Index

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All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

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, 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(VcfEntry, long) - Method in class org.snpsift.annotate.VcfIndex
Add an interval parse from 'line'
addChild(Individual) - Method in class org.snpsift.pedigree.Individual
 
addEffect(String) - Method in class org.snpsift.caseControl.VariantCounter
 
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_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(String, String, String[]) - Method in class org.snpsift.testCases.TestCasesZzz
Annotate
annotate(String, String, String[]) - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate
annotate(String, String, String[]) - Method in class org.snpsift.testCases.unit.TestCasesDbNsfp
 
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.SnpSift
 
annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdAnnotate
 
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
 
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(VcfFileIterator) - Method in class org.snpsift.SnpSift
 
annotateFinish(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdDbNsfp
 
annotateFinish(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdGwasCatalog
 
annotateGetFiledTypes(String, String, String[]) - Method in class org.snpsift.testCases.unit.TestCasesDbNsfp
 
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.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
 
annotateOut(String, String, String[]) - Method in class org.snpsift.testCases.TestCasesZzz
Annotate and return STDOUT as a string
annotateOut(String, String, String[]) - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate and return STDOUT as a string
annotateTest(String, String) - Method in class org.snpsift.testCases.TestCasesZzz
 
annotateTest(String, String) - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
 
annotateTest(String, String, String[]) - Method in class org.snpsift.testCases.TestCasesZzz
Annotate a file and check that the new annotation matches the expected one
annotateTest(String, String, String[]) - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate a file and check that the new annotation matches the expected one
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
 
argsList(String, String, String[]) - Method in class org.snpsift.testCases.TestCasesZzz
 
argsList(String, String, String[]) - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
 
argsList(String, String, String[]) - Method in class org.snpsift.testCases.unit.TestCasesDbNsfp
 
argsList(String, String, String[]) - Method in class org.snpsift.testCases.unit.TestCasesFilterChrPos
 
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

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
 
build() - Method in class org.snpsift.annotate.VcfIndexTree
 
BUILD - Static variable in class org.snpsift.SnpSift
 

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?
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
 
checkFieldsToAdd() - Method in class org.snpsift.SnpSiftCmdDbNsfp
Check that all fields to add are available
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
 
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.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
 
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
 
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, Boolean, VariantEffect.FunctionalClass, String, int) - Method in class org.snpsift.caseControl.Summary
 
countAnnotated - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
countBadRef - Variable in class org.snpsift.SnpSiftCmdAnnotate
 
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.SnpSiftCmdDbNsfp
 
covariance() - Method in class org.snpsift.SnpSiftCmdCovarianceMatrix
Calculate covariance matrix
currentDbEntry - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 

D

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
 
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
 
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.testCases.TestCasesZzz
 
debug - Static variable in class org.snpsift.testCases.unit.TestCasesAnnotate
 
debug - Static variable in class org.snpsift.testCases.unit.TestCasesCaseControl
 
debug - Static variable in class org.snpsift.testCases.unit.TestCasesConcordance
 
debug - Static variable in class org.snpsift.testCases.unit.TestCasesDbNsfp
 
debug - Static variable in class org.snpsift.testCases.unit.TestCasesExtractFields
 
debug - Static variable in class org.snpsift.testCases.unit.TestCasesFilterChrPos
 
debug - Static variable in class org.snpsift.testCases.unit.TestCasesGeneSets
 
debug - Static variable in class org.snpsift.testCases.unit.TestCasesGt
 
debug - Static variable in class org.snpsift.testCases.unit.TestCasesIndex
 
debug - Static variable in class org.snpsift.testCases.unit.TestCasesPrivate
 
debug - Static variable in class org.snpsift.testCases.unit.TestCasesSort
 
debug - Static variable in class org.snpsift.testCases.unit.TestCasesSplit
 
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
 
defaultExtraArgs - Variable in class org.snpsift.testCases.TestCasesZzz
 
defaultExtraArgs - Variable in class org.snpsift.testCases.unit.TestCasesAnnotate
 
defaultExtraArgs - Variable in class org.snpsift.testCases.unit.TestCasesDbNsfp
 
defaultExtraArgs - Variable in class org.snpsift.testCases.unit.TestCasesFilterChrPos
 
deleteIndexFile - Variable in class org.snpsift.testCases.TestCasesZzz
 
deleteIndexFile - Variable in class org.snpsift.testCases.unit.TestCasesAnnotate
 
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
 
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 in SnpSiftParser.expression().
enterExpressionComp(SnpSiftParser.ExpressionCompContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by the expressionComp labeled alternative in SnpSiftParser.expression().
enterExpressionCond(SnpSiftParser.ExpressionCondContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Enter a parse tree produced by the expressionCond labeled alternative in SnpSiftParser.expression().
enterExpressionCond(SnpSiftParser.ExpressionCondContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by the expressionCond labeled alternative in SnpSiftParser.expression().
enterExpressionExists(SnpSiftParser.ExpressionExistsContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Enter a parse tree produced by the expressionExists labeled alternative in SnpSiftParser.expression().
enterExpressionExists(SnpSiftParser.ExpressionExistsContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by the expressionExists labeled alternative in SnpSiftParser.expression().
enterExpressionLogic(SnpSiftParser.ExpressionLogicContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Enter a parse tree produced by the expressionLogic labeled alternative in SnpSiftParser.expression().
enterExpressionLogic(SnpSiftParser.ExpressionLogicContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by the expressionLogic labeled alternative in SnpSiftParser.expression().
enterExpressionParen(SnpSiftParser.ExpressionParenContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Enter a parse tree produced by the expressionParen labeled alternative in SnpSiftParser.expression().
enterExpressionParen(SnpSiftParser.ExpressionParenContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by the expressionParen labeled alternative in SnpSiftParser.expression().
enterExpressionPlus(SnpSiftParser.ExpressionPlusContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Enter a parse tree produced by the expressionPlus labeled alternative in SnpSiftParser.expression().
enterExpressionPlus(SnpSiftParser.ExpressionPlusContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by the expressionPlus labeled alternative in SnpSiftParser.expression().
enterExpressionSet(SnpSiftParser.ExpressionSetContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Enter a parse tree produced by the expressionSet labeled alternative in SnpSiftParser.expression().
enterExpressionSet(SnpSiftParser.ExpressionSetContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by the expressionSet labeled alternative in SnpSiftParser.expression().
enterExpressionTimes(SnpSiftParser.ExpressionTimesContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Enter a parse tree produced by the expressionTimes labeled alternative in SnpSiftParser.expression().
enterExpressionTimes(SnpSiftParser.ExpressionTimesContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by the expressionTimes labeled alternative in SnpSiftParser.expression().
enterExpressionUnary(SnpSiftParser.ExpressionUnaryContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Enter a parse tree produced by the expressionUnary labeled alternative in SnpSiftParser.expression().
enterExpressionUnary(SnpSiftParser.ExpressionUnaryContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by the expressionUnary labeled alternative in SnpSiftParser.expression().
enterFunctionCall(SnpSiftParser.FunctionCallContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Enter a parse tree produced by the functionCall labeled alternative in SnpSiftParser.expression().
enterFunctionCall(SnpSiftParser.FunctionCallContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by the functionCall labeled alternative in SnpSiftParser.expression().
enterLiteralBool(SnpSiftParser.LiteralBoolContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Enter a parse tree produced by the literalBool labeled alternative in SnpSiftParser.expression().
enterLiteralBool(SnpSiftParser.LiteralBoolContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by the literalBool labeled alternative in SnpSiftParser.expression().
enterLiteralFloat(SnpSiftParser.LiteralFloatContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Enter a parse tree produced by the literalFloat labeled alternative in SnpSiftParser.expression().
enterLiteralFloat(SnpSiftParser.LiteralFloatContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by the literalFloat labeled alternative in SnpSiftParser.expression().
enterLiteralIndex(SnpSiftParser.LiteralIndexContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Enter a parse tree produced by the literalIndex labeled alternative in SnpSiftParser.expression().
enterLiteralIndex(SnpSiftParser.LiteralIndexContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by the literalIndex labeled alternative in SnpSiftParser.expression().
enterLiteralInt(SnpSiftParser.LiteralIntContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Enter a parse tree produced by the literalInt labeled alternative in SnpSiftParser.expression().
enterLiteralInt(SnpSiftParser.LiteralIntContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by the literalInt labeled alternative in SnpSiftParser.expression().
enterLiteralString(SnpSiftParser.LiteralStringContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Enter a parse tree produced by the literalString labeled alternative in SnpSiftParser.expression().
enterLiteralString(SnpSiftParser.LiteralStringContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by the literalString labeled alternative in SnpSiftParser.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 in SnpSiftParser.expression().
enterVarReference(SnpSiftParser.VarReferenceContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by the varReference labeled alternative in SnpSiftParser.expression().
enterVarReferenceList(SnpSiftParser.VarReferenceListContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Enter a parse tree produced by the varReferenceList labeled alternative in SnpSiftParser.expression().
enterVarReferenceList(SnpSiftParser.VarReferenceListContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by the varReferenceList labeled alternative in SnpSiftParser.expression().
enterVarReferenceListSub(SnpSiftParser.VarReferenceListSubContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Enter a parse tree produced by the varReferenceListSub labeled alternative in SnpSiftParser.expression().
enterVarReferenceListSub(SnpSiftParser.VarReferenceListSubContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by the varReferenceListSub labeled alternative in SnpSiftParser.expression().
EOF() - Method in class org.snpsift.antlr.SnpSiftParser.CompilationUnitContext
 
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 in SnpSiftParser.expression().
exitExpressionComp(SnpSiftParser.ExpressionCompContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by the expressionComp labeled alternative in SnpSiftParser.expression().
exitExpressionCond(SnpSiftParser.ExpressionCondContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Exit a parse tree produced by the expressionCond labeled alternative in SnpSiftParser.expression().
exitExpressionCond(SnpSiftParser.ExpressionCondContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by the expressionCond labeled alternative in SnpSiftParser.expression().
exitExpressionExists(SnpSiftParser.ExpressionExistsContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Exit a parse tree produced by the expressionExists labeled alternative in SnpSiftParser.expression().
exitExpressionExists(SnpSiftParser.ExpressionExistsContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by the expressionExists labeled alternative in SnpSiftParser.expression().
exitExpressionLogic(SnpSiftParser.ExpressionLogicContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Exit a parse tree produced by the expressionLogic labeled alternative in SnpSiftParser.expression().
exitExpressionLogic(SnpSiftParser.ExpressionLogicContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by the expressionLogic labeled alternative in SnpSiftParser.expression().
exitExpressionParen(SnpSiftParser.ExpressionParenContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Exit a parse tree produced by the expressionParen labeled alternative in SnpSiftParser.expression().
exitExpressionParen(SnpSiftParser.ExpressionParenContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by the expressionParen labeled alternative in SnpSiftParser.expression().
exitExpressionPlus(SnpSiftParser.ExpressionPlusContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Exit a parse tree produced by the expressionPlus labeled alternative in SnpSiftParser.expression().
exitExpressionPlus(SnpSiftParser.ExpressionPlusContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by the expressionPlus labeled alternative in SnpSiftParser.expression().
exitExpressionSet(SnpSiftParser.ExpressionSetContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Exit a parse tree produced by the expressionSet labeled alternative in SnpSiftParser.expression().
exitExpressionSet(SnpSiftParser.ExpressionSetContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by the expressionSet labeled alternative in SnpSiftParser.expression().
exitExpressionTimes(SnpSiftParser.ExpressionTimesContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Exit a parse tree produced by the expressionTimes labeled alternative in SnpSiftParser.expression().
exitExpressionTimes(SnpSiftParser.ExpressionTimesContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by the expressionTimes labeled alternative in SnpSiftParser.expression().
exitExpressionUnary(SnpSiftParser.ExpressionUnaryContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Exit a parse tree produced by the expressionUnary labeled alternative in SnpSiftParser.expression().
exitExpressionUnary(SnpSiftParser.ExpressionUnaryContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by the expressionUnary labeled alternative in SnpSiftParser.expression().
exitFunctionCall(SnpSiftParser.FunctionCallContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Exit a parse tree produced by the functionCall labeled alternative in SnpSiftParser.expression().
exitFunctionCall(SnpSiftParser.FunctionCallContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by the functionCall labeled alternative in SnpSiftParser.expression().
exitLiteralBool(SnpSiftParser.LiteralBoolContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Exit a parse tree produced by the literalBool labeled alternative in SnpSiftParser.expression().
exitLiteralBool(SnpSiftParser.LiteralBoolContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by the literalBool labeled alternative in SnpSiftParser.expression().
exitLiteralFloat(SnpSiftParser.LiteralFloatContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Exit a parse tree produced by the literalFloat labeled alternative in SnpSiftParser.expression().
exitLiteralFloat(SnpSiftParser.LiteralFloatContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by the literalFloat labeled alternative in SnpSiftParser.expression().
exitLiteralIndex(SnpSiftParser.LiteralIndexContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Exit a parse tree produced by the literalIndex labeled alternative in SnpSiftParser.expression().
exitLiteralIndex(SnpSiftParser.LiteralIndexContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by the literalIndex labeled alternative in SnpSiftParser.expression().
exitLiteralInt(SnpSiftParser.LiteralIntContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Exit a parse tree produced by the literalInt labeled alternative in SnpSiftParser.expression().
exitLiteralInt(SnpSiftParser.LiteralIntContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by the literalInt labeled alternative in SnpSiftParser.expression().
exitLiteralString(SnpSiftParser.LiteralStringContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Exit a parse tree produced by the literalString labeled alternative in SnpSiftParser.expression().
exitLiteralString(SnpSiftParser.LiteralStringContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by the literalString labeled alternative in SnpSiftParser.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 in SnpSiftParser.expression().
exitVarReference(SnpSiftParser.VarReferenceContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by the varReference labeled alternative in SnpSiftParser.expression().
exitVarReferenceList(SnpSiftParser.VarReferenceListContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Exit a parse tree produced by the varReferenceList labeled alternative in SnpSiftParser.expression().
exitVarReferenceList(SnpSiftParser.VarReferenceListContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by the varReferenceList labeled alternative in SnpSiftParser.expression().
exitVarReferenceListSub(SnpSiftParser.VarReferenceListSubContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Exit a parse tree produced by the varReferenceListSub labeled alternative in SnpSiftParser.expression().
exitVarReferenceListSub(SnpSiftParser.VarReferenceListSubContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by the varReferenceListSub labeled alternative in SnpSiftParser.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.SnpSiftCmdVcfOperator
 
fieldsDescription - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
fieldsNamesToAdd - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
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
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(String, String, int) - Method in class org.snpsift.testCases.unit.TestCasesFilterChrPos
 
filter(String, String, String[], int) - Method in class org.snpsift.testCases.unit.TestCasesFilterChrPos
Filter
filter(VcfEntry) - Method in class org.snpsift.SnpSiftCmdFilterChrPos
Filter this line?
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
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(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.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
 
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
 
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
 
getCountEntries() - Method in class org.snpsift.SnpSiftCmdConcordance
 
getD() - Method in class org.snpsift.VcfLd
 
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
 
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
 
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.lang.expression.Field
 
getName() - Method in class org.snpsift.lang.expression.FieldEff
 
getName() - Method in class org.snpsift.lang.expression.FieldLof
 
getNames2index() - Method in class org.snpsift.fileIterator.DbNsfp
 
getOrCreate(String) - Method in class org.snpsift.annotate.VcfIndex
Get IntervalFileChromo by chromosome name.
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
 
getPosition() - Method in class org.snpsift.pedigree.Individual
 
getQa() - Method in class org.snpsift.VcfLd
 
getQb() - Method in class org.snpsift.VcfLd
 
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
 
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
 
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(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
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
 
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.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.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
 
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.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
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
 
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
 
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.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
 
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
 
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(DataInputStream) - Method in class org.snpsift.annotate.VcfIndexTree
Read data from input stream
load(String) - Method in class org.snpsift.gwasCatalog.GwasCatalog
Load data from file
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.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
 
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
 
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.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.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
 
numWorkers - Variable in class org.snpsift.SnpSift
 

O

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
 
org.snpsift - package org.snpsift
 
org.snpsift.annotate - package org.snpsift.annotate
 
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.testCases - package org.snpsift.testCases
 
org.snpsift.testCases.unit - package org.snpsift.testCases.unit
 
org.snpsift.util - package org.snpsift.util
 
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.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'.
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
 
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

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_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
 
removeDataTypesCache - Variable in class org.snpsift.testCases.unit.TestCasesDbNsfp
 
replicationSampleSize - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
reportedGene - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
reset() - Method in class org.snpsift.lang.expression.FieldIterator
Reset all counters
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.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.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(DataOutputStream) - Method in class org.snpsift.annotate.VcfIndexTree
Save to output stream
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
 
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
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
 
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
 
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
 
setOrder(int) - Method in class org.snpsift.pedigree.Individual
 
setPrependInfoFieldName(String) - Method in class org.snpsift.annotate.AnnotateVcfDb
 
setQuiet(boolean) - Method in class org.snpsift.SnpSift
 
setRmFilterField(String) - Method in class org.snpsift.SnpSiftCmdFilter
 
setSaveOutput(boolean) - Method in class org.snpsift.SnpSift
 
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.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
 
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_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
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.VcfIndexDataChromo
 
size() - Method in class org.snpsift.annotate.VcfIndexTree
 
sizeByDepth(int[]) - Method in class org.snpsift.pedigree.Individual
Size by depth
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
 
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
 
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
 
STDOUT_BUFFER_SIZE - Static variable in class org.snpsift.testCases.unit.TestCasesFilter
 
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
 
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
 
test_00() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
Check headers vs map2num
test_01() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
 
test_01() - Method in class org.snpsift.testCases.unit.TestCasesCaseControl
 
test_01() - Method in class org.snpsift.testCases.unit.TestCasesConcordance
 
test_01() - Method in class org.snpsift.testCases.unit.TestCasesDbNsfp
 
test_01() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
Extract fields
test_01() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by quality
test_01() - Method in class org.snpsift.testCases.unit.TestCasesFilterChrPos
 
test_01() - Method in class org.snpsift.testCases.unit.TestCasesFilterGt
Filter
test_01() - Method in class org.snpsift.testCases.unit.TestCasesGeneSets
 
test_01() - Method in class org.snpsift.testCases.unit.TestCasesGt
 
test_01() - Method in class org.snpsift.testCases.unit.TestCasesGwasCatalog
 
test_01() - Method in class org.snpsift.testCases.unit.TestCasesHwe
Calculate p-value using ChiSquare approximation
test_01() - Method in class org.snpsift.testCases.unit.TestCasesIndex
Index a VCF file and query all entries
test_01() - Method in class org.snpsift.testCases.unit.TestCasesIntervals
Filter VCF entries
test_01() - Method in class org.snpsift.testCases.unit.TestCasesLd
Calculate LD parameters Example from "Principles of population genetics", pages 79,80
test_01() - Method in class org.snpsift.testCases.unit.TestCasesPrivate
Non private
test_01() - Method in class org.snpsift.testCases.unit.TestCasesSort
Vcf Header bug: FORMAT and INFO having the same ID
test_01() - Method in class org.snpsift.testCases.unit.TestCasesSplit
Split by chromosome
test_01() - Method in class org.snpsift.testCases.unit.TestCasesVcfCheck
 
test_01_SNP() - Method in class org.snpsift.testCases.unit.TestCasesVarType
 
test_01_Str() - Method in class org.snpsift.testCases.unit.TestCasesCaseControl
 
test_02() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
 
test_02() - Method in class org.snpsift.testCases.unit.TestCasesCaseControl
 
test_02() - Method in class org.snpsift.testCases.unit.TestCasesConcordance
 
test_02() - Method in class org.snpsift.testCases.unit.TestCasesDbNsfp
Test dbnsfp having multiple lines per variant
test_02() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_02() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by chromosome
test_02() - Method in class org.snpsift.testCases.unit.TestCasesFilterChrPos
 
test_02() - Method in class org.snpsift.testCases.unit.TestCasesFilterGt
Filter
test_02() - Method in class org.snpsift.testCases.unit.TestCasesGwasCatalog
 
test_02() - Method in class org.snpsift.testCases.unit.TestCasesHwe
Calculate p-value using exact formula
test_02() - Method in class org.snpsift.testCases.unit.TestCasesIndex
Index a VCF file and query all entries
test_02() - Method in class org.snpsift.testCases.unit.TestCasesIntervals
Filter VCF entries
test_02() - Method in class org.snpsift.testCases.unit.TestCasesPrivate
Non private
test_02() - Method in class org.snpsift.testCases.unit.TestCasesSplit
Split by number
test_02_MNP() - Method in class org.snpsift.testCases.unit.TestCasesVarType
 
test_02_Str() - Method in class org.snpsift.testCases.unit.TestCasesCaseControl
 
test_02_Str2() - Method in class org.snpsift.testCases.unit.TestCasesCaseControl
 
test_02_table_1() - Method in class org.snpsift.testCases.unit.TestCasesHwe
Calculate "P[ n12 | n1, n2]" according to Table 1 in the paper "A Note on Exact test of Hardy Weinberg Equilibrium", G.
test_03() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
 
test_03() - Method in class org.snpsift.testCases.unit.TestCasesCaseControl
 
test_03() - Method in class org.snpsift.testCases.unit.TestCasesConcordance
 
test_03() - Method in class org.snpsift.testCases.unit.TestCasesDbNsfp
Test dbnsfp having multiple lines per variant, without collapsing
test_03() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_03() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by position
test_03() - Method in class org.snpsift.testCases.unit.TestCasesFilterChrPos
 
test_03() - Method in class org.snpsift.testCases.unit.TestCasesPrivate
Private variant
test_03() - Method in class org.snpsift.testCases.unit.TestCasesSplit
Split and join
test_03_INS() - Method in class org.snpsift.testCases.unit.TestCasesVarType
 
test_03_page_59() - Method in class org.snpsift.testCases.unit.TestCasesHwe
Calculate "P[ n12 | n1, n2]" according to Page 59 in the "Principles of population genetics"
test_03_Str() - Method in class org.snpsift.testCases.unit.TestCasesCaseControl
 
test_03_Str2() - Method in class org.snpsift.testCases.unit.TestCasesCaseControl
 
test_03_Str3() - Method in class org.snpsift.testCases.unit.TestCasesCaseControl
 
test_04() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
 
test_04() - Method in class org.snpsift.testCases.unit.TestCasesCaseControl
 
test_04() - Method in class org.snpsift.testCases.unit.TestCasesConcordance
 
test_04() - Method in class org.snpsift.testCases.unit.TestCasesDbNsfp
 
test_04() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_04() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by position
test_04() - Method in class org.snpsift.testCases.unit.TestCasesPrivate
Private variant
test_04_DEL() - Method in class org.snpsift.testCases.unit.TestCasesVarType
 
test_04_pChi2_table_1() - Method in class org.snpsift.testCases.unit.TestCasesHwe
Calculate "P_{HWE}" using Chi-square approximation.
test_04_pHwe_table_1() - Method in class org.snpsift.testCases.unit.TestCasesHwe
Calculate "P_{HWE}" according to Table 1 in the paper "A Note on Exact test of Hardy Weinberg Equilibrium", G.
test_04_Str() - Method in class org.snpsift.testCases.unit.TestCasesCaseControl
 
test_05() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Chromosomes in VCF file are called 'chr22' instead of '22'.
test_05() - Method in class org.snpsift.testCases.unit.TestCasesCaseControl
 
test_05() - Method in class org.snpsift.testCases.unit.TestCasesConcordance
 
test_05() - Method in class org.snpsift.testCases.unit.TestCasesDbNsfp
 
test_05() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_05() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by position
test_05() - Method in class org.snpsift.testCases.unit.TestCasesPrivate
 
test_05_multiple() - Method in class org.snpsift.testCases.unit.TestCasesVarType
 
test_06() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate info fields
test_06() - Method in class org.snpsift.testCases.unit.TestCasesCaseControl
 
test_06() - Method in class org.snpsift.testCases.unit.TestCasesConcordance
 
test_06() - Method in class org.snpsift.testCases.unit.TestCasesDbNsfp
 
test_06() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_06() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by position
test_06() - Method in class org.snpsift.testCases.unit.TestCasesPrivate
 
test_07() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate only some info fields
test_07() - Method in class org.snpsift.testCases.unit.TestCasesCaseControl
 
test_07() - Method in class org.snpsift.testCases.unit.TestCasesConcordance
 
test_07() - Method in class org.snpsift.testCases.unit.TestCasesDbNsfp
Check header values are correctly inferred.
test_07() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_07() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by position (AND test)
test_07() - Method in class org.snpsift.testCases.unit.TestCasesPrivate
 
test_08() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Do not annotate ID column
test_08() - Method in class org.snpsift.testCases.unit.TestCasesCaseControl
 
test_08() - Method in class org.snpsift.testCases.unit.TestCasesConcordance
 
test_08() - Method in class org.snpsift.testCases.unit.TestCasesDbNsfp
Missing annotations
test_08() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_08() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by position (OR test)
test_08() - Method in class org.snpsift.testCases.unit.TestCasesPrivate
 
test_09() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate only some info fields
test_09() - Method in class org.snpsift.testCases.unit.TestCasesCaseControl
Compare to results from PLINK using ChiSquare approximation
test_09() - Method in class org.snpsift.testCases.unit.TestCasesConcordance
 
test_09() - Method in class org.snpsift.testCases.unit.TestCasesDbNsfp
Invalid INFO keys
test_09() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_09() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Regexp test
test_10() - Method in class org.snpsift.testCases.unit.TestCasesCaseControl
Compare to results from PLINK using Fisher exact test
test_10() - Method in class org.snpsift.testCases.unit.TestCasesConcordance
 
test_10() - Method in class org.snpsift.testCases.unit.TestCasesDbNsfp
Missing database entries
test_10() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_10() - Method in class org.snpsift.testCases.unit.TestCasesFilter
REF and ALT values
test_11() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate only some info fields
test_11() - Method in class org.snpsift.testCases.unit.TestCasesConcordance
 
test_11() - Method in class org.snpsift.testCases.unit.TestCasesDbNsfp
Missing database entries + non-missing entry
test_11() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_11() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by coverage
test_12() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate without REF/ALT fields
test_12() - Method in class org.snpsift.testCases.unit.TestCasesConcordance
 
test_12() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_12() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by INDEL info tag
test_13() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate using "reserved" VCF fields (e.g.
test_13() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_13() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by INDEL info tag
test_14() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
 
test_14() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_14() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by PL genottype tag
test_15() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
 
test_15() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_15() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by GT genottype tag
test_16() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
 
test_16() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_16() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by GT genottype functions
test_17() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
 
test_17() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_17() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by GT genottype functions
test_18() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
 
test_18() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_18() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by GT genottype functions
test_19() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
 
test_19() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_19() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by GT genottype functions
test_20() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate info fields
test_20() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_20() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by GT genottype functions
test_21() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate two consecutive variants in the same position
test_21() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by GT genottype functions
test_22() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate first base in a chromosome
test_22() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by GT genottype functions
test_22_3() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by GT genottype functions
test_23() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_23() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by GT[*] (any genottype)
test_23_allele_specific_annotation_missing_R() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Database has one entry and VCF has multiple ALTs
test_24() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate using "-name" to prepend a name to VCF fields (e.g.
test_24() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_24() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by GT[0].VV[*] (any sub field in a genottype)
test_25() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate using "-name" to prepend a name to VCF fields (e.g.
test_25() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_25() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by GT[*].VV[*] (any sub field in any genottype)
test_26() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_26() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by EFF[0].EFFECT (effect)
test_26_ann() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by ANN[0].EFFECT (effect)
test_26_repeat_db_entry() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate ID using entries that are duplicated in db.vcf
test_27() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_27() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by EFF[*].EFFECT (any effect)
test_27_ann() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by ANN[*].EFFECT (any effect)
test_27_ann2() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by ANN[*].EFFECT (any effect)
test_27_repeat_db_entry() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate INFO fields using entries that are duplicated in db.vcf
test_28() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
Extract fields using sample names
test_28() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Test countHom function
test_28_exists() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate if a VCF entry exists in the database file
test_29() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
Extract fields using sample names
test_29() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Test countHet function
test_29_repeated_IDs() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate if a VCF entry's ID might have multiple repeated entries
test_30() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
Extract fields using sample names
test_30() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Test countRef function
test_31() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
Extract fields using sample names
test_31() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Test countVariant function
test_31_ann() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
Extract fields using sample names
test_31_annotate_minimal_representation_db() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Issue when database has REF several variants which have to be converted into minimal representation
test_32() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
Extract fields using sample names
test_32() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by EFF[*].CODING
test_32_ann() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by ANN[*].CODING
test_32_annotate_minimal_representation_input() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Issue when query has REF several variants which have to be converted into minimal representation
test_33() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
Extract fields using sample names
test_33() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by EFF[*].CODING
test_33_ann() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by ANN[*].CODING
test_33_empty_db() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Empty database
test_34() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
Extract fields using sample names
test_34() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by EFF[ALL].EFFECT
test_34() - Method in class org.snpsift.testCases.unit.TestCasesFilterALL
Filter by EFF[ALL].EFFECT
test_34_ann() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by ANN[ALL].EFFECT
test_34_dbStartsOnDifferentChromo() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Database has one entry and VCF has multiple ALTs
test_35() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate flags without '=true'
test_35() - Method in class org.snpsift.testCases.unit.TestCasesExtractFields
 
test_35() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by EFF[*].GENE
test_35_ann() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by EFF[*].GENE
test_36() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate multi-allelic
test_36() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Inverse of a filter
test_37() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Use filter field (add 'PASS' if expression is true)
test_38() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Input VCf triggers a seek to a position after chromosome sections ends in database.
test_38() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Add a string to FILTER if expression is true)
test_39() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate issues with discovered info fields (when annotating ALL info fields)
test_39() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Remove FILTER strings
test_40() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Problems when tabix database file has 'chr' in chromosome names and VCF file does not
test_40() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Inverse FILTER strings
test_41() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
 
test_41() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Remove filter option '-rmFilter' Bug reported by Jim Johnson
test_42() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Test multiple CAF annotations
test_42() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Test compare to missing field
test_43() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate empty
test_43() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Test compare to missing field
test_44() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate GnomAd with multiple entries
test_44() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Test compare to missing field
test_45() - Method in class org.snpsift.testCases.TestCasesZzz
Annotate GnomAd with multiple entries
test_45() - Method in class org.snpsift.testCases.unit.TestCasesAnnotate
Annotate GnomAd with multiple entries
test_45() - Method in class org.snpsift.testCases.unit.TestCasesFilter
LOF[*].PERC > 0.1
test_46() - Method in class org.snpsift.testCases.unit.TestCasesFilter
 
test_47() - Method in class org.snpsift.testCases.unit.TestCasesFilter
 
test_48() - Method in class org.snpsift.testCases.unit.TestCasesFilter
 
test_49() - Method in class org.snpsift.testCases.unit.TestCasesFilter
 
test_50() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by EFF[*] (whole field comparison)
test_51() - Method in class org.snpsift.testCases.unit.TestCasesFilter
LOF[*] : Whole field
test_52() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter by "(Cases[0] = 3) invalid input: '&' (Controls[0] = 0)" Bug in Field.getReturnType() was causing some trouble.
test_53() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter using 'has' operator
test_54() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Filter: Operator precedence issue
test_55() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Test compare a field having 'Number=A' INFO header
test_55_2() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Test compare a field having 'Number=A' INFO header
test_55_3() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Test compare a field having 'Number=A' INFO header
test_56_empty_vcf() - Method in class org.snpsift.testCases.unit.TestCasesFilter
If header is shown when input file is empty
test_57_short_circuit_AND_OR_operators() - Method in class org.snpsift.testCases.unit.TestCasesFilter
In AND operators, second expression should not be evaluated if first one is FALSE
test_58_rmFilter_info_field() - Method in class org.snpsift.testCases.unit.TestCasesFilter
Remove filter option '-rmFilter'.
TestCasesAnnotate - Class in org.snpsift.testCases.unit
Annotate test case
TestCasesAnnotate() - Constructor for class org.snpsift.testCases.unit.TestCasesAnnotate
 
TestCasesAnnotateCreateIndex - Class in org.snpsift.testCases.unit
Annotate test case Deletes index files to make sure they are properly built
TestCasesAnnotateCreateIndex() - Constructor for class org.snpsift.testCases.unit.TestCasesAnnotateCreateIndex
 
TestCasesAnnotateMem - Class in org.snpsift.testCases.unit
Annotate test case
TestCasesAnnotateMem() - Constructor for class org.snpsift.testCases.unit.TestCasesAnnotateMem
 
TestCasesAnnotateTabix - Class in org.snpsift.testCases.unit
Annotate test case using TABIX indexed files
TestCasesAnnotateTabix() - Constructor for class org.snpsift.testCases.unit.TestCasesAnnotateTabix
 
TestCasesAnnotateUseIndex - Class in org.snpsift.testCases.unit
Annotate test case Uses the index files created during the execution of TestCasesAnnotateCreateIndex test suite
TestCasesAnnotateUseIndex() - Constructor for class org.snpsift.testCases.unit.TestCasesAnnotateUseIndex
 
TestCasesCaseControl - Class in org.snpsift.testCases.unit
Case control test cases
TestCasesCaseControl() - Constructor for class org.snpsift.testCases.unit.TestCasesCaseControl
 
TestCasesConcordance - Class in org.snpsift.testCases.unit
Concordance test cases
TestCasesConcordance() - Constructor for class org.snpsift.testCases.unit.TestCasesConcordance
 
TestCasesDbNsfp - Class in org.snpsift.testCases.unit
Test cases for dbNSFP database annotations Note: This class tries to use 'data type cache' files
TestCasesDbNsfp() - Constructor for class org.snpsift.testCases.unit.TestCasesDbNsfp
 
TestCasesDbNsfpDeleteCache - Class in org.snpsift.testCases.unit
Test cases for dbNSFP database annotations Note: This class deletes and re-builds 'data type cache' files
TestCasesDbNsfpDeleteCache() - Constructor for class org.snpsift.testCases.unit.TestCasesDbNsfpDeleteCache
 
TestCasesExtractFields - Class in org.snpsift.testCases.unit
Extract fields test cases
TestCasesExtractFields() - Constructor for class org.snpsift.testCases.unit.TestCasesExtractFields
 
TestCasesFilter - Class in org.snpsift.testCases.unit
Filter test cases
TestCasesFilter() - Constructor for class org.snpsift.testCases.unit.TestCasesFilter
 
TestCasesFilterALL - Class in org.snpsift.testCases.unit
Filter test cases for 'ALL' index
TestCasesFilterALL() - Constructor for class org.snpsift.testCases.unit.TestCasesFilterALL
 
TestCasesFilterChrPos - Class in org.snpsift.testCases.unit
Test cases for SnpSift filterChrPos
TestCasesFilterChrPos() - Constructor for class org.snpsift.testCases.unit.TestCasesFilterChrPos
 
TestCasesFilterGt - Class in org.snpsift.testCases.unit
Filter test cases for 'GT Filter'
TestCasesFilterGt() - Constructor for class org.snpsift.testCases.unit.TestCasesFilterGt
 
TestCasesGeneSets - Class in org.snpsift.testCases.unit
SnpSift 'gt' test cases
TestCasesGeneSets() - Constructor for class org.snpsift.testCases.unit.TestCasesGeneSets
 
TestCasesGt - Class in org.snpsift.testCases.unit
SnpSift 'gt' test cases
TestCasesGt() - Constructor for class org.snpsift.testCases.unit.TestCasesGt
 
TestCasesGwasCatalog - Class in org.snpsift.testCases.unit
Test GWAS catalog classes
TestCasesGwasCatalog() - Constructor for class org.snpsift.testCases.unit.TestCasesGwasCatalog
 
TestCasesHwe - Class in org.snpsift.testCases.unit
HWE test cases
TestCasesHwe() - Constructor for class org.snpsift.testCases.unit.TestCasesHwe
 
TestCasesIndex - Class in org.snpsift.testCases.unit
Annotate test case
TestCasesIndex() - Constructor for class org.snpsift.testCases.unit.TestCasesIndex
 
TestCasesIntervals - Class in org.snpsift.testCases.unit
SnpSIft intervals
TestCasesIntervals() - Constructor for class org.snpsift.testCases.unit.TestCasesIntervals
 
TestCasesLd - Class in org.snpsift.testCases.unit
Linkage disequilibrium test cases
TestCasesLd() - Constructor for class org.snpsift.testCases.unit.TestCasesLd
 
TestCasesPrivate - Class in org.snpsift.testCases.unit
SnpSift 'private' test cases
TestCasesPrivate() - Constructor for class org.snpsift.testCases.unit.TestCasesPrivate
 
TestCasesSort - Class in org.snpsift.testCases.unit
SnpSift 'split' test cases
TestCasesSort() - Constructor for class org.snpsift.testCases.unit.TestCasesSort
 
TestCasesSplit - Class in org.snpsift.testCases.unit
SnpSift 'split' test cases
TestCasesSplit() - Constructor for class org.snpsift.testCases.unit.TestCasesSplit
 
TestCasesVarType - Class in org.snpsift.testCases.unit
VarType test cases
TestCasesVarType() - Constructor for class org.snpsift.testCases.unit.TestCasesVarType
 
TestCasesVcfCheck - Class in org.snpsift.testCases.unit
VarType test cases
TestCasesVcfCheck() - Constructor for class org.snpsift.testCases.unit.TestCasesVcfCheck
 
TestCasesZzz - Class in org.snpsift.testCases
Try test cases in this class before adding them to long test cases
TestCasesZzz() - Constructor for class org.snpsift.testCases.TestCasesZzz
 
TestSuiteAll - Class in org.snpsift.testCases
Invoke all test cases
TestSuiteAll() - Constructor for class org.snpsift.testCases.TestSuiteAll
 
tfamFile - Variable in class org.snpsift.SnpSiftCmdCaseControl
 
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.
toString() - Method in class org.snpsift.annotate.AnnotateVcfDb
 
toString() - Method in class org.snpsift.annotate.MarkerFile
 
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
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.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.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.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
 
VariantCounter - Class in org.snpsift.caseControl
A counnter for genotypes
VariantCounter(int) - Constructor for class org.snpsift.caseControl.VariantCounter
 
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
vcfDbFile - Variable in class org.snpsift.annotate.AnnotateVcfDb
 
vcfFile - Variable in class org.snpsift.SnpSiftCmdAnnotate
 
vcfFile - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
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
 
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
 
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
 
verbose - Static variable in class org.snpsift.testCases.TestCasesZzz
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesAnnotate
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesCaseControl
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesConcordance
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesDbNsfp
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesFilter
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesFilterALL
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesFilterChrPos
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesFilterGt
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesGeneSets
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesGt
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesGwasCatalog
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesHwe
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesIndex
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesIntervals
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesLd
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesPrivate
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesSort
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesSplit
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesVarType
 
verbose - Static variable in class org.snpsift.testCases.unit.TestCasesVcfCheck
 
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 in SnpSiftParser.expression().
visitExpressionComp(SnpSiftParser.ExpressionCompContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by the expressionComp labeled alternative in SnpSiftParser.expression().
visitExpressionCond(SnpSiftParser.ExpressionCondContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
Visit a parse tree produced by the expressionCond labeled alternative in SnpSiftParser.expression().
visitExpressionCond(SnpSiftParser.ExpressionCondContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by the expressionCond labeled alternative in SnpSiftParser.expression().
visitExpressionExists(SnpSiftParser.ExpressionExistsContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
Visit a parse tree produced by the expressionExists labeled alternative in SnpSiftParser.expression().
visitExpressionExists(SnpSiftParser.ExpressionExistsContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by the expressionExists labeled alternative in SnpSiftParser.expression().
visitExpressionLogic(SnpSiftParser.ExpressionLogicContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
Visit a parse tree produced by the expressionLogic labeled alternative in SnpSiftParser.expression().
visitExpressionLogic(SnpSiftParser.ExpressionLogicContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by the expressionLogic labeled alternative in SnpSiftParser.expression().
visitExpressionParen(SnpSiftParser.ExpressionParenContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
Visit a parse tree produced by the expressionParen labeled alternative in SnpSiftParser.expression().
visitExpressionParen(SnpSiftParser.ExpressionParenContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by the expressionParen labeled alternative in SnpSiftParser.expression().
visitExpressionPlus(SnpSiftParser.ExpressionPlusContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
Visit a parse tree produced by the expressionPlus labeled alternative in SnpSiftParser.expression().
visitExpressionPlus(SnpSiftParser.ExpressionPlusContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by the expressionPlus labeled alternative in SnpSiftParser.expression().
visitExpressionSet(SnpSiftParser.ExpressionSetContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
Visit a parse tree produced by the expressionSet labeled alternative in SnpSiftParser.expression().
visitExpressionSet(SnpSiftParser.ExpressionSetContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by the expressionSet labeled alternative in SnpSiftParser.expression().
visitExpressionTimes(SnpSiftParser.ExpressionTimesContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
Visit a parse tree produced by the expressionTimes labeled alternative in SnpSiftParser.expression().
visitExpressionTimes(SnpSiftParser.ExpressionTimesContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by the expressionTimes labeled alternative in SnpSiftParser.expression().
visitExpressionUnary(SnpSiftParser.ExpressionUnaryContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
Visit a parse tree produced by the expressionUnary labeled alternative in SnpSiftParser.expression().
visitExpressionUnary(SnpSiftParser.ExpressionUnaryContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by the expressionUnary labeled alternative in SnpSiftParser.expression().
visitFunctionCall(SnpSiftParser.FunctionCallContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
Visit a parse tree produced by the functionCall labeled alternative in SnpSiftParser.expression().
visitFunctionCall(SnpSiftParser.FunctionCallContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by the functionCall labeled alternative in SnpSiftParser.expression().
visitLiteralBool(SnpSiftParser.LiteralBoolContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
Visit a parse tree produced by the literalBool labeled alternative in SnpSiftParser.expression().
visitLiteralBool(SnpSiftParser.LiteralBoolContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by the literalBool labeled alternative in SnpSiftParser.expression().
visitLiteralFloat(SnpSiftParser.LiteralFloatContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
Visit a parse tree produced by the literalFloat labeled alternative in SnpSiftParser.expression().
visitLiteralFloat(SnpSiftParser.LiteralFloatContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by the literalFloat labeled alternative in SnpSiftParser.expression().
visitLiteralIndex(SnpSiftParser.LiteralIndexContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
Visit a parse tree produced by the literalIndex labeled alternative in SnpSiftParser.expression().
visitLiteralIndex(SnpSiftParser.LiteralIndexContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by the literalIndex labeled alternative in SnpSiftParser.expression().
visitLiteralInt(SnpSiftParser.LiteralIntContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
Visit a parse tree produced by the literalInt labeled alternative in SnpSiftParser.expression().
visitLiteralInt(SnpSiftParser.LiteralIntContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by the literalInt labeled alternative in SnpSiftParser.expression().
visitLiteralString(SnpSiftParser.LiteralStringContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
Visit a parse tree produced by the literalString labeled alternative in SnpSiftParser.expression().
visitLiteralString(SnpSiftParser.LiteralStringContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by the literalString labeled alternative in SnpSiftParser.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 in SnpSiftParser.expression().
visitVarReference(SnpSiftParser.VarReferenceContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by the varReference labeled alternative in SnpSiftParser.expression().
visitVarReferenceList(SnpSiftParser.VarReferenceListContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
Visit a parse tree produced by the varReferenceList labeled alternative in SnpSiftParser.expression().
visitVarReferenceList(SnpSiftParser.VarReferenceListContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by the varReferenceList labeled alternative in SnpSiftParser.expression().
visitVarReferenceListSub(SnpSiftParser.VarReferenceListSubContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
Visit a parse tree produced by the varReferenceListSub labeled alternative in SnpSiftParser.expression().
visitVarReferenceListSub(SnpSiftParser.VarReferenceListSubContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by the varReferenceListSub labeled alternative in SnpSiftParser.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
 

_

_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
 
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