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
|
| 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
|