# All Classes and Interfaces

Class
Description
And
And expression
AnnotateVcfDb
Annotate using a VCF "database"
AnnotateVcfDbMem
Annotate using a VCF "database" Note: Reads and loads the whole VCF file into memory
AnnotateVcfDbSorted
Annotate using a VCF "database" Note: Assumes that the VCF database file is sorted.
AnnotateVcfDbTabix
Annotate using a tabix indexed VCF "database"
BoolArray
BoolArray is a class that provides a compact representation of a boolean array using a byte array.
CountHet
Count number of heterozygous samples
CountHom
Count number of homozygous samples
CountRef
Count number of refernces samples
CountVariant
Count number of ALT samples
DataFrame
A set of DataColumns, indexed by position.
DataFrameColumn<T>
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.
DataFrameColumnBool
A column of boolean values, that can also be null The bollean values are stored in a BoolArray
DataFrameColumnChar
DataFrameColumnDouble
DataFrameColumnInt
DataFrameColumnLong
DataFrameColumnString
DataFrameDel
DataFrameDel is a specialized subclass of DataFrame designed to handle deletion variants.
DataFrameIns
DataFrameIns is a specialized subclass of DataFrame designed to handle insertion variants.
DataFrameMixed
DataFrameMixed is a specialized subclass of DataFrame that is designed to handle mixed data types.
DataFrameMnp
DataFrameMnp is a specialized subclass of DataFrame designed to handle multi-nucleotide polymorphisms (MNPs).
DataFrameOther
DataFrameOther is a subclass of DataFrame that is specifically tailored for handling variant type counting and categorization.
DataFrameRow
The DataFrameRow class represents a row in a DataFrame.
DataFrameSnp
The DataFrameSnp class extends the DataFrame class and represents a specific type of data frame that deals with single nucleotide polymorphisms (SNPs).
DbMarker<Q,R>
Use a file as a 'marker' database.
DbNsfp
DbNSFP database: Reference https://sites.google.com/site/jpopgen/dbNSFP
DbNsfpEntry
DbNSFP database entry: Reference https://sites.google.com/site/jpopgen/dbNSFP Added lazy parsing of key/value pairs
DbVcf
Use a VCF file as a database for annotations A VCF database consists of a VCF file and an index.
DbVcfMem
Loads a VCF file into memory.
DbVcfSorted
Use an uncompressed sorted VCF file as a database for annotations Note: Assumes that the VCF database file is sorted and uncompressed.
DbVcfTabix
Use a bgzip-compressed, tabix indexed VCF file as a database for annotations
Div
And expression
EnumArray
The EnumArray class is a specialized array for storing and managing strings as enumerated values.
Eq
Equal
Exists
Exists operator (true if a field exists)
Expression
A generic expresion Expressions have values (VcfInfoType)
ExpressionBinary
Binary condition
ExpressionUnary
An expression that can be negated
FastaSample
Get a region from a fasta file
Field
A field: E.g.: 'DP', 'CHROM'
FieldConstant
A 'constant' field: e.g.
FieldConstant.FieldConstantNames
FieldConstantFloat
A 'constant' field: e.g.
FieldEff
An 'EFF' field form SnpEff: E.g.: 'EFF[2].GENE'
FieldGenotype
A field: E.g.: 'GEN[2].GT'
FieldGenotypeSub
A field: E.g.: 'GEN[2].PL[3]'
FieldIterator
Iterates on fields / sub-fields It's a singleton
FieldIterator.IteratorType
FieldLof
A LOF field form SnpEff: E.g.: 'LOF[2].GENE'
FieldNmd
A NMD field form SnpEff: E.g.: 'NMD[2].GENE'
Fields
The Fields class represents a collection of VCF (Variant Call Format) header information fields.
FieldSub
A field that has sub fields (e.g.
FormatUtil
Function
A function that returns an expression (i.e.
FunctionBoolGenotype
A function that returns a bool type (i.e.
Ge
Greater equal
Gt
Greater equal
GwasCatalog
GWAS catalog table.
GwasCatalogEntry
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
GwasCatalogFileIterator
Iterate on each line of a GWAS catalog (TXT, tab separated format)
Has
Equal
In
Is an expression in a set?
Individual
An individual in the pedigree Individuals are like TfamEntries but have drawing info (coordinates, color, etc.)
IsHet
Is 'genotypeNum' heterozygous?
IsHom
Is 'genotypeNum' homozygous?
IsRef
Is 'genotypeNum' reference?
IsVariant
Is 'genotypeNum' reference?
LangFactory
Creates objects from an AST
Le
Less or equal than
Literal
Lt
Greater equal
MarkerFile
Represents a marker in a file (located at 'fileIdx' bytes since the beginning of the file)
Match
Match a regular expression (string)
Minus
And expression
Mod
And expression
Na
Exists operator (true if a field exists)
Neq
Not equal
Not
Not expression
NotMatch
Match a regular expression (string)
Or
Or expression
PedigreeDraw
Draws a pedigree using SVG
PhastCons
Conservation score
Plus
And expression
PosIndex
The PosIndex class is designed to manage and index chromosome positions efficiently converting chromosome positions to zero-based indices.
QueryResult
A database query and a result.
RandomUtil
ShowProgress
SnpSift
Generic SnpSift tool caller
SnpSiftBaseListener
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.
SnpSiftBaseVisitor<T>
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.
SnpSiftCmdAlleleMatrix
Convert VCf file to allele matrix Note: Only use SNPs Note: Only variants with two possible alleles.
SnpSiftCmdAnnotate
Annotate a VCF file with ID from another VCF file (database)
SnpSiftCmdAnnotateDf
Annotate a VCF file from another VCF file (database) by creating "DataFrames" for each chromosome.
SnpSiftCmdCaseControl
Count number of cases and controls
SnpSiftCmdCaseControlSummary
Summarize a VCF annotated file
SnpSiftCmdConcordance
Calculate genotyping concordance between two VCF files.
SnpSiftCmdCovarianceMatrix
Convert allele 'matrix' file into Covariance matrix Note: Only variants with two possible alleles.
SnpSiftCmdDbNsfp
Annotate a VCF file with dbNSFP.
SnpSiftCmdExtractFields
Extract fields from VCF file to a TXT (tab separated) format
SnpSiftCmdFilter
Generic SnpSift filter Filter out data based on VCF attributes: - Chromosome, Position, etc.
SnpSiftCmdFilterChrPos
Filter using CHROM:POS only
SnpSiftCmdFilterGt
Generic SnpSift genotype filter Removes genotypes matching the filter: e.g.
SnpSiftCmdGeneSets
Annotate a VCF file using Gene sets (MSigDb) or gene ontology (GO)
SnpSiftCmdGt
Add genotype information to INFO fields
SnpSiftCmdGwasCatalog
Annotate a VCF file using GWAS catalog database Loads GWAS catalog in memory, thus it makes no assumption about order.
SnpSiftCmdHwe
Calculate Hardy-Weinberg equilibrium and goodness of fit for each entry in a VCF file
SnpSiftCmdIntersect
Intersect intervals
SnpSiftCmdIntervals
Filter variants that hit intervals
SnpSiftCmdIntervalsIndex
Filter variants that hit intervals Use an indexed VCF file.
SnpSiftCmdJoin
Annotate a VCF file with ID from another VCF file (database)
SnpSiftCmdPedShow
Draws a pedigree using SVG according to a VCF file
SnpSiftCmdPhastCons
Annotate using PhastCons score files
SnpSiftCmdPrivate
Annotate if a variant is 'private'.
SnpSiftCmdRemoveReferenceGenotypes
Removes reference genotypes.
SnpSiftCmdRmInfo
Removes INFO fields
SnpSiftCmdSort
Sort VCF file/s by chromosome invalid input: '&' position
SnpSiftCmdSplit
Split a large VCF file by chromosome or bby number of lines
SnpSiftCmdTsTv
Calculate Ts/Tv rations per sample (transitions vs transversions)
SnpSiftCmdVarType
Annotate a VCF file with variant type
SnpSiftCmdVcf2Tped
Transform a VCF to a TPED file
SnpSiftCmdVcf2Tped.UseMissing
SnpSiftCmdVcfCheck
Check VCF files (run some simple checks)
SnpSiftCmdVcfOperator
Annotate a field based on an operation (max, min, etc.) of other VCF fields
SnpSiftCmdVcfOperator.Operator
SnpSiftLexer
SnpSiftListener
This interface defines a complete listener for a parse tree produced by `SnpSiftParser`.
SnpSiftParser
SnpSiftParser.CompilationUnitContext
SnpSiftParser.ExpressionCompContext
SnpSiftParser.ExpressionCondContext
SnpSiftParser.ExpressionContext
SnpSiftParser.ExpressionExistsContext
SnpSiftParser.ExpressionLogicContext
SnpSiftParser.ExpressionParenContext
SnpSiftParser.ExpressionPlusContext
SnpSiftParser.ExpressionSetContext
SnpSiftParser.ExpressionTimesContext
SnpSiftParser.ExpressionUnaryContext
SnpSiftParser.FunctionCallContext
SnpSiftParser.LiteralBoolContext
SnpSiftParser.LiteralFloatContext
SnpSiftParser.LiteralIndexContext
SnpSiftParser.LiteralIntContext
SnpSiftParser.LiteralStringContext
SnpSiftParser.VarReferenceContext
SnpSiftParser.VarReferenceListContext
SnpSiftParser.VarReferenceListSubContext
SnpSiftVisitor<T>
This interface defines a complete generic visitor for a parse tree produced by `SnpSiftParser`.
SortedVariantsVcfIterator
This is a class that reads a VCF file and returns the variants in sorted order.
StringArray
The StringArray class implements a memory-efficient array of strings.
StringArrayBase
Abstract base class for a string array that supports iteration and serialization.
Summary
Summarize a VCF annotated file
Times
And expression
Value
VariantCategory
The `VariantCategory` enum represents different categories of genetic variants.
VariantCounter
A counnter for genotypes
VariantDatabase
A database of variant's data used to annotate a VCF file (i.e.
VariantDataFrame
A DataFrame of variant's data that is indexed "variant type AND chromosome possition".
VariantTypeCounter
VariantTypeCounter is a class that counts the number of variants in a VCF (Variant Call Format) file.
VariantTypeCounters
The VariantTypeCounters class is responsible for counting the number of variants in VCF (Variant Call Format) files.
VcfHwe
Calculate Hardy-Weimberg equilibrium and goodness of fit.
VcfIndex
An index for a VCF file
VcfIndexDataChromo
Represents a set of VCF entries stored in an (uncompressed) file All entries belong to the same chromosome
VcfIndexTree
Interval tree structure for an 'VcfIndexChromo' The whole tree is stored in a single class as a set of arrays.
VcfLd
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.
Xor
Or expression
Zzz
Test: This class loaads a "database" VCF file and then annotates another VCF file.