All Classes Interface Summary Class Summary Enum Summary
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"
|
CountHet |
Count number of heterozygous samples
|
CountHom |
Count number of homozygous samples
|
CountRef |
Count number of refernces samples
|
CountVariant |
Count number of ALT samples
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DbMarker<Q extends org.snpeff.interval.Marker,R extends org.snpeff.interval.Marker> |
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
|
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'
|
FieldSub |
A field that has sub fields (e.g.
|
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
|
QueryResult |
A database query and a result.
|
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)
|
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 & 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 .
|
Summary |
Summarize a VCF annotated file
|
TestCasesAnnotate |
Annotate test case
|
TestCasesAnnotateCreateIndex |
Annotate test case
Deletes index files to make sure they are properly built
|
TestCasesAnnotateMem |
Annotate test case
|
TestCasesAnnotateTabix |
Annotate test case using TABIX indexed files
|
TestCasesAnnotateUseIndex |
Annotate test case
Uses the index files created during the execution of TestCasesAnnotateCreateIndex test suite
|
TestCasesCaseControl |
Case control test cases
|
TestCasesConcordance |
Concordance test cases
|
TestCasesDbNsfp |
Test cases for dbNSFP database annotations
Note: This class tries to use 'data type cache' files
|
TestCasesDbNsfpDeleteCache |
Test cases for dbNSFP database annotations
Note: This class deletes and re-builds 'data type cache' files
|
TestCasesExtractFields |
Extract fields test cases
|
TestCasesFilter |
Filter test cases
|
TestCasesFilterALL |
Filter test cases for 'ALL' index
|
TestCasesFilterChrPos |
Test cases for SnpSift filterChrPos
|
TestCasesFilterGt |
Filter test cases for 'GT Filter'
|
TestCasesGeneSets |
SnpSift 'gt' test cases
|
TestCasesGt |
SnpSift 'gt' test cases
|
TestCasesGwasCatalog |
Test GWAS catalog classes
|
TestCasesHwe |
HWE test cases
|
TestCasesIndex |
Annotate test case
|
TestCasesIntervals |
SnpSIft intervals
|
TestCasesLd |
Linkage disequilibrium test cases
|
TestCasesPrivate |
SnpSift 'private' test cases
|
TestCasesSort |
SnpSift 'split' test cases
|
TestCasesSplit |
SnpSift 'split' test cases
|
TestCasesVarType |
VarType test cases
|
TestCasesVcfCheck |
VarType test cases
|
TestCasesZzz |
Try test cases in this class before adding them to long test cases
|
TestSuiteAll |
Invoke all test cases
|
Times |
And expression
|
Value |
|
VariantCounter |
A counnter for genotypes
|
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 & Clark, pages 73 to 81
Note: I try to follow the same notation as the book.
|
Xor |
Or expression
|