiles() - Method in class org.snpsift.SnpSiftCmdSort
-
Load VCF files
- LOF - Enum constant in enum class org.snpsift.lang.expression.FieldIterator.IteratorType
- log - Variable in class org.snpsift.SnpSift
- Lt - Class in org.snpsift.lang.expression
-
Greater equal
- Lt(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Lt
M
- main(String[]) - Static method in class org.snpsift.annotate.mem.Zzz
-
Main
- main(String[]) - Static method in class org.snpsift.hwe.SnpSiftCmdHwe
-
Main
- main(String[]) - Static method in class org.snpsift.SnpSift
-
Main
- main(String[]) - Static method in class org.snpsift.util.FastaSample
-
Main
- male(Individual) - Method in class org.snpsift.pedigree.PedigreeDraw
- mappedGene - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- mappedTrait - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- mappedTraitUri - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- marker(int) - Method in class org.snpsift.annotate.VcfIndexDataChromo
-
Create a marker form data at position 'idx'
- MarkerFile - Class in org.snpsift.annotate
-
Represents a marker in a file (located at 'fileIdx' bytes since the beginning of the file)
- MarkerFile(Marker, int, int, long) - Constructor for class org.snpsift.annotate.MarkerFile
- match(Variant, VariantVcfEntry) - Method in class org.snpsift.annotate.AnnotateVcfDb
-
Does database entry 'dbVcfEntry' match 'variant'?
- match(Variant, DbNsfpEntry) - Method in class org.snpsift.fileIterator.DbNsfp
-
Does database entry 'DbNsfpEntry' match 'variant'?
- Match - Class in org.snpsift.lang.expression
-
Match a regular expression (string)
- Match(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Match
- MAX - Enum constant in enum class org.snpsift.SnpSiftCmdVcfOperator.Operator
- MAX_DIFF_COLLAPSE - Static variable in class org.snpsift.annotate.VcfIndexTree
- MAX_ERRORS - Static variable in class org.snpsift.annotate.AnnotateVcfDb
- MAX_NUM_STRING_TO_SHOW - Static variable in class org.snpsift.annotate.mem.arrays.EnumArray
- MAX_NUM_STRING_TO_SHOW - Static variable in class org.snpsift.annotate.mem.arrays.StringArray
- MAX_NUMBER_OF_ELEMENTS_TO_SHOW - Static variable in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
- MAX_NUMBER_OF_ENUM_VALUES - Static variable in class org.snpsift.annotate.mem.arrays.EnumArray
- MAX_ROWS_TO_SHOW - Static variable in class org.snpsift.annotate.mem.dataFrame.DataFrame
- maxBlockSize - Variable in class org.snpsift.SnpSiftCmdAnnotate
- maxChrPosRefAltIdx - Variable in class org.snpsift.fileIterator.DbNsfp
- mean() - Method in class org.snpsift.SnpSiftCmdCovarianceMatrix
-
Calculate mean
- merged - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- method - Variable in class org.snpsift.SnpSiftCmdAnnotate
- MIN - Enum constant in enum class org.snpsift.SnpSiftCmdVcfOperator.Operator
- MIN_JUMP - Static variable in class org.snpsift.SnpSiftCmdDbNsfp
- Minus - Class in org.snpsift.lang.expression
-
And expression
- Minus(Expression) - Constructor for class org.snpsift.lang.expression.Minus
- Minus(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Minus
- MISSING - Enum constant in enum class org.snpsift.SnpSiftCmdVcf2Tped.UseMissing
- MISSING_ENTRY - Static variable in class org.snpsift.SnpSiftCmdConcordance
- MISSING_GENOTYPE - Static variable in class org.snpsift.SnpSiftCmdConcordance
- MIXED - Enum constant in enum class org.snpsift.annotate.mem.VariantCategory
- MNP - Enum constant in enum class org.snpsift.annotate.mem.VariantCategory
- Mod - Class in org.snpsift.lang.expression
-
And expression
- Mod(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Mod
- modeNames - Static variable in class org.snpsift.antlr.SnpSiftLexer
- moveIfLeft(int, int, Set<Individual>) - Method in class org.snpsift.pedigree.PedigreeDraw
-
Move if the object is located to the left of posX
- moveIfRight(int, int, Set<Individual>) - Method in class org.snpsift.pedigree.PedigreeDraw
-
Move if the object is located to the right of posX
- multipleValues - Variable in class org.snpsift.fileIterator.DbNsfp
N
- Na - Class in org.snpsift.lang.expression
-
Exists operator (true if a field exists)
- Na(Expression) - Constructor for class org.snpsift.lang.expression.Na
- name - Variable in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
- name - Variable in class org.snpsift.lang.expression.Field
- names2index - Variable in class org.snpsift.fileIterator.DbNsfp
- NaN - Enum constant in enum class org.snpsift.lang.expression.FieldConstant.FieldConstantNames
- needsConfig - Variable in class org.snpsift.SnpSift
- needsDb - Variable in class org.snpsift.SnpSift
- needsGenome - Variable in class org.snpsift.SnpSift
- negated - Variable in class org.snpsift.lang.expression.Expression
- Neq - Class in org.snpsift.lang.expression
-
Not equal
- Neq(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Neq
- next() - Method in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
- next() - Method in class org.snpsift.lang.expression.FieldIterator
-
Next in iteration
- NMD - Enum constant in enum class org.snpsift.lang.expression.FieldIterator.IteratorType
- Not - Class in org.snpsift.lang.expression
-
Not expression
- Not(Expression) - Constructor for class org.snpsift.lang.expression.Not
- NotMatch - Class in org.snpsift.lang.expression
-
Match a regular expression (string)
- NotMatch(Expression, Expression) - Constructor for class org.snpsift.lang.expression.NotMatch
- NULL - Static variable in class org.snpsift.lang.Value
- number - Variable in class org.snpsift.lang.expression.Field
- numEnums() - Method in class org.snpsift.annotate.mem.arrays.EnumArray
-
Number of enums in the array
- numWorkers - Variable in class org.snpsift.SnpSift
O
- of(String[]) - Static method in class org.snpsift.annotate.mem.arrays.StringArray
-
Create a StringArray from an array of strings
- of(String, String[]) - Static method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnString
-
Create a StringColumn from an array of strings
- of(Collection<String>) - Static method in class org.snpsift.annotate.mem.arrays.StringArray
-
Create a StringArray from a collection of strings
- of(Variant) - Static method in enum class org.snpsift.annotate.mem.VariantCategory
- offset - Variable in class org.snpsift.annotate.mem.arrays.StringArray
- op - Variable in class org.snpsift.antlr.SnpSiftParser.ExpressionCompContext
- op - Variable in class org.snpsift.antlr.SnpSiftParser.ExpressionExistsContext
- op - Variable in class org.snpsift.antlr.SnpSiftParser.ExpressionLogicContext
- op - Variable in class org.snpsift.antlr.SnpSiftParser.ExpressionPlusContext
- op - Variable in class org.snpsift.antlr.SnpSiftParser.ExpressionTimesContext
- op - Variable in class org.snpsift.antlr.SnpSiftParser.ExpressionUnaryContext
- open() - Method in class org.snpsift.annotate.AnnotateVcfDb
- open() - Method in interface org.snpsift.annotate.DbMarker
-
Open database (load index in memory if required)
- open() - Method in class org.snpsift.annotate.DbVcf
- open() - Method in class org.snpsift.annotate.DbVcfMem
-
Open database annotation file
- open() - Method in class org.snpsift.annotate.DbVcfSorted
-
Open VCF database annotation file
- open() - Method in class org.snpsift.annotate.DbVcfTabix
-
Open database annotation file
- open() - Method in class org.snpsift.annotate.VcfIndex
-
Open file
- open() - Method in class org.snpsift.fileIterator.DbNsfp
- openVcfInputFile() - Method in class org.snpsift.SnpSift
-
Open VCF input file
- operator - Variable in class org.snpsift.lang.expression.Expression
- operator - Variable in class org.snpsift.SnpSiftCmdVcfOperator
- Or - Class in org.snpsift.lang.expression
-
Or expression
- Or(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Or
- orBeta - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- ord2enum - Variable in class org.snpsift.annotate.mem.arrays.EnumArray
- org.snpsift - package org.snpsift
- org.snpsift.annotate - package org.snpsift.annotate
- org.snpsift.annotate.mem - package org.snpsift.annotate.mem
- org.snpsift.annotate.mem.arrays - package org.snpsift.annotate.mem.arrays
- org.snpsift.annotate.mem.database - package org.snpsift.annotate.mem.database
- org.snpsift.annotate.mem.dataFrame - package org.snpsift.annotate.mem.dataFrame
- org.snpsift.annotate.mem.dataFrame.dataFrameColumn - package org.snpsift.annotate.mem.dataFrame.dataFrameColumn
- org.snpsift.annotate.mem.variantTypeCounter - package org.snpsift.annotate.mem.variantTypeCounter
- org.snpsift.antlr - package org.snpsift.antlr
- org.snpsift.caseControl - package org.snpsift.caseControl
- org.snpsift.fileIterator - package org.snpsift.fileIterator
- org.snpsift.gwasCatalog - package org.snpsift.gwasCatalog
- org.snpsift.hwe - package org.snpsift.hwe
- org.snpsift.lang - package org.snpsift.lang
- org.snpsift.lang.expression - package org.snpsift.lang.expression
- org.snpsift.lang.function - package org.snpsift.lang.function
- org.snpsift.pedigree - package org.snpsift.pedigree
- org.snpsift.phatsCons - package org.snpsift.phatsCons
- org.snpsift.util - package org.snpsift.util
- OTHER - Enum constant in enum class org.snpsift.annotate.mem.VariantCategory
- outField - Variable in class org.snpsift.SnpSiftCmdVcfOperator
- output - Variable in class org.snpsift.SnpSift
P
- pAllelic(int[], int[], double) - Method in class org.snpsift.SnpSiftCmdCaseControl
-
Allelic model: Count number of SNPs
- parseArgs(String[]) - Method in class org.snpsift.caseControl.SnpSiftCmdCaseControlSummary
- parseArgs(String[]) - Method in class org.snpsift.hwe.SnpSiftCmdHwe
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSift
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdAlleleMatrix
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdAnnotate
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdAnnotateMem
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdCaseControl
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdConcordance
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdCovarianceMatrix
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdDbNsfp
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdExtractFields
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdFilter
-
Parse command line options
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdFilterChrPos
-
Parse command line options
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdFilterGt
-
Parse command line options
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdGeneSets
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdGt
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdGwasCatalog
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdIntersect
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdIntervals
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdIntervalsIndex
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdJoin
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdPedShow
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdPhastCons
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdPrivate
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdRemoveReferenceGenotypes
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdRmInfo
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdSort
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdSplit
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdTsTv
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdVarType
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdVcf2Tped
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdVcfCheck
-
Parse command line arguments
- parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdVcfOperator
- parseChrPosRefAlt() - Method in class org.snpsift.fileIterator.DbNsfpEntry
-
Parse dbSNFP 'Chr, pos, ref, alt' values from a single line
- parseExpression(String) - Method in class org.snpsift.SnpSiftCmdFilter
-
Parse expression
- parseExpression(String) - Method in class org.snpsift.SnpSiftCmdFilterGt
-
Parse expression
- parseGenotypes(VcfEntry) - Method in class org.snpsift.caseControl.VariantCounter
-
Update genotype counts
- parseKeyValues() - Method in class org.snpsift.fileIterator.DbNsfpEntry
-
Parse dbSNFP ALL values from a single line and store them in 'values' hash
- parsePosition(String) - Method in class org.snpsift.fileIterator.DbNsfpEntry
-
Parse a string as a 'position'.
- parseVcfHeaderFields(String) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
-
Read VCF header and get columns data types
- parseVcfHeaderFields(VcfFileIterator) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
-
Read VCF header and get columns data types
- pDominant(int[], int[], double) - Method in class org.snpsift.SnpSiftCmdCaseControl
-
Dominant model: Either a/A or A/A causes the disease
- pedigree - Variable in class org.snpsift.SnpSiftCmdCaseControl
- PedigreeDraw - Class in org.snpsift.pedigree
-
Draws a pedigree using SVG
- PedigreeDraw(String) - Constructor for class org.snpsift.pedigree.PedigreeDraw
- PedigreeDraw(PedPedigree) - Constructor for class org.snpsift.pedigree.PedigreeDraw
- pGenotypic(int[], int[]) - Method in class org.snpsift.SnpSiftCmdCaseControl
-
Genotypic model (Chi Square)
- PhastCons - Class in org.snpsift.phatsCons
-
Conservation score
- PhastCons() - Constructor for class org.snpsift.phatsCons.PhastCons
- platform - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- Plus - Class in org.snpsift.lang.expression
-
And expression
- Plus(Expression) - Constructor for class org.snpsift.lang.expression.Plus
- Plus(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Plus
- PLUS - Enum constant in enum class org.snpsift.SnpSiftCmdVcfOperator.Operator
- PosIndex - Class in org.snpsift.annotate.mem.arrays
-
An index by possition
- PosIndex(int) - Constructor for class org.snpsift.annotate.mem.arrays.PosIndex
- pRecessive(int[], int[], double) - Method in class org.snpsift.SnpSiftCmdCaseControl
-
Recessive model: Only A/A causes the disease
- prependInfoFieldName - Variable in class org.snpsift.annotate.AnnotateVcfDb
- prependInfoFieldName - Variable in class org.snpsift.SnpSiftCmdAnnotate
- prependInfoName(String) - Method in class org.snpsift.annotate.AnnotateVcfDb
-
Prepend 'prependInfoFieldName' to all info fields
- processStr(VcfEntry, StringBuilder) - Method in class org.snpsift.SnpSiftCmdAlleleMatrix
-
Process a VCF entry and return a string (tab separated values)
- processVcfHeader(VcfFileIterator) - Method in class org.snpsift.SnpSift
-
Process VCF header related issues
- processVcfHeader(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdCaseControl
- PRODUCT - Enum constant in enum class org.snpsift.SnpSiftCmdVcfOperator.Operator
- pTrend(int[], int[]) - Method in class org.snpsift.SnpSiftCmdCaseControl
-
Trend model
- pubmedId - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- pValue - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- pValueMlog - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- pValueText - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- pvalueThreshold - Variable in class org.snpsift.SnpSiftCmdCaseControl
Q
- query(Interval) - Method in class org.snpsift.annotate.VcfIndexTree
-
Query index to find all VCF entries intersecting 'marker' Store VCF entries in 'results'
- query(Interval, int, Markers) - Method in class org.snpsift.annotate.VcfIndexTree
-
Query index to find all VCF entries intersecting 'marker', starting from node 'idx' Store VCF entries in 'results'
- query(Marker) - Method in class org.snpsift.annotate.VcfIndex
-
Query interval forest
- query(Variant) - Method in class org.snpsift.annotate.AnnotateVcfDb
-
Query database and find results matching 'variant'
- query(Variant) - Method in class org.snpsift.annotate.DbVcf
-
Find matching entries in the database
- query(Variant) - Method in class org.snpsift.annotate.DbVcfMem
- query(Variant) - Method in class org.snpsift.annotate.DbVcfSorted
- query(Variant) - Method in class org.snpsift.annotate.DbVcfTabix
- query(Variant) - Method in class org.snpsift.fileIterator.DbNsfp
-
Query tabix file to get dbNsfp entries (or cached entries from latest results)
- query(Q) - Method in interface org.snpsift.annotate.DbMarker
-
Find matching entries in the database
- queryIntersects(Interval, int, Markers) - Method in class org.snpsift.annotate.VcfIndexTree
-
Query VCF entries intersecting 'marker' at node 'idx'
- QueryResult - Class in org.snpsift.annotate
-
A database query and a result.
- QueryResult(Variant, Collection<VariantVcfEntry>) - Constructor for class org.snpsift.annotate.QueryResult
- quiet - Variable in class org.snpsift.SnpSift
R
- rand() - Method in class org.snpsift.util.RandomUtil
- randAcgt() - Method in class org.snpsift.util.RandomUtil
- randBase(String) - Method in class org.snpsift.util.RandomUtil
- randBases(int) - Method in class org.snpsift.util.RandomUtil
- randBases(int, String) - Method in class org.snpsift.util.RandomUtil
- randBool() - Method in class org.snpsift.util.RandomUtil
- randBoolOrNull() - Method in class org.snpsift.util.RandomUtil
- randChar() - Method in class org.snpsift.util.RandomUtil
- randCharOrNull() - Method in class org.snpsift.util.RandomUtil
- randDouble(double) - Method in class org.snpsift.util.RandomUtil
- randDoubleOrNull() - Method in class org.snpsift.util.RandomUtil
- randEnum(ArrayList<String>) - Method in class org.snpsift.util.RandomUtil
- randEnumOrNull(ArrayList<String>) - Method in class org.snpsift.util.RandomUtil
- randInt() - Method in class org.snpsift.util.RandomUtil
- randInt(int) - Method in class org.snpsift.util.RandomUtil
- randIntOrNull() - Method in class org.snpsift.util.RandomUtil
- randIntOrNull(int) - Method in class org.snpsift.util.RandomUtil
- randLong() - Method in class org.snpsift.util.RandomUtil
- randLong(long) - Method in class org.snpsift.util.RandomUtil
- randLongOrNull() - Method in class org.snpsift.util.RandomUtil
- randLongOrNull(long) - Method in class org.snpsift.util.RandomUtil
- RandomUtil - Class in org.snpsift.util
- RandomUtil() - Constructor for class org.snpsift.util.RandomUtil
- RandomUtil(int) - Constructor for class org.snpsift.util.RandomUtil
- randString(int) - Method in class org.snpsift.util.RandomUtil
- randStringOrNull() - Method in class org.snpsift.util.RandomUtil
- randStringOrNull(int) - Method in class org.snpsift.util.RandomUtil
- randVariant(VariantCategory) - Method in class org.snpsift.util.RandomUtil
- randVariantAlt(VariantCategory, String) - Method in class org.snpsift.util.RandomUtil
- randVariantRef(VariantCategory) - Method in class org.snpsift.util.RandomUtil
- read(long) - Method in class org.snpsift.annotate.VcfIndex
-
Read a VcfEntry at position 'fileIdx'
- read(MarkerFile) - Method in class org.snpsift.annotate.VcfIndex
-
Read a VcfEntry referenced by 'markerFile'
- readDb() - Method in class org.snpsift.SnpSiftCmdGwasCatalog
-
Read database
- REF - Static variable in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
- REF_NAME - Static variable in class org.snpsift.fileIterator.DbNsfp
- REFERENCE - Enum constant in enum class org.snpsift.SnpSiftCmdVcf2Tped.UseMissing
- refIdx - Variable in class org.snpsift.fileIterator.DbNsfp
- region - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- removeChild(Individual) - Method in class org.snpsift.pedigree.Individual
- replicationSampleSize - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- reportedGene - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- reset() - Method in class org.snpsift.annotate.mem.arrays.BoolArray
- reset() - Method in class org.snpsift.lang.expression.FieldIterator
-
Reset all counters
- reset() - Method in class org.snpsift.util.RandomUtil
- resize() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
-
Resize and memory optimize the data
- resize() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
-
Resize and memory optimize the data
- resize() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnString
-
Resize and memory optimize the data
- results - Variable in class org.snpsift.annotate.QueryResult
- returnType - Variable in class org.snpsift.lang.expression.Field
- returnType(VcfEntry) - Method in class org.snpsift.lang.expression.Field
- returnType(VcfGenotype) - Method in class org.snpsift.lang.expression.Field
- REVISION - Static variable in class org.snpsift.SnpSift
- right - Variable in class org.snpsift.lang.expression.ExpressionBinary
- riskAllele - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- riskAlleleFrequency - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- RULE_compilationUnit - Static variable in class org.snpsift.antlr.SnpSiftParser
- RULE_expression - Static variable in class org.snpsift.antlr.SnpSiftParser
- ruleNames - Static variable in class org.snpsift.antlr.SnpSiftLexer
- ruleNames - Static variable in class org.snpsift.antlr.SnpSiftParser
- run() - Method in class org.snpsift.caseControl.SnpSiftCmdCaseControlSummary
-
Run summary
- run() - Method in class org.snpsift.hwe.SnpSiftCmdHwe
-
Analyze the file (run multi-thread mode)
- run() - Method in class org.snpsift.SnpSift
- run() - Method in class org.snpsift.SnpSiftCmdAlleleMatrix
-
Process the whole VCF file
- run() - Method in class org.snpsift.SnpSiftCmdAnnotate
-
Annotate each entry of a VCF file
- run() - Method in class org.snpsift.SnpSiftCmdAnnotateMem
-
Annotate each entry of a VCF file
- run() - Method in class org.snpsift.SnpSiftCmdCaseControl
-
Load a file compare calls
- run() - Method in class org.snpsift.SnpSiftCmdConcordance
- run() - Method in class org.snpsift.SnpSiftCmdCovarianceMatrix
-
Process the whole file
- run() - Method in class org.snpsift.SnpSiftCmdDbNsfp
- run() - Method in class org.snpsift.SnpSiftCmdExtractFields
-
Run main algorithm
- run() - Method in class org.snpsift.SnpSiftCmdFilter
- run() - Method in class org.snpsift.SnpSiftCmdFilterChrPos
- run() - Method in class org.snpsift.SnpSiftCmdFilterGt
- run() - Method in class org.snpsift.SnpSiftCmdGeneSets
-
Annotate entries
- run() - Method in class org.snpsift.SnpSiftCmdGt
-
Process a VCF entry and return a string (tab separated values)
- run() - Method in class org.snpsift.SnpSiftCmdGwasCatalog
-
Annotate entries
- run() - Method in class org.snpsift.SnpSiftCmdIntersect
-
Run annotations
- run() - Method in class org.snpsift.SnpSiftCmdIntervals
- run() - Method in class org.snpsift.SnpSiftCmdIntervalsIndex
-
Load a file compare calls
- run() - Method in class org.snpsift.SnpSiftCmdJoin
-
Run algorithm
- run() - Method in class org.snpsift.SnpSiftCmdPedShow
-
Run: Main method
- run() - Method in class org.snpsift.SnpSiftCmdPhastCons
-
Run
- run() - Method in class org.snpsift.SnpSiftCmdPrivate
-
Run annotations
- run() - Method in class org.snpsift.SnpSiftCmdRemoveReferenceGenotypes
-
Analyze the file
- run() - Method in class org.snpsift.SnpSiftCmdRmInfo
-
Analyze the file
- run() - Method in class org.snpsift.SnpSiftCmdSort
-
Run
- run() - Method in class org.snpsift.SnpSiftCmdSplit
-
Run
- run() - Method in class org.snpsift.SnpSiftCmdTsTv
-
Analyze the file
- run() - Method in class org.snpsift.SnpSiftCmdVarType
-
Annotate entries
- run() - Method in class org.snpsift.SnpSiftCmdVcf2Tped
-
Run annotations
- run() - Method in class org.snpsift.SnpSiftCmdVcfCheck
-
Process the whole VCF file
- run() - Method in class org.snpsift.SnpSiftCmdVcfOperator
-
Annotate
- run() - Method in class org.snpsift.util.FastaSample
- run(boolean) - Method in class org.snpsift.SnpSiftCmdAnnotate
-
Run annotations
- run(boolean) - Method in class org.snpsift.SnpSiftCmdAnnotateMem
-
Run annotations
- run(boolean) - Method in class org.snpsift.SnpSiftCmdCaseControl
-
Run
- run(boolean) - Method in class org.snpsift.SnpSiftCmdDbNsfp
-
Run annotation algorithm
- run(boolean) - Method in class org.snpsift.SnpSiftCmdExtractFields
- run(boolean) - Method in class org.snpsift.SnpSiftCmdFilter
-
Run filter
- run(boolean) - Method in class org.snpsift.SnpSiftCmdFilterChrPos
-
Run filter
- run(boolean) - Method in class org.snpsift.SnpSiftCmdFilterGt
-
Run filter
- run(boolean) - Method in class org.snpsift.SnpSiftCmdGeneSets
- run(boolean) - Method in class org.snpsift.SnpSiftCmdGwasCatalog
- run(boolean) - Method in class org.snpsift.SnpSiftCmdIntervals
-
Load a file compare calls
- run(boolean) - Method in class org.snpsift.SnpSiftCmdPhastCons
-
Run annotations
- run(boolean) - Method in class org.snpsift.SnpSiftCmdPrivate
-
Run annotations.
- run(boolean) - Method in class org.snpsift.SnpSiftCmdSort
- run(boolean) - Method in class org.snpsift.SnpSiftCmdVcfOperator
-
Run filter
S
- sanityCheck(VcfEntry, VcfEntry) - Method in class org.snpsift.VcfLd
-
Return an error message if any problem is found or empty string if it is OK.
- save() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
- save(DataOutputStream) - Method in class org.snpsift.annotate.VcfIndexTree
-
Save to output stream
- save(String) - Method in class org.snpsift.annotate.mem.Fields
-
Save to file
- save(String) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
- save(String) - Method in class org.snpsift.annotate.VcfIndex
-
Save index file
- saveDataTypesCache(String) - Method in class org.snpsift.fileIterator.DbNsfp
-
Save data types to cache file
- saveOutput - Variable in class org.snpsift.SnpSift
- sempred(RuleContext, int, int) - Method in class org.snpsift.antlr.SnpSiftParser
- SEP - Static variable in class org.snpsift.SnpSiftCmdConcordance
- SEP_GT - Static variable in class org.snpsift.SnpSiftCmdConcordance
- SEPARATOR - Static variable in class org.snpsift.SnpSiftCmdAlleleMatrix
- set(int) - Method in class org.snpsift.annotate.mem.arrays.BoolArray
-
Set data to null
- set(int, boolean) - Method in class org.snpsift.annotate.mem.arrays.BoolArray
- set(int, int) - Method in class org.snpsift.annotate.mem.arrays.PosIndex
-
Set position to entry number 'i'
- set(int, Object) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
-
Set value at index i, consideting null data
- set(int, String) - Method in class org.snpsift.annotate.mem.arrays.EnumArray
-
Add a string to the array WARNING: Typically you use either 'add' or 'set', but not both
- set(int, String) - Method in class org.snpsift.annotate.mem.arrays.StringArray
-
Add a string to the array WARNING: Typically you use either 'add' or 'set', but not both
- set(int, String) - Method in class org.snpsift.annotate.mem.arrays.StringArrayBase
-
Add a string to the array Return the index of the next element
- set(String, int, Object) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
-
Set data in a column
- set(String, Object) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
- setAddFilterField(String) - Method in class org.snpsift.SnpSiftCmdFilter
- setAffected(Boolean) - Method in class org.snpsift.pedigree.Individual
- setAnnotateEmpty(boolean) - Method in class org.snpsift.annotate.AnnotateVcfDb
- setAnnotateEmpty(boolean) - Method in class org.snpsift.SnpSiftCmdAnnotate
- setColor(String) - Method in class org.snpsift.pedigree.Individual
- setCommand(Class) - Method in class org.snpsift.SnpSift
- setCommand(String) - Method in class org.snpsift.SnpSift
- setConfig(Config) - Method in class org.snpsift.SnpSift
- setConfigFile(String) - Method in class org.snpsift.SnpSift
- setCount(int, int, int, int, int, int, int, int) - Method in class org.snpsift.VcfLd
-
Set counters in order to calculate LD parameters
- setData(int, Object) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
-
Set data at index i
- setData(int, Object) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnBool
- setData(int, Object) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnChar
- setData(int, Object) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnDouble
- setData(int, Object) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnInt
- setData(int, Object) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnLong
- setData(int, Object) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnString
- setDataFrame() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
-
Populate row in DataFrame with the values in this row
- setDataFrame(String) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
-
Set the data frame with a value from this row
- setDataFrame(String, Object) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
-
Set the data frame with a specific value
- setDbDir(String) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
- setDbFileName(String) - Method in class org.snpsift.SnpSift
- setDebug(boolean) - Method in class org.snpsift.annotate.AnnotateVcfDb
- setDebug(boolean) - Method in interface org.snpsift.annotate.DbMarker
- setDebug(boolean) - Method in class org.snpsift.annotate.DbVcf
- setDebug(boolean) - Method in class org.snpsift.annotate.VcfIndex
- setDebug(boolean) - Method in class org.snpsift.annotate.VcfIndexTree
- setDebug(boolean) - Method in class org.snpsift.fileIterator.DbNsfp
- setDebug(boolean) - Method in class org.snpsift.SnpSift
- setDepth(int) - Method in class org.snpsift.pedigree.Individual
- setExceptionIfNotFound(boolean) - Method in class org.snpsift.lang.expression.Field
- setExceptionIfNotFound(boolean) - Method in class org.snpsift.SnpSiftCmdFilter
- setExistsInfoField(String) - Method in class org.snpsift.annotate.AnnotateVcfDb
- setExpression(String) - Method in class org.snpsift.SnpSiftCmdFilter
- setFather(Individual) - Method in class org.snpsift.pedigree.Individual
- setFieldNamesAnnotate(String[]) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
- setFieldsNamesToAdd(String) - Method in class org.snpsift.SnpSiftCmdDbNsfp
- setFilePosEnd(long) - Method in class org.snpsift.annotate.VcfIndexDataChromo
- setFilterId(String) - Method in class org.snpsift.SnpSiftCmdFilter
- setFormatVersion(EffFormatVersion) - Method in class org.snpsift.SnpSiftCmdFilter
- setGenotype(int, int) - Method in class org.snpsift.caseControl.VariantCounter
- setId(String) - Method in class org.snpsift.pedigree.Individual
- setIdx(int) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
- setInfoFields(boolean, Collection<String>) - Method in class org.snpsift.annotate.AnnotateVcfDb
- setInOffset(int) - Method in class org.snpsift.SnpSiftCmdIntervalsIndex
- setInverse(boolean) - Method in class org.snpsift.SnpSiftCmdFilter
- setLabel(String) - Method in class org.snpsift.pedigree.Individual
- setMax(FieldIterator.IteratorType, int) - Method in class org.snpsift.lang.expression.FieldIterator
-
Set 'max' parameter for an iterator
- setMaxBlockSize(int) - Method in class org.snpsift.annotate.DbVcfSorted
- setMaxBlockSize(int) - Method in class org.snpsift.annotate.VcfIndex
- setMaxBlockSize(int) - Method in class org.snpsift.annotate.VcfIndexTree
- setMother(Individual) - Method in class org.snpsift.pedigree.Individual
- setMsigdb(String) - Method in class org.snpsift.SnpSiftCmdGeneSets
- setNegated(boolean) - Method in class org.snpsift.lang.expression.Expression
- setNullRatio(double) - Method in class org.snpsift.util.RandomUtil
- setOrder(int) - Method in class org.snpsift.pedigree.Individual
- setPrefix(String) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
- setPrefix(String) - Method in class org.snpsift.annotate.mem.database.VariantDataFrame
- setPrependInfoFieldName(String) - Method in class org.snpsift.annotate.AnnotateVcfDb
- setQuiet(boolean) - Method in class org.snpsift.SnpSift
- setRand(Random) - Method in class org.snpsift.util.RandomUtil
- setRmFilterField(String) - Method in class org.snpsift.SnpSiftCmdFilter
- setSaveOutput(boolean) - Method in class org.snpsift.SnpSift
- setSeed(long) - Method in class org.snpsift.util.RandomUtil
- setSets(ArrayList<HashSet<String>>) - Method in class org.snpsift.SnpSiftCmdFilter
- setSex(Sex) - Method in class org.snpsift.pedigree.Individual
- setShowVcfHeader(boolean) - Method in class org.snpsift.SnpSift
- setShowVersion(boolean) - Method in class org.snpsift.SnpSift
- setSuppressOutput(boolean) - Method in class org.snpsift.SnpSift
- setTabixCheck(boolean) - Method in class org.snpsift.SnpSiftCmdDbNsfp
- setType(int) - Method in class org.snpsift.lang.expression.FieldIterator
- setUseId(boolean) - Method in class org.snpsift.annotate.AnnotateVcfDb
- setUsePassField(boolean) - Method in class org.snpsift.SnpSiftCmdFilter
- setUseRefAlt(boolean) - Method in class org.snpsift.annotate.AnnotateVcfDb
- setVcf(VcfFileIterator) - Method in class org.snpsift.annotate.VcfIndexTree
- setVcfHeaderAddProgramVersion(boolean) - Method in class org.snpsift.SnpSift
- setVerbose(boolean) - Method in class org.snpsift.annotate.AnnotateVcfDb
- setVerbose(boolean) - Method in interface org.snpsift.annotate.DbMarker
- setVerbose(boolean) - Method in class org.snpsift.annotate.DbVcf
- setVerbose(boolean) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
- setVerbose(boolean) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
- setVerbose(boolean) - Method in class org.snpsift.annotate.VcfIndex
- setVerbose(boolean) - Method in class org.snpsift.annotate.VcfIndexTree
- setVerbose(boolean) - Method in class org.snpsift.fileIterator.DbNsfp
- setVerbose(boolean) - Method in class org.snpsift.SnpSift
- setWriteBySampleFile(boolean) - Method in class org.snpsift.SnpSiftCmdConcordance
- setWriteSummaryFile(boolean) - Method in class org.snpsift.SnpSiftCmdConcordance
- shiftArgs - Variable in class org.snpsift.SnpSift
- SHORT_VARIANT_LEN - Static variable in class org.snpsift.util.RandomUtil
- SHOW - Static variable in class org.snpsift.annotate.DbVcfMem
- SHOW - Static variable in class org.snpsift.SnpSiftCmdAnnotate
- SHOW - Static variable in class org.snpsift.SnpSiftCmdExtractFields
- SHOW - Static variable in class org.snpsift.SnpSiftCmdGeneSets
- SHOW - Static variable in class org.snpsift.SnpSiftCmdGwasCatalog
- SHOW - Static variable in class org.snpsift.SnpSiftCmdSort
- SHOW - Static variable in class org.snpsift.SnpSiftCmdSplit
- SHOW - Static variable in class org.snpsift.SnpSiftCmdVarType
- SHOW_EVERY - Static variable in class org.snpsift.annotate.VcfIndex
- SHOW_EVERY - Static variable in class org.snpsift.hwe.SnpSiftCmdHwe
- SHOW_EVERY - Static variable in class org.snpsift.SnpSiftCmdAlleleMatrix
- SHOW_EVERY - Static variable in class org.snpsift.SnpSiftCmdCaseControl
- SHOW_EVERY - Static variable in class org.snpsift.SnpSiftCmdConcordance
- SHOW_EVERY - Static variable in class org.snpsift.SnpSiftCmdCovarianceMatrix
- SHOW_EVERY - Static variable in class org.snpsift.SnpSiftCmdDbNsfp
- SHOW_EVERY - Static variable in class org.snpsift.SnpSiftCmdGt
- SHOW_EVERY - Static variable in class org.snpsift.SnpSiftCmdPhastCons
- SHOW_EVERY - Static variable in class org.snpsift.SnpSiftCmdRemoveReferenceGenotypes
- SHOW_EVERY - Static variable in class org.snpsift.SnpSiftCmdTsTv
- SHOW_EVERY - Static variable in class org.snpsift.util.ShowProgress
- SHOW_EVERY_LINE - Static variable in class org.snpsift.util.ShowProgress
- SHOW_EVERY_NL - Static variable in class org.snpsift.SnpSiftCmdRemoveReferenceGenotypes
- SHOW_EVERY_NL - Static variable in class org.snpsift.SnpSiftCmdTsTv
- SHOW_EVERY_VCFLINES - Static variable in class org.snpsift.SnpSift
- SHOW_LINES - Static variable in class org.snpsift.annotate.DbVcfMem
- SHOW_LINES - Static variable in class org.snpsift.SnpSiftCmdGeneSets
- SHOW_LINES - Static variable in class org.snpsift.SnpSiftCmdGwasCatalog
- SHOW_LINES - Static variable in class org.snpsift.SnpSiftCmdSort
- SHOW_LINES - Static variable in class org.snpsift.SnpSiftCmdSplit
- SHOW_LINES - Static variable in class org.snpsift.SnpSiftCmdVarType
- showCmd() - Method in class org.snpsift.SnpSift
-
Show command line
- ShowProgress - Class in org.snpsift.util
- ShowProgress() - Constructor for class org.snpsift.util.ShowProgress
- ShowProgress(int, int) - Constructor for class org.snpsift.util.ShowProgress
- showVcfHeader - Variable in class org.snpsift.SnpSift
- showVersion - Variable in class org.snpsift.SnpSift
- showVersion() - Method in class org.snpsift.SnpSift
-
Show version number
- size() - Method in class org.snpsift.annotate.mem.arrays.BoolArray
- size() - Method in class org.snpsift.annotate.mem.arrays.EnumArray
-
Size of the data array (capacity of number of bytes)
- size() - Method in class org.snpsift.annotate.mem.arrays.PosIndex
-
Number of entries in use
- size() - Method in class org.snpsift.annotate.mem.arrays.StringArray
-
Size of the data array (capacity of number of bytes)
- size() - Method in class org.snpsift.annotate.mem.arrays.StringArrayBase
-
Number of different strings in the array
- size() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
-
Number of elements in this DataColumn
- size() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnBool
- size() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnChar
- size() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnDouble
- size() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnInt
- size() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnLong
- size() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnString
- size() - Static method in enum class org.snpsift.annotate.mem.VariantCategory
- size() - Method in class org.snpsift.annotate.VcfIndexDataChromo
- size() - Method in class org.snpsift.annotate.VcfIndexTree
- sizeByDepth(int[]) - Method in class org.snpsift.pedigree.Individual
-
Size by depth
- sizeBytes() - Method in class org.snpsift.annotate.mem.arrays.BoolArray
- sizeBytes() - Method in class org.snpsift.annotate.mem.arrays.EnumArray
-
Memory size of this object (approximate size in bytes)
- sizeBytes() - Method in class org.snpsift.annotate.mem.arrays.PosIndex
-
Memory size of this object (approximate size in bytes)
- sizeBytes() - Method in class org.snpsift.annotate.mem.arrays.StringArray
-
Memory size of this object (approximate size in bytes)
- sizeBytes() - Method in class org.snpsift.annotate.mem.arrays.StringArrayBase
-
Memory size of this object (approximate size in bytes)
- sizeBytes() - Method in class org.snpsift.annotate.mem.database.VariantDataFrame
- sizeBytes() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
-
Memory size of this object
- sizeBytes() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
-
Memory size of this object (approximate size in bytes)
- sizeBytes() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnBool
-
Memory size of this object (approximate size in bytes)
- sizeBytes() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnChar
-
Memory size of this object (approximate size in bytes)
- sizeBytes() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnDouble
-
Memory size of this object (approximate size in bytes)
- sizeBytes() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnInt
-
Memory size of this object (approximate size in bytes)
- sizeBytes() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnLong
-
Memory size of this object (approximate size in bytes)
- sizeBytes() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnString
-
Memory size of this object (approximate size in bytes)
- sizeOf(String) - Static method in class org.snpsift.annotate.mem.arrays.StringArray
-
Calculate the size of a string in memory
- sizeOf(String[]) - Static method in class org.snpsift.annotate.mem.arrays.StringArray
- sizeOf(Collection<String>) - Static method in class org.snpsift.annotate.mem.arrays.StringArray
- sizesByField - Variable in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
- SNP_A - Enum constant in enum class org.snpsift.annotate.mem.VariantCategory
- SNP_C - Enum constant in enum class org.snpsift.annotate.mem.VariantCategory
- SNP_G - Enum constant in enum class org.snpsift.annotate.mem.VariantCategory
- SNP_T - Enum constant in enum class org.snpsift.annotate.mem.VariantCategory
- snpGeneIds - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- snpIdCurrent - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- snps - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- SnpSift - Class in org.snpsift
-
Generic SnpSift tool caller
- SnpSift() - Constructor for class org.snpsift.SnpSift
- SnpSift(String[]) - Constructor for class org.snpsift.SnpSift
- SnpSiftBaseListener - Class in org.snpsift.antlr
-
This class provides an empty implementation of
SnpSiftListener
, which can be extended to create a listener which only needs to handle a subset of the available methods. - SnpSiftBaseListener() - Constructor for class org.snpsift.antlr.SnpSiftBaseListener
- SnpSiftBaseVisitor<T> - Class in org.snpsift.antlr
-
This class provides an empty implementation of
SnpSiftVisitor
, which can be extended to create a visitor which only needs to handle a subset of the available methods. - SnpSiftBaseVisitor() - Constructor for class org.snpsift.antlr.SnpSiftBaseVisitor
- SnpSiftCmdAlleleMatrix - Class in org.snpsift
-
Convert VCf file to allele matrix Note: Only use SNPs Note: Only variants with two possible alleles.
- SnpSiftCmdAlleleMatrix() - Constructor for class org.snpsift.SnpSiftCmdAlleleMatrix
- SnpSiftCmdAnnotate - Class in org.snpsift
-
Annotate a VCF file with ID from another VCF file (database)
- SnpSiftCmdAnnotate() - Constructor for class org.snpsift.SnpSiftCmdAnnotate
- SnpSiftCmdAnnotate(String[]) - Constructor for class org.snpsift.SnpSiftCmdAnnotate
- SnpSiftCmdAnnotateMem - Class in org.snpsift
-
Annotate a VCF file from another VCF file (database) The database file is loaded into memory.
- SnpSiftCmdAnnotateMem() - Constructor for class org.snpsift.SnpSiftCmdAnnotateMem
- SnpSiftCmdAnnotateMem(String[]) - Constructor for class org.snpsift.SnpSiftCmdAnnotateMem
- SnpSiftCmdCaseControl - Class in org.snpsift
-
Count number of cases and controls
- SnpSiftCmdCaseControl() - Constructor for class org.snpsift.SnpSiftCmdCaseControl
- SnpSiftCmdCaseControl(String[]) - Constructor for class org.snpsift.SnpSiftCmdCaseControl
- SnpSiftCmdCaseControlSummary - Class in org.snpsift.caseControl
-
Summarize a VCF annotated file
- SnpSiftCmdCaseControlSummary() - Constructor for class org.snpsift.caseControl.SnpSiftCmdCaseControlSummary
- SnpSiftCmdCaseControlSummary(String[]) - Constructor for class org.snpsift.caseControl.SnpSiftCmdCaseControlSummary
- SnpSiftCmdConcordance - Class in org.snpsift
-
Calculate genotyping concordance between two VCF files.
- SnpSiftCmdConcordance() - Constructor for class org.snpsift.SnpSiftCmdConcordance
- SnpSiftCmdConcordance(String[]) - Constructor for class org.snpsift.SnpSiftCmdConcordance
- SnpSiftCmdCovarianceMatrix - Class in org.snpsift
-
Convert allele 'matrix' file into Covariance matrix Note: Only variants with two possible alleles.
- SnpSiftCmdCovarianceMatrix() - Constructor for class org.snpsift.SnpSiftCmdCovarianceMatrix
- SnpSiftCmdCovarianceMatrix(String[]) - Constructor for class org.snpsift.SnpSiftCmdCovarianceMatrix
- SnpSiftCmdDbNsfp - Class in org.snpsift
-
Annotate a VCF file with dbNSFP.
- SnpSiftCmdDbNsfp() - Constructor for class org.snpsift.SnpSiftCmdDbNsfp
- SnpSiftCmdDbNsfp(String[]) - Constructor for class org.snpsift.SnpSiftCmdDbNsfp
- SnpSiftCmdExtractFields - Class in org.snpsift
-
Extract fields from VCF file to a TXT (tab separated) format
- SnpSiftCmdExtractFields() - Constructor for class org.snpsift.SnpSiftCmdExtractFields
- SnpSiftCmdExtractFields(String[]) - Constructor for class org.snpsift.SnpSiftCmdExtractFields
- SnpSiftCmdFilter - Class in org.snpsift
-
Generic SnpSift filter Filter out data based on VCF attributes: - Chromosome, Position, etc.
- SnpSiftCmdFilter() - Constructor for class org.snpsift.SnpSiftCmdFilter
- SnpSiftCmdFilter(String[]) - Constructor for class org.snpsift.SnpSiftCmdFilter
- SnpSiftCmdFilterChrPos - Class in org.snpsift
-
Filter using CHROM:POS only
- SnpSiftCmdFilterChrPos() - Constructor for class org.snpsift.SnpSiftCmdFilterChrPos
- SnpSiftCmdFilterChrPos(String[]) - Constructor for class org.snpsift.SnpSiftCmdFilterChrPos
- SnpSiftCmdFilterGt - Class in org.snpsift
-
Generic SnpSift genotype filter Removes genotypes matching the filter: e.g.
- SnpSiftCmdFilterGt() - Constructor for class org.snpsift.SnpSiftCmdFilterGt
- SnpSiftCmdFilterGt(String[]) - Constructor for class org.snpsift.SnpSiftCmdFilterGt
- SnpSiftCmdGeneSets - Class in org.snpsift
-
Annotate a VCF file using Gene sets (MSigDb) or gene ontology (GO)
- SnpSiftCmdGeneSets() - Constructor for class org.snpsift.SnpSiftCmdGeneSets
- SnpSiftCmdGeneSets(String[]) - Constructor for class org.snpsift.SnpSiftCmdGeneSets
- SnpSiftCmdGt - Class in org.snpsift
-
Add genotype information to INFO fields
- SnpSiftCmdGt() - Constructor for class org.snpsift.SnpSiftCmdGt
- SnpSiftCmdGt(String[]) - Constructor for class org.snpsift.SnpSiftCmdGt
- SnpSiftCmdGwasCatalog - Class in org.snpsift
-
Annotate a VCF file using GWAS catalog database Loads GWAS catalog in memory, thus it makes no assumption about order.
- SnpSiftCmdGwasCatalog() - Constructor for class org.snpsift.SnpSiftCmdGwasCatalog
- SnpSiftCmdGwasCatalog(String[]) - Constructor for class org.snpsift.SnpSiftCmdGwasCatalog
- SnpSiftCmdHwe - Class in org.snpsift.hwe
-
Calculate Hardy-Weinberg equilibrium and goodness of fit for each entry in a VCF file
- SnpSiftCmdHwe() - Constructor for class org.snpsift.hwe.SnpSiftCmdHwe
- SnpSiftCmdHwe(String[]) - Constructor for class org.snpsift.hwe.SnpSiftCmdHwe
- SnpSiftCmdIntersect - Class in org.snpsift
-
Intersect intervals
- SnpSiftCmdIntersect() - Constructor for class org.snpsift.SnpSiftCmdIntersect
- SnpSiftCmdIntersect(String[]) - Constructor for class org.snpsift.SnpSiftCmdIntersect
- SnpSiftCmdIntervals - Class in org.snpsift
-
Filter variants that hit intervals
- SnpSiftCmdIntervals() - Constructor for class org.snpsift.SnpSiftCmdIntervals
- SnpSiftCmdIntervals(String[]) - Constructor for class org.snpsift.SnpSiftCmdIntervals
- SnpSiftCmdIntervalsIndex - Class in org.snpsift
-
Filter variants that hit intervals Use an indexed VCF file.
- SnpSiftCmdIntervalsIndex() - Constructor for class org.snpsift.SnpSiftCmdIntervalsIndex
- SnpSiftCmdIntervalsIndex(String[]) - Constructor for class org.snpsift.SnpSiftCmdIntervalsIndex
- SnpSiftCmdJoin - Class in org.snpsift
-
Annotate a VCF file with ID from another VCF file (database)
- SnpSiftCmdJoin() - Constructor for class org.snpsift.SnpSiftCmdJoin
- SnpSiftCmdJoin(String[]) - Constructor for class org.snpsift.SnpSiftCmdJoin
- SnpSiftCmdPedShow - Class in org.snpsift
-
Draws a pedigree using SVG according to a VCF file
- SnpSiftCmdPedShow() - Constructor for class org.snpsift.SnpSiftCmdPedShow
- SnpSiftCmdPedShow(String[]) - Constructor for class org.snpsift.SnpSiftCmdPedShow
- SnpSiftCmdPhastCons - Class in org.snpsift
-
Annotate using PhastCons score files
- SnpSiftCmdPhastCons() - Constructor for class org.snpsift.SnpSiftCmdPhastCons
- SnpSiftCmdPhastCons(String[]) - Constructor for class org.snpsift.SnpSiftCmdPhastCons
- SnpSiftCmdPrivate - Class in org.snpsift
-
Annotate if a variant is 'private'.
- SnpSiftCmdPrivate() - Constructor for class org.snpsift.SnpSiftCmdPrivate
- SnpSiftCmdPrivate(String[]) - Constructor for class org.snpsift.SnpSiftCmdPrivate
- SnpSiftCmdRemoveReferenceGenotypes - Class in org.snpsift
-
Removes reference genotypes.
- SnpSiftCmdRemoveReferenceGenotypes() - Constructor for class org.snpsift.SnpSiftCmdRemoveReferenceGenotypes
- SnpSiftCmdRemoveReferenceGenotypes(String[]) - Constructor for class org.snpsift.SnpSiftCmdRemoveReferenceGenotypes
- SnpSiftCmdRmInfo - Class in org.snpsift
-
Removes INFO fields
- SnpSiftCmdRmInfo() - Constructor for class org.snpsift.SnpSiftCmdRmInfo
- SnpSiftCmdRmInfo(String[]) - Constructor for class org.snpsift.SnpSiftCmdRmInfo
- SnpSiftCmdSort - Class in org.snpsift
-
Sort VCF file/s by chromosome invalid input: '&' position
- SnpSiftCmdSort() - Constructor for class org.snpsift.SnpSiftCmdSort
- SnpSiftCmdSort(String[]) - Constructor for class org.snpsift.SnpSiftCmdSort
- SnpSiftCmdSplit - Class in org.snpsift
-
Split a large VCF file by chromosome or bby number of lines
- SnpSiftCmdSplit() - Constructor for class org.snpsift.SnpSiftCmdSplit
- SnpSiftCmdSplit(String[]) - Constructor for class org.snpsift.SnpSiftCmdSplit
- SnpSiftCmdTsTv - Class in org.snpsift
-
Calculate Ts/Tv rations per sample (transitions vs transversions)
- SnpSiftCmdTsTv() - Constructor for class org.snpsift.SnpSiftCmdTsTv
- SnpSiftCmdTsTv(String[]) - Constructor for class org.snpsift.SnpSiftCmdTsTv
- SnpSiftCmdVarType - Class in org.snpsift
-
Annotate a VCF file with variant type
- SnpSiftCmdVarType() - Constructor for class org.snpsift.SnpSiftCmdVarType
- SnpSiftCmdVarType(String[]) - Constructor for class org.snpsift.SnpSiftCmdVarType
- SnpSiftCmdVcf2Tped - Class in org.snpsift
-
Transform a VCF to a TPED file
- SnpSiftCmdVcf2Tped() - Constructor for class org.snpsift.SnpSiftCmdVcf2Tped
- SnpSiftCmdVcf2Tped(String[]) - Constructor for class org.snpsift.SnpSiftCmdVcf2Tped
- SnpSiftCmdVcf2Tped.UseMissing - Enum Class in org.snpsift
- SnpSiftCmdVcfCheck - Class in org.snpsift
-
Check VCF files (run some simple checks)
- SnpSiftCmdVcfCheck() - Constructor for class org.snpsift.SnpSiftCmdVcfCheck
- SnpSiftCmdVcfCheck(String[]) - Constructor for class org.snpsift.SnpSiftCmdVcfCheck
- SnpSiftCmdVcfOperator - Class in org.snpsift
-
Annotate a field based on an operation (max, min, etc.) of other VCF fields
- SnpSiftCmdVcfOperator() - Constructor for class org.snpsift.SnpSiftCmdVcfOperator
- SnpSiftCmdVcfOperator(String[]) - Constructor for class org.snpsift.SnpSiftCmdVcfOperator
- SnpSiftCmdVcfOperator.Operator - Enum Class in org.snpsift
- SnpSiftLexer - Class in org.snpsift.antlr
- SnpSiftLexer(CharStream) - Constructor for class org.snpsift.antlr.SnpSiftLexer
- SnpSiftListener - Interface in org.snpsift.antlr
-
This interface defines a complete listener for a parse tree produced by
SnpSiftParser
. - SnpSiftParser - Class in org.snpsift.antlr
- SnpSiftParser(TokenStream) - Constructor for class org.snpsift.antlr.SnpSiftParser
- SnpSiftParser.CompilationUnitContext - Class in org.snpsift.antlr
- SnpSiftParser.ExpressionCompContext - Class in org.snpsift.antlr
- SnpSiftParser.ExpressionCondContext - Class in org.snpsift.antlr
- SnpSiftParser.ExpressionContext - Class in org.snpsift.antlr
- SnpSiftParser.ExpressionExistsContext - Class in org.snpsift.antlr
- SnpSiftParser.ExpressionLogicContext - Class in org.snpsift.antlr
- SnpSiftParser.ExpressionParenContext - Class in org.snpsift.antlr
- SnpSiftParser.ExpressionPlusContext - Class in org.snpsift.antlr
- SnpSiftParser.ExpressionSetContext - Class in org.snpsift.antlr
- SnpSiftParser.ExpressionTimesContext - Class in org.snpsift.antlr
- SnpSiftParser.ExpressionUnaryContext - Class in org.snpsift.antlr
- SnpSiftParser.FunctionCallContext - Class in org.snpsift.antlr
- SnpSiftParser.LiteralBoolContext - Class in org.snpsift.antlr
- SnpSiftParser.LiteralFloatContext - Class in org.snpsift.antlr
- SnpSiftParser.LiteralIndexContext - Class in org.snpsift.antlr
- SnpSiftParser.LiteralIntContext - Class in org.snpsift.antlr
- SnpSiftParser.LiteralStringContext - Class in org.snpsift.antlr
- SnpSiftParser.VarReferenceContext - Class in org.snpsift.antlr
- SnpSiftParser.VarReferenceListContext - Class in org.snpsift.antlr
- SnpSiftParser.VarReferenceListSubContext - Class in org.snpsift.antlr
- SnpSiftVisitor<T> - Interface in org.snpsift.antlr
-
This interface defines a complete generic visitor for a parse tree produced by
SnpSiftParser
. - SOFTWARE_NAME - Static variable in class org.snpsift.SnpSift
- SortedVariantsVcfIterator - Class in org.snpsift.annotate.mem
-
This is a class that reads a VCF file and returns the variants in sorted order.
- SortedVariantsVcfIterator(BufferedReader) - Constructor for class org.snpsift.annotate.mem.SortedVariantsVcfIterator
- SortedVariantsVcfIterator(String) - Constructor for class org.snpsift.annotate.mem.SortedVariantsVcfIterator
- SPLIT_REGEX - Static variable in class org.snpsift.lang.expression.Has
- splitValuesField(String) - Static method in class org.snpsift.fileIterator.DbNsfpEntry
- square(int, int, int, int, String, int, String) - Method in class org.snpsift.pedigree.PedigreeDraw
- stab(int) - Method in class org.snpsift.annotate.VcfIndexTree
- START_FIELD - Static variable in class org.snpsift.SnpSiftCmdPhastCons
- startIdx - Variable in class org.snpsift.fileIterator.DbNsfp
- STRING_LITERAL - Static variable in class org.snpsift.antlr.SnpSiftLexer
- STRING_LITERAL - Static variable in class org.snpsift.antlr.SnpSiftParser
- STRING_LITERAL() - Method in class org.snpsift.antlr.SnpSiftParser.LiteralStringContext
- StringArray - Class in org.snpsift.annotate.mem.arrays
-
Implement a memory efficient array of strings It only stores bytes (i.e.
- StringArray(int, int) - Constructor for class org.snpsift.annotate.mem.arrays.StringArray
-
Constructor
- StringArrayBase - Class in org.snpsift.annotate.mem.arrays
-
Implement a memory efficient array of strings It only stores bytes (i.e.
- StringArrayBase() - Constructor for class org.snpsift.annotate.mem.arrays.StringArrayBase
-
Constructor
- study - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- SUBFIELD_SEPARATOR - Static variable in class org.snpsift.fileIterator.DbNsfp
- SUBFIELD_SEPARATOR_2 - Static variable in class org.snpsift.fileIterator.DbNsfp
- SUBFIELD_SEPARATOR_CHAR - Static variable in class org.snpsift.fileIterator.DbNsfp
- SUBFIELD_SEPARATOR_CHAR_2 - Static variable in class org.snpsift.fileIterator.DbNsfp
- Summary - Class in org.snpsift.caseControl
-
Summarize a VCF annotated file
- Summary() - Constructor for class org.snpsift.caseControl.Summary
- suppressOutput - Variable in class org.snpsift.SnpSift
- swapMinorAllele(int[], int[]) - Method in class org.snpsift.SnpSiftCmdCaseControl
-
Swap counts if REF is minor allele (instead of ALT)
T
- T__0 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__0 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__1 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__1 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__10 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__10 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__11 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__11 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__12 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__12 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__13 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__13 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__14 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__14 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__15 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__15 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__16 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__16 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__17 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__17 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__18 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__18 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__19 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__19 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__2 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__2 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__20 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__20 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__21 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__21 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__22 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__22 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__23 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__23 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__24 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__24 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__25 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__25 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__26 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__26 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__27 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__27 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__28 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__28 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__29 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__29 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__3 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__3 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__30 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__30 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__31 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__31 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__32 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__32 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__33 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__33 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__34 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__34 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__4 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__4 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__5 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__5 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__6 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__6 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__7 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__7 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__8 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__8 - Static variable in class org.snpsift.antlr.SnpSiftParser
- T__9 - Static variable in class org.snpsift.antlr.SnpSiftLexer
- T__9 - Static variable in class org.snpsift.antlr.SnpSiftParser
- tabixCheck - Variable in class org.snpsift.SnpSiftCmdDbNsfp
- tabixReader - Variable in class org.snpsift.annotate.DbVcfTabix
- tabixReader - Variable in class org.snpsift.fileIterator.DbNsfp
- tfamFile - Variable in class org.snpsift.SnpSiftCmdCaseControl
- tick(int) - Method in class org.snpsift.util.ShowProgress
- tick(int, VariantVcfEntry) - Method in class org.snpsift.util.ShowProgress
- tick(int, VcfEntry) - Method in class org.snpsift.util.ShowProgress
-
Call this method every iteration
- Times - Class in org.snpsift.lang.expression
-
And expression
- Times(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Times
- tokenNames - Static variable in class org.snpsift.antlr.SnpSiftLexer
-
Deprecated.
- tokenNames - Static variable in class org.snpsift.antlr.SnpSiftParser
-
Deprecated.Use
SnpSiftParser.VOCABULARY
instead. - toString() - Method in class org.snpsift.annotate.AnnotateVcfDb
- toString() - Method in class org.snpsift.annotate.MarkerFile
- toString() - Method in class org.snpsift.annotate.mem.arrays.EnumArray
- toString() - Method in class org.snpsift.annotate.mem.arrays.StringArray
- toString() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
- toString() - Method in class org.snpsift.annotate.mem.database.VariantDataFrame
- toString() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
- toString() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
- toString() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
- toString() - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
- toString() - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
- toString() - Method in class org.snpsift.annotate.QueryResult
- toString() - Method in class org.snpsift.annotate.VcfIndex
- toString() - Method in class org.snpsift.annotate.VcfIndexDataChromo
- toString() - Method in class org.snpsift.annotate.VcfIndexTree
- toString() - Method in class org.snpsift.caseControl.VariantCounter
- toString() - Method in class org.snpsift.fileIterator.DbNsfpEntry
- toString() - Method in class org.snpsift.gwasCatalog.GwasCatalogEntry
- toString() - Method in class org.snpsift.lang.expression.ExpressionBinary
- toString() - Method in class org.snpsift.lang.expression.ExpressionUnary
- toString() - Method in class org.snpsift.lang.expression.Field
- toString() - Method in class org.snpsift.lang.expression.FieldEff
- toString() - Method in class org.snpsift.lang.expression.FieldGenotype
- toString() - Method in class org.snpsift.lang.expression.FieldGenotypeSub
- toString() - Method in class org.snpsift.lang.expression.FieldIterator
- toString() - Method in class org.snpsift.lang.expression.FieldLof
- toString() - Method in class org.snpsift.lang.expression.FieldSub
- toString() - Method in class org.snpsift.lang.expression.Literal
- toString() - Method in class org.snpsift.lang.function.Function
- toString() - Method in class org.snpsift.lang.function.FunctionBoolGenotype
- toString() - Method in class org.snpsift.lang.function.In
- toString() - Method in class org.snpsift.lang.Value
- toString() - Method in class org.snpsift.pedigree.Individual
- toString() - Method in class org.snpsift.SnpSiftCmdCovarianceMatrix
- toString(int) - Method in class org.snpsift.annotate.VcfIndexTree
- toString(List<String>) - Method in class org.snpsift.caseControl.Summary
- toStringAll() - Method in class org.snpsift.annotate.VcfIndex
-
Show all entries
- toStringAll() - Method in class org.snpsift.annotate.VcfIndexTree
- toStringTitle(List<String>) - Method in class org.snpsift.caseControl.Summary
- toStringTree() - Method in class org.snpsift.pedigree.Individual
- trait - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- TRUE - Static variable in class org.snpsift.lang.Value
- type() - Method in class org.snpsift.lang.Value
- TYPE_ALL - Static variable in class org.snpsift.lang.expression.Field
- TYPE_ANY - Static variable in class org.snpsift.lang.expression.Field
- types - Variable in class org.snpsift.fileIterator.DbNsfp
U
- uniqueIds(Set<String>, String) - Method in class org.snpsift.annotate.AnnotateVcfDb
-
IDs from database not present in VCF
- unknown(Individual) - Method in class org.snpsift.pedigree.PedigreeDraw
- unSanitize(String) - Method in class org.snpsift.SnpSift
-
Convert a sanitized expression (from Galaxy) back to the original string References: http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg00530.html
- updateSizes(VariantCategory, String, String) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
-
Update sizes for a field
- upstreamGeneDistance - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- upstreamGeneId - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
- usage(String) - Method in class org.snpsift.caseControl.SnpSiftCmdCaseControlSummary
-
Show usage message
- usage(String) - Method in class org.snpsift.hwe.SnpSiftCmdHwe
-
Show usage and exit
- usage(String) - Method in class org.snpsift.SnpSift
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdAlleleMatrix
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdAnnotate
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdAnnotateMem
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdCaseControl
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdConcordance
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdCovarianceMatrix
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdDbNsfp
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdExtractFields
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdFilter
-
Usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdFilterChrPos
-
Usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdFilterGt
-
Usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdGeneSets
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdGt
- usage(String) - Method in class org.snpsift.SnpSiftCmdGwasCatalog
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdIntersect
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdIntervals
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdIntervalsIndex
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdJoin
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdPedShow
- usage(String) - Method in class org.snpsift.SnpSiftCmdPhastCons
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdPrivate
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdRemoveReferenceGenotypes
-
Show usage and exit
- usage(String) - Method in class org.snpsift.SnpSiftCmdRmInfo
-
Show usage and exit
- usage(String) - Method in class org.snpsift.SnpSiftCmdSort
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdSplit
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdTsTv
-
Show usage and exit
- usage(String) - Method in class org.snpsift.SnpSiftCmdVarType
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdVcf2Tped
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdVcfCheck
-
Show usage message
- usage(String) - Method in class org.snpsift.SnpSiftCmdVcfOperator
- usageGenericAndDb() - Method in class org.snpsift.SnpSift
-
Options common to all commands
- useAllInfoFields - Variable in class org.snpsift.annotate.AnnotateVcfDb
- useChiSquare - Variable in class org.snpsift.SnpSiftCmdCaseControl
- useId - Variable in class org.snpsift.annotate.AnnotateVcfDb
- useId - Variable in class org.snpsift.SnpSiftCmdAnnotate
- useInfoField - Variable in class org.snpsift.SnpSiftCmdAnnotate
- useInfoFields - Variable in class org.snpsift.annotate.AnnotateVcfDb
- useRefAlt - Variable in class org.snpsift.annotate.AnnotateVcfDb
- useRefAlt - Variable in class org.snpsift.SnpSiftCmdAnnotate
V
- Value - Class in org.snpsift.lang
- Value(Object) - Constructor for class org.snpsift.lang.Value
- valueOf(String) - Static method in enum class org.snpsift.annotate.mem.VariantCategory
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpsift.lang.expression.FieldConstant.FieldConstantNames
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpsift.lang.expression.FieldIterator.IteratorType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpsift.SnpSiftCmdVcf2Tped.UseMissing
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class org.snpsift.SnpSiftCmdVcfOperator.Operator
-
Returns the enum constant of this class with the specified name.
- values() - Static method in enum class org.snpsift.annotate.mem.VariantCategory
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpsift.lang.expression.FieldConstant.FieldConstantNames
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpsift.lang.expression.FieldIterator.IteratorType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpsift.SnpSiftCmdVcf2Tped.UseMissing
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class org.snpsift.SnpSiftCmdVcfOperator.Operator
-
Returns an array containing the constants of this enum class, in the order they are declared.
- VAR - Enum constant in enum class org.snpsift.lang.expression.FieldIterator.IteratorType
- variant - Variable in class org.snpsift.annotate.QueryResult
- VARIANT_DATABASE_EXT - Static variable in class org.snpsift.annotate.mem.database.VariantDatabase
- VARIANT_DATAFRAME_EXT - Static variable in class org.snpsift.annotate.mem.database.VariantDatabase
- VariantCategory - Enum Class in org.snpsift.annotate.mem
- VariantCounter - Class in org.snpsift.caseControl
-
A counnter for genotypes
- VariantCounter(int) - Constructor for class org.snpsift.caseControl.VariantCounter
- VariantDatabase - Class in org.snpsift.annotate.mem.database
-
A database of variant's data used to annotate a VCF file (i.e.
- VariantDatabase() - Constructor for class org.snpsift.annotate.mem.database.VariantDatabase
- VariantDatabase(String, String, String[]) - Constructor for class org.snpsift.annotate.mem.database.VariantDatabase
-
Constructor used to create a database
- VariantDatabase(String, String, String[], String, boolean) - Constructor for class org.snpsift.annotate.mem.database.VariantDatabase
-
Constructor used to annotate a database
- VariantDataFrame - Class in org.snpsift.annotate.mem.database
-
A DataFrame of variant's data that is indexed "variant type AND chromosome possition".
- VariantDataFrame(VariantTypeCounter) - Constructor for class org.snpsift.annotate.mem.database.VariantDataFrame
- variantsMinHeap - Variable in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
- VariantTypeCounter - Class in org.snpsift.annotate.mem.variantTypeCounter
-
Count different types of variants These statistics are used to create data sets
- VariantTypeCounter(Fields) - Constructor for class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
- VariantTypeCounters - Class in org.snpsift.annotate.mem.variantTypeCounter
-
Variant type counters for each chromosome
- VariantTypeCounters(boolean) - Constructor for class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
- VariantTypeCounters(Fields, boolean) - Constructor for class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
- VarReferenceContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.VarReferenceContext
- VarReferenceListContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.VarReferenceListContext
- VarReferenceListSubContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.VarReferenceListSubContext
- VARTYPE - Static variable in class org.snpsift.SnpSiftCmdVarType
- vcf - Variable in class org.snpsift.annotate.DbVcfTabix
- VCF_INFO_CASE - Static variable in class org.snpsift.SnpSiftCmdCaseControl
- VCF_INFO_CC_ALL - Static variable in class org.snpsift.SnpSiftCmdCaseControl
- VCF_INFO_CC_DOM - Static variable in class org.snpsift.SnpSiftCmdCaseControl
- VCF_INFO_CC_GENO - Static variable in class org.snpsift.SnpSiftCmdCaseControl
- VCF_INFO_CC_REC - Static variable in class org.snpsift.SnpSiftCmdCaseControl
- VCF_INFO_CC_TREND - Static variable in class org.snpsift.SnpSiftCmdCaseControl
- VCF_INFO_CONTROL - Static variable in class org.snpsift.SnpSiftCmdCaseControl
- VCF_INFO_FILTER_DELETED - Static variable in class org.snpsift.SnpSiftCmdFilter
- VCF_INFO_PHASTCONS_FIELD - Static variable in class org.snpsift.SnpSiftCmdPhastCons
- vcf2Tped(String, String, String, String) - Method in class org.snpsift.SnpSiftCmdVcf2Tped
-
Convert a VCF to a TPED file
- vcfChr - Variable in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
- vcfDbFile - Variable in class org.snpsift.annotate.AnnotateVcfDb
- vcfEntryPending - Variable in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
- vcfFile - Variable in class org.snpsift.SnpSiftCmdAnnotate
- vcfFile - Variable in class org.snpsift.SnpSiftCmdDbNsfp
- vcfFileIterator - Variable in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
- vcfFileName - Variable in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
- vcfFileName - Variable in class org.snpsift.SnpSiftCmdDbNsfp
- vcfHeader - Variable in class org.snpsift.annotate.DbVcf
- vcfHeaderAddProgramVersion - Variable in class org.snpsift.SnpSift
- vcfHeaderProcessed - Variable in class org.snpsift.SnpSift
- vcfHeaders() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
- vcfHeaders(String) - Method in class org.snpsift.annotate.mem.Fields
-
Get VCF headers
- VcfHwe - Class in org.snpsift.hwe
-
Calculate Hardy-Weimberg equilibrium and goodness of fit.
- VcfHwe() - Constructor for class org.snpsift.hwe.VcfHwe
- VcfIndex - Class in org.snpsift.annotate
-
An index for a VCF file
- VcfIndex(String) - Constructor for class org.snpsift.annotate.VcfIndex
- VcfIndexDataChromo - Class in org.snpsift.annotate
-
Represents a set of VCF entries stored in an (uncompressed) file All entries belong to the same chromosome
- VcfIndexDataChromo(Genome) - Constructor for class org.snpsift.annotate.VcfIndexDataChromo
- VcfIndexDataChromo(Genome, String) - Constructor for class org.snpsift.annotate.VcfIndexDataChromo
- VcfIndexTree - Class in org.snpsift.annotate
-
Interval tree structure for an 'VcfIndexChromo' The whole tree is stored in a single class as a set of arrays.
- VcfIndexTree() - Constructor for class org.snpsift.annotate.VcfIndexTree
- VcfIndexTree(VcfFileIterator, VcfIndexDataChromo) - Constructor for class org.snpsift.annotate.VcfIndexTree
- vcfInfo - Variable in class org.snpsift.lang.expression.Field
- vcfInfoNumber - Variable in class org.snpsift.lang.expression.Field
- vcfInfoPerAllele - Variable in class org.snpsift.annotate.AnnotateVcfDb
- vcfInfoPerAlleleRef - Variable in class org.snpsift.annotate.AnnotateVcfDb
- vcfInputFile - Variable in class org.snpsift.SnpSift
- VcfLd - Class in org.snpsift
-
Calculate Linkage Disequilibrium Reference: "Principles of population genetics (4th edition)" Hartl invalid input: '&' Clark, pages 73 to 81 Note: I try to follow the same notation as the book.
- VcfLd() - Constructor for class org.snpsift.VcfLd
- vcfPos - Variable in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
- verbose - Variable in class org.snpsift.annotate.AnnotateVcfDb
- verbose - Variable in class org.snpsift.annotate.DbVcf
- verbose - Variable in class org.snpsift.fileIterator.DbNsfp
- verbose - Variable in class org.snpsift.SnpSift
- VERSION - Static variable in class org.snpsift.SnpSift
- VERSION_MAJOR - Static variable in class org.snpsift.SnpSift
- VERSION_NO_NAME - Static variable in class org.snpsift.SnpSift
- VERSION_SHORT - Static variable in class org.snpsift.SnpSift
- visitCompilationUnit(SnpSiftParser.CompilationUnitContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by
SnpSiftParser.compilationUnit()
. - visitCompilationUnit(SnpSiftParser.CompilationUnitContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by
SnpSiftParser.compilationUnit()
. - visitErrorNode(ErrorNode) - Method in class org.snpsift.antlr.SnpSiftBaseListener
- visitExpressionComp(SnpSiftParser.ExpressionCompContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by the
expressionComp
labeled alternative inSnpSiftParser.expression()
. - visitExpressionComp(SnpSiftParser.ExpressionCompContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by the
expressionComp
labeled alternative inSnpSiftParser.expression()
. - visitExpressionCond(SnpSiftParser.ExpressionCondContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by the
expressionCond
labeled alternative inSnpSiftParser.expression()
. - visitExpressionCond(SnpSiftParser.ExpressionCondContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by the
expressionCond
labeled alternative inSnpSiftParser.expression()
. - visitExpressionExists(SnpSiftParser.ExpressionExistsContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by the
expressionExists
labeled alternative inSnpSiftParser.expression()
. - visitExpressionExists(SnpSiftParser.ExpressionExistsContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by the
expressionExists
labeled alternative inSnpSiftParser.expression()
. - visitExpressionLogic(SnpSiftParser.ExpressionLogicContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by the
expressionLogic
labeled alternative inSnpSiftParser.expression()
. - visitExpressionLogic(SnpSiftParser.ExpressionLogicContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by the
expressionLogic
labeled alternative inSnpSiftParser.expression()
. - visitExpressionParen(SnpSiftParser.ExpressionParenContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by the
expressionParen
labeled alternative inSnpSiftParser.expression()
. - visitExpressionParen(SnpSiftParser.ExpressionParenContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by the
expressionParen
labeled alternative inSnpSiftParser.expression()
. - visitExpressionPlus(SnpSiftParser.ExpressionPlusContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by the
expressionPlus
labeled alternative inSnpSiftParser.expression()
. - visitExpressionPlus(SnpSiftParser.ExpressionPlusContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by the
expressionPlus
labeled alternative inSnpSiftParser.expression()
. - visitExpressionSet(SnpSiftParser.ExpressionSetContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by the
expressionSet
labeled alternative inSnpSiftParser.expression()
. - visitExpressionSet(SnpSiftParser.ExpressionSetContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by the
expressionSet
labeled alternative inSnpSiftParser.expression()
. - visitExpressionTimes(SnpSiftParser.ExpressionTimesContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by the
expressionTimes
labeled alternative inSnpSiftParser.expression()
. - visitExpressionTimes(SnpSiftParser.ExpressionTimesContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by the
expressionTimes
labeled alternative inSnpSiftParser.expression()
. - visitExpressionUnary(SnpSiftParser.ExpressionUnaryContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by the
expressionUnary
labeled alternative inSnpSiftParser.expression()
. - visitExpressionUnary(SnpSiftParser.ExpressionUnaryContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by the
expressionUnary
labeled alternative inSnpSiftParser.expression()
. - visitFunctionCall(SnpSiftParser.FunctionCallContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by the
functionCall
labeled alternative inSnpSiftParser.expression()
. - visitFunctionCall(SnpSiftParser.FunctionCallContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by the
functionCall
labeled alternative inSnpSiftParser.expression()
. - visitLiteralBool(SnpSiftParser.LiteralBoolContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by the
literalBool
labeled alternative inSnpSiftParser.expression()
. - visitLiteralBool(SnpSiftParser.LiteralBoolContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by the
literalBool
labeled alternative inSnpSiftParser.expression()
. - visitLiteralFloat(SnpSiftParser.LiteralFloatContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by the
literalFloat
labeled alternative inSnpSiftParser.expression()
. - visitLiteralFloat(SnpSiftParser.LiteralFloatContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by the
literalFloat
labeled alternative inSnpSiftParser.expression()
. - visitLiteralIndex(SnpSiftParser.LiteralIndexContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by the
literalIndex
labeled alternative inSnpSiftParser.expression()
. - visitLiteralIndex(SnpSiftParser.LiteralIndexContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by the
literalIndex
labeled alternative inSnpSiftParser.expression()
. - visitLiteralInt(SnpSiftParser.LiteralIntContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by the
literalInt
labeled alternative inSnpSiftParser.expression()
. - visitLiteralInt(SnpSiftParser.LiteralIntContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by the
literalInt
labeled alternative inSnpSiftParser.expression()
. - visitLiteralString(SnpSiftParser.LiteralStringContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by the
literalString
labeled alternative inSnpSiftParser.expression()
. - visitLiteralString(SnpSiftParser.LiteralStringContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by the
literalString
labeled alternative inSnpSiftParser.expression()
. - visitTerminal(TerminalNode) - Method in class org.snpsift.antlr.SnpSiftBaseListener
- visitVarReference(SnpSiftParser.VarReferenceContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by the
varReference
labeled alternative inSnpSiftParser.expression()
. - visitVarReference(SnpSiftParser.VarReferenceContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by the
varReference
labeled alternative inSnpSiftParser.expression()
. - visitVarReferenceList(SnpSiftParser.VarReferenceListContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by the
varReferenceList
labeled alternative inSnpSiftParser.expression()
. - visitVarReferenceList(SnpSiftParser.VarReferenceListContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by the
varReferenceList
labeled alternative inSnpSiftParser.expression()
. - visitVarReferenceListSub(SnpSiftParser.VarReferenceListSubContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
-
Visit a parse tree produced by the
varReferenceListSub
labeled alternative inSnpSiftParser.expression()
. - visitVarReferenceListSub(SnpSiftParser.VarReferenceListSubContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
-
Visit a parse tree produced by the
varReferenceListSub
labeled alternative inSnpSiftParser.expression()
. - VOCABULARY - Static variable in class org.snpsift.antlr.SnpSiftLexer
- VOCABULARY - Static variable in class org.snpsift.antlr.SnpSiftParser
W
- warn(String) - Method in class org.snpsift.annotate.AnnotateVcfDb
-
Show a warning message (up to MAX_ERRORS times)
- WS - Static variable in class org.snpsift.antlr.SnpSiftLexer
- WS - Static variable in class org.snpsift.antlr.SnpSiftParser
X
- Xor - Class in org.snpsift.lang.expression
-
Or expression
- Xor(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Xor
Z
- Zzz - Class in org.snpsift.annotate.mem
-
Test: This class loaads a "database" VCF file and then annotates another VCF file.
- Zzz() - Constructor for class org.snpsift.annotate.mem.Zzz
_
- _ATN - Static variable in class org.snpsift.antlr.SnpSiftLexer
- _ATN - Static variable in class org.snpsift.antlr.SnpSiftParser
- _decisionToDFA - Static variable in class org.snpsift.antlr.SnpSiftLexer
- _decisionToDFA - Static variable in class org.snpsift.antlr.SnpSiftParser
- _serializedATN - Static variable in class org.snpsift.antlr.SnpSiftLexer
- _serializedATN - Static variable in class org.snpsift.antlr.SnpSiftParser
- _sharedContextCache - Static variable in class org.snpsift.antlr.SnpSiftLexer
- _sharedContextCache - Static variable in class org.snpsift.antlr.SnpSiftParser
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form
SnpSiftLexer.VOCABULARY
instead.