Index

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

A

ACGT - Static variable in class org.snpsift.util.RandomUtil
 
action(RuleContext, int, int) - Method in class org.snpsift.antlr.SnpSiftLexer
 
add(int, int, long) - Method in class org.snpsift.annotate.VcfIndexDataChromo
Add [start, end] => filePos
add(String) - Method in class org.snpsift.annotate.mem.arrays.StringArrayBase
Add a string to the array WARNING: Typically you use either 'add' or 'set', but not both
add(String) - Method in class org.snpsift.SnpSiftCmdAnnotateMem
Add a database file
add(String, String) - Method in class org.snpsift.fileIterator.DbNsfpEntry
Add a value
add(Marker) - Method in class org.snpsift.annotate.VcfIndexTree
 
add(Markers) - Method in class org.snpsift.annotate.VcfIndexTree
 
add(VariantVcfEntry) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
Add a VCF entry to the database
add(VcfEntry, long) - Method in class org.snpsift.annotate.VcfIndex
Add an interval parse from 'line'
add(VcfHeaderInfo) - Method in class org.snpsift.annotate.mem.Fields
 
add(DataFrameRow) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
Add a row to the data frame
addChild(Individual) - Method in class org.snpsift.pedigree.Individual
 
addEffect(String) - Method in class org.snpsift.caseControl.VariantCounter
 
addEnum(String) - Method in class org.snpsift.annotate.mem.arrays.EnumArray
Add an enum, return the ordinal
addHeaders(VcfFileIterator) - Method in class org.snpsift.SnpSift
Add VCF headers
addHeaders(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdDbNsfp
Add some lines to header before showing it
addSet(String) - Method in class org.snpsift.SnpSiftCmdFilter
Read a file as a string set
addSet(String) - Method in class org.snpsift.SnpSiftCmdFilterGt
Read a file as a string set
ALT - Static variable in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
 
ALT_NAME - Static variable in class org.snpsift.fileIterator.DbNsfp
 
altIdx - Variable in class org.snpsift.fileIterator.DbNsfp
 
And - Class in org.snpsift.lang.expression
And expression
And(Expression, Expression) - Constructor for class org.snpsift.lang.expression.And
 
annotate(Variant, Map<String, String>) - Method in class org.snpsift.SnpSiftCmdDbNsfp
Annotate a VCF entry
annotate(VcfEntry) - Method in class org.snpsift.annotate.AnnotateVcfDb
Annotate a VCF entry
annotate(VcfEntry) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
This method is used to annotate a VCF entry The annotations are added to the INFO field of the VCF entry
annotate(VcfEntry) - Method in class org.snpsift.SnpSift
 
annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdAnnotate
 
annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdAnnotateMem
 
annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdCaseControl
Annotate VCF entry
annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdDbNsfp
 
annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdFilter
 
annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdGeneSets
Annotate one entry
annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdGwasCatalog
 
annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdPrivate
Parse a single VCF entry
annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdVarType
Annotate one entry
annotate(VcfEntry) - Method in class org.snpsift.SnpSiftCmdVcfOperator
 
annotate(VcfEntry, String[]) - Method in class org.snpsift.annotate.mem.database.VariantDataFrame
Annotate a VCF entry with the fields in this VariantDataFrame
annotateDb - Variable in class org.snpsift.SnpSiftCmdAnnotate
 
annotateEmpty - Variable in class org.snpsift.annotate.AnnotateVcfDb
 
annotateEmpty - Variable in class org.snpsift.SnpSiftCmdAnnotate
 
annotateEmpty - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
annotateExists(VcfEntry) - Method in class org.snpsift.annotate.AnnotateVcfDb
Add 'exists' flag to INFO fields
annotateFinish() - Method in class org.snpsift.SnpSiftCmdAnnotateMem
 
annotateFinish(VcfFileIterator) - Method in class org.snpsift.SnpSift
 
annotateFinish(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdDbNsfp
 
annotateFinish(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdGwasCatalog
 
annotateIds(VcfEntry, Set<String>) - Method in class org.snpsift.annotate.AnnotateVcfDb
Add ID information.
annotateInfo(VcfEntry, Map<String, String>) - Method in class org.snpsift.annotate.AnnotateVcfDb
Add INFO fields.
annotateInit(VcfFileIterator) - Method in class org.snpsift.SnpSift
 
annotateInit(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdAnnotate
Initialize database for annotation process
annotateInit(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdAnnotateMem
Initialize database for annotation process
annotateInit(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdDbNsfp
Initialize annotation process
annotateInit(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdFilter
 
annotateInit(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdGeneSets
 
annotateInit(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdGwasCatalog
 
annotateInit(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdPrivate
 
annotateMissing - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
AnnotateVcfDb - Class in org.snpsift.annotate
Annotate using a VCF "database"
AnnotateVcfDb() - Constructor for class org.snpsift.annotate.AnnotateVcfDb
 
AnnotateVcfDbMem - Class in org.snpsift.annotate
Annotate using a VCF "database" Note: Reads and loads the whole VCF file into memory
AnnotateVcfDbMem(String) - Constructor for class org.snpsift.annotate.AnnotateVcfDbMem
 
AnnotateVcfDbSorted - Class in org.snpsift.annotate
Annotate using a VCF "database" Note: Assumes that the VCF database file is sorted.
AnnotateVcfDbSorted(String, int) - Constructor for class org.snpsift.annotate.AnnotateVcfDbSorted
 
AnnotateVcfDbTabix - Class in org.snpsift.annotate
Annotate using a tabix indexed VCF "database"
AnnotateVcfDbTabix(String) - Constructor for class org.snpsift.annotate.AnnotateVcfDbTabix
 
applyOp(List<Double>) - Method in class org.snpsift.SnpSiftCmdVcfOperator
 
args - Variable in class org.snpsift.SnpSift
 
asBool() - Method in class org.snpsift.lang.Value
 
asFloat() - Method in class org.snpsift.lang.Value
 
asInt() - Method in class org.snpsift.lang.Value
 
assignOrder() - Method in class org.snpsift.pedigree.PedigreeDraw
Assign order
asString() - Method in class org.snpsift.lang.Value
 

B

benchmarkSortedVariantsVcfIterator(String) - Method in class org.snpsift.annotate.mem.Zzz
 
benchmarkVcfIterator(String) - Method in class org.snpsift.annotate.mem.Zzz
 
BOOL_LITERAL - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
BOOL_LITERAL - Static variable in class org.snpsift.antlr.SnpSiftParser
 
BOOL_LITERAL() - Method in class org.snpsift.antlr.SnpSiftParser.LiteralBoolContext
 
BoolArray - Class in org.snpsift.annotate.mem.arrays
A "memory efficient" boolean array Is is implemented as an array of bytes, where each bit is a boolean value.
BoolArray(int) - Constructor for class org.snpsift.annotate.mem.arrays.BoolArray
 
build() - Method in class org.snpsift.annotate.VcfIndexTree
 
BUILD - Static variable in class org.snpsift.SnpSift
 
bytes - Variable in class org.snpsift.annotate.mem.arrays.BoolArray
 

C

calcDepth() - Method in class org.snpsift.pedigree.Individual
Depth in the graph.
calcDepth() - Method in class org.snpsift.pedigree.PedigreeDraw
Max depth in this pedigree
canBeFloat() - Method in class org.snpsift.lang.Value
 
canBeInt() - Method in class org.snpsift.lang.Value
 
canCompare(Value) - Method in class org.snpsift.lang.Value
Can these values be compared?
capacity() - Method in class org.snpsift.annotate.mem.arrays.PosIndex
 
caseControl - Variable in class org.snpsift.SnpSiftCmdCaseControl
 
CaseControl - Static variable in class org.snpsift.caseControl.SnpSiftCmdCaseControlSummary
 
channelNames - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
check() - Method in class org.snpsift.annotate.mem.arrays.PosIndex
Check that all positions are in non-decreasing order.
check() - Method in class org.snpsift.annotate.mem.database.VariantDataFrame
This is used after creating the data to verify there are no issues with the dataFrames and indeces
check() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
 
check() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
Check data consistency
checkFields(String[], boolean) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
Check that all `fieldNames` are available in `fields`
checkFieldsToAdd() - Method in class org.snpsift.SnpSiftCmdDbNsfp
Check that all fields to add are available
CHR1_NUM_ENTRIES - Static variable in class org.snpsift.annotate.mem.Zzz
 
chrId - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
chromosomeIdx - Variable in class org.snpsift.fileIterator.DbNsfp
 
chrPos - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
chrPrepend - Variable in class org.snpsift.annotate.DbVcfTabix
 
chrPrev - Variable in class org.snpsift.annotate.AnnotateVcfDb
 
chrPrev - Variable in class org.snpsift.SnpSiftCmdAnnotate
 
ci95 - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
circle(int, int, int, String, int, String) - Method in class org.snpsift.pedigree.PedigreeDraw
 
clear(int) - Method in class org.snpsift.annotate.mem.arrays.BoolArray
Clear null data
cloneShallow() - Method in class org.snpsift.fileIterator.DbNsfpEntry
 
close() - Method in class org.snpsift.annotate.AnnotateVcfDb
 
close() - Method in interface org.snpsift.annotate.DbMarker
Close database, free resources
close() - Method in class org.snpsift.annotate.DbVcf
 
close() - Method in class org.snpsift.annotate.DbVcfMem
 
close() - Method in class org.snpsift.annotate.DbVcfSorted
 
close() - Method in class org.snpsift.annotate.DbVcfTabix
 
close() - Method in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
 
close() - Method in class org.snpsift.annotate.VcfIndex
Close file and free memory
close() - Method in class org.snpsift.fileIterator.DbNsfp
 
cmd() - Method in class org.snpsift.SnpSift
Run: Executes the appropriate class
cnv - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
COLLAPSE_MAX_NUM_ENTRIES - Static variable in class org.snpsift.annotate.VcfIndexTree
 
collapseRepeatedValues - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
colorAffected() - Method in class org.snpsift.pedigree.PedigreeDraw
Color individuals by affected status
COLUMN_CHR_NAME - Static variable in class org.snpsift.fileIterator.DbNsfp
 
COLUMN_POS_NAME_v2 - Static variable in class org.snpsift.fileIterator.DbNsfp
 
COLUMN_POS_NAME_v3 - Static variable in class org.snpsift.fileIterator.DbNsfp
 
COLUMN_SEPARATOR - Static variable in class org.snpsift.fileIterator.DbNsfp
 
columnNames() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
 
command - Variable in class org.snpsift.SnpSift
 
commandLineStr() - Method in class org.snpsift.SnpSift
Show command line
COMMENT_HASH - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
COMMENT_HASH - Static variable in class org.snpsift.antlr.SnpSiftParser
 
COMMENT_SL - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
COMMENT_SL - Static variable in class org.snpsift.antlr.SnpSiftParser
 
compareTo(Value) - Method in class org.snpsift.lang.Value
 
compareTo(Individual) - Method in class org.snpsift.pedigree.Individual
 
compilationUnit() - Method in class org.snpsift.antlr.SnpSiftParser
 
CompilationUnitContext(ParserRuleContext, int) - Constructor for class org.snpsift.antlr.SnpSiftParser.CompilationUnitContext
 
compile(String) - Method in class org.snpsift.lang.LangFactory
Create an AST from a program (using ANTLR lexer invalid input: '&' parser) Returns null if error Use 'alreadyIncluded' to keep track of from 'include' statements
config - Variable in class org.snpsift.SnpSift
 
CONFIG_DBNSFP_DB_NAME - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
CONFIG_GWAS_DB_NAME - Variable in class org.snpsift.SnpSiftCmdGwasCatalog
 
configFile - Variable in class org.snpsift.SnpSift
 
contains(int) - Method in class org.snpsift.annotate.mem.arrays.PosIndex
 
context - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
copyFrom(SnpSiftParser.ExpressionContext) - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionContext
 
count - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
count(String) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
Count the number of variants in a VCF file
count(String, Boolean, VariantEffect.FunctionalClass, String, int) - Method in class org.snpsift.caseControl.Summary
 
count(VcfFileIterator) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
 
count(VcfEntry) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
Count the number of variants in a VCF file
count(VcfEntry) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
Count the number of variants in a VCF file
countAnnotated - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
countBadRef - Variable in class org.snpsift.SnpSiftCmdAnnotate
 
countByCategory - Variable in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
 
CountHet - Class in org.snpsift.lang.function
Count number of heterozygous samples
CountHet() - Constructor for class org.snpsift.lang.function.CountHet
 
CountHom - Class in org.snpsift.lang.function
Count number of homozygous samples
CountHom() - Constructor for class org.snpsift.lang.function.CountHom
 
countNonZeroGenotypes() - Method in class org.snpsift.caseControl.VariantCounter
 
CountRef - Class in org.snpsift.lang.function
Count number of refernces samples
CountRef() - Constructor for class org.snpsift.lang.function.CountRef
 
CountVariant - Class in org.snpsift.lang.function
Count number of ALT samples
CountVariant() - Constructor for class org.snpsift.lang.function.CountVariant
 
countVariants - Variable in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
 
countVariants - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
countVariants(String) - Static method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
Count variants in a string of VCF lines (i.e.
countVcfEntries - Variable in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
 
covariance() - Method in class org.snpsift.SnpSiftCmdCovarianceMatrix
Calculate covariance matrix
create() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
Create a database from a VCF file
create() - Method in class org.snpsift.SnpSiftCmdAnnotateMem
Create all databases
create(String) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
Create a database from a VCF file content (as a string) This is used for testing
createColumn(VcfHeaderInfo) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
Create a column of a given type
createColumns() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
Create columns based on fields
currentDbEntry - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
currentIndex - Variable in class org.snpsift.annotate.mem.arrays.StringArrayBase
 

D

data - Variable in class org.snpsift.annotate.mem.arrays.EnumArray
 
data - Variable in class org.snpsift.annotate.mem.arrays.StringArray
 
DATA_TYPES_CACHE_EXT - Static variable in class org.snpsift.fileIterator.DbNsfp
 
DATA_TYPES_MAX_LINES - Static variable in class org.snpsift.fileIterator.DbNsfp
 
DATA_TYPES_MIN_LINES - Static variable in class org.snpsift.fileIterator.DbNsfp
 
databaseDownload() - Method in class org.snpsift.SnpSift
Download a database
databaseFind() - Method in class org.snpsift.SnpSift
Find database file name.
dataDir - Variable in class org.snpsift.SnpSift
 
DataFrame - Class in org.snpsift.annotate.mem.dataFrame
A set of DataColumns, indexed by position This is used to store data for a chromosome
DataFrame(VariantTypeCounter, VariantCategory, boolean, boolean) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrame
 
DataFrameColumn<T> - Class in org.snpsift.annotate.mem.dataFrame.dataFrameColumn
A wrapper for a data column of primitive type T A Data Column is a column of a specific data tyle (String, Float, Long, etc.) that is stored using primitive types for memory efficiency.
DataFrameColumn(String, int) - Constructor for class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
 
DataFrameColumnBool - Class in org.snpsift.annotate.mem.dataFrame.dataFrameColumn
A column of boolean values, that can also be null The bollean values are stored in a BoolArray
DataFrameColumnBool(String, int) - Constructor for class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnBool
 
DataFrameColumnChar - Class in org.snpsift.annotate.mem.dataFrame.dataFrameColumn
 
DataFrameColumnChar(String, int) - Constructor for class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnChar
 
DataFrameColumnDouble - Class in org.snpsift.annotate.mem.dataFrame.dataFrameColumn
 
DataFrameColumnDouble(String, int) - Constructor for class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnDouble
 
DataFrameColumnInt - Class in org.snpsift.annotate.mem.dataFrame.dataFrameColumn
 
DataFrameColumnInt(String, int) - Constructor for class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnInt
 
DataFrameColumnLong - Class in org.snpsift.annotate.mem.dataFrame.dataFrameColumn
 
DataFrameColumnLong(String, int) - Constructor for class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnLong
 
DataFrameColumnString - Class in org.snpsift.annotate.mem.dataFrame.dataFrameColumn
 
DataFrameColumnString(String, int, int) - Constructor for class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnString
Constructor
DataFrameDel - Class in org.snpsift.annotate.mem.dataFrame
 
DataFrameDel(VariantTypeCounter, VariantCategory) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameDel
 
DataFrameIns - Class in org.snpsift.annotate.mem.dataFrame
 
DataFrameIns(VariantTypeCounter, VariantCategory) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameIns
 
DataFrameMixed - Class in org.snpsift.annotate.mem.dataFrame
 
DataFrameMixed(VariantTypeCounter, VariantCategory) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameMixed
 
DataFrameMnp - Class in org.snpsift.annotate.mem.dataFrame
 
DataFrameMnp(VariantTypeCounter, VariantCategory) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameMnp
 
DataFrameOther - Class in org.snpsift.annotate.mem.dataFrame
 
DataFrameOther(VariantTypeCounter, VariantCategory) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameOther
 
DataFrameRow - Class in org.snpsift.annotate.mem.dataFrame
A DataFrame 'row'.
DataFrameRow(DataFrame, int, String, String) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameRow
 
DataFrameRow(DataFrame, int, String, String, int) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameRow
 
DataFrameSnp - Class in org.snpsift.annotate.mem.dataFrame
A set of DataColumns specific SNP 'alt' (e.g.
DataFrameSnp(VariantTypeCounter, VariantCategory) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameSnp
 
dataTypes() - Method in class org.snpsift.fileIterator.DbNsfp
Guess field types: Read many lines and guess the data type for each column
date - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
dateAddedtoCatalog - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
dbDirFromVcfFileName(String) - Static method in class org.snpsift.annotate.mem.database.VariantDatabase
Get the database directory name from a "VCF database" file name buy just appending ".snpsift.vardb"
dbFileName - Variable in class org.snpsift.annotate.DbVcf
 
dbFileName - Variable in class org.snpsift.SnpSift
 
DbMarker<Q,R> - Interface in org.snpsift.annotate
Use a file as a 'marker' database.
dbNsfp - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
DbNsfp - Class in org.snpsift.fileIterator
DbNSFP database: Reference https://sites.google.com/site/jpopgen/dbNSFP
DbNsfp(String) - Constructor for class org.snpsift.fileIterator.DbNsfp
 
DBNSFP_VCF_INFO_PREFIX - Static variable in class org.snpsift.SnpSiftCmdDbNsfp
 
DbNsfpEntry - Class in org.snpsift.fileIterator
DbNSFP database entry: Reference https://sites.google.com/site/jpopgen/dbNSFP Added lazy parsing of key/value pairs
DbNsfpEntry(DbNsfp, String) - Constructor for class org.snpsift.fileIterator.DbNsfpEntry
 
dbTabix - Variable in class org.snpsift.SnpSift
 
dbType - Variable in class org.snpsift.SnpSift
 
dbVcf - Variable in class org.snpsift.annotate.AnnotateVcfDb
 
DbVcf - Class in org.snpsift.annotate
Use a VCF file as a database for annotations A VCF database consists of a VCF file and an index.
DbVcf(String) - Constructor for class org.snpsift.annotate.DbVcf
 
DbVcfMem - Class in org.snpsift.annotate
Loads a VCF file into memory.
DbVcfMem(String) - Constructor for class org.snpsift.annotate.DbVcfMem
 
DbVcfSorted - Class in org.snpsift.annotate
Use an uncompressed sorted VCF file as a database for annotations Note: Assumes that the VCF database file is sorted and uncompressed.
DbVcfSorted(String) - Constructor for class org.snpsift.annotate.DbVcfSorted
 
DbVcfTabix - Class in org.snpsift.annotate
Use a bgzip-compressed, tabix indexed VCF file as a database for annotations
DbVcfTabix(String) - Constructor for class org.snpsift.annotate.DbVcfTabix
 
debug - Variable in class org.snpsift.annotate.AnnotateVcfDb
 
debug - Variable in class org.snpsift.annotate.DbVcf
 
debug - Variable in class org.snpsift.fileIterator.DbNsfp
 
debug - Static variable in class org.snpsift.hwe.VcfHwe
 
debug - Static variable in class org.snpsift.lang.expression.Expression
 
debug - Static variable in class org.snpsift.lang.LangFactory
 
debug - Static variable in class org.snpsift.lang.Value
 
debug - Static variable in class org.snpsift.pedigree.PedigreeDraw
 
debug - Variable in class org.snpsift.SnpSift
 
debug - Static variable in class org.snpsift.VcfLd
 
DEFAULT_FIELDS_NAMES_TO_ADD - Static variable in class org.snpsift.SnpSiftCmdDbNsfp
 
DEFAULT_MAX_BLOCK_SIZE - Static variable in class org.snpsift.annotate.VcfIndexTree
 
DEL - Enum constant in enum class org.snpsift.annotate.mem.VariantCategory
 
diamond(int, int, int, int, String, int, String) - Method in class org.snpsift.pedigree.PedigreeDraw
Draw a diamond (unknown sex)
discoverInfoFields() - Method in class org.snpsift.annotate.AnnotateVcfDb
 
discoverInfoFields(VcfEntry) - Method in class org.snpsift.annotate.AnnotateVcfDb
If 'ALL' info fields are being used, we can try to discover new fields that have not already been added to the annotation list (e.g.
Div - Class in org.snpsift.lang.expression
And expression
Div(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Div
 
DO_NOT_USE - Enum constant in enum class org.snpsift.SnpSiftCmdVcf2Tped.UseMissing
 
download - Variable in class org.snpsift.SnpSift
 
downstreamGeneDistance - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
downstreamGeneId - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
drawSvg() - Method in class org.snpsift.pedigree.PedigreeDraw
Draw the full pedigree as an SVG graph
drawSvgByFamily(String, String) - Method in class org.snpsift.pedigree.PedigreeDraw
Draw each family

E

EFFECT - Enum constant in enum class org.snpsift.lang.expression.FieldIterator.IteratorType
 
elapsedSec() - Method in class org.snpsift.util.ShowProgress
 
EMPTY_ARGS - Static variable in class org.snpsift.SnpSift
 
enterCompilationUnit(SnpSiftParser.CompilationUnitContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Enter a parse tree produced by SnpSiftParser.compilationUnit().
enterCompilationUnit(SnpSiftParser.CompilationUnitContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Enter a parse tree produced by SnpSiftParser.compilationUnit().
enterEveryRule(ParserRuleContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
enterExpressionComp(SnpSiftParser.ExpressionCompContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Enter a parse tree produced by the expressionComp labeled alternative 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().
enum2ord - Variable in class org.snpsift.annotate.mem.arrays.EnumArray
 
EnumArray - Class in org.snpsift.annotate.mem.arrays
Implement a memory efficient array of enums It only stores bytes (i.e.
EnumArray(int) - Constructor for class org.snpsift.annotate.mem.arrays.EnumArray
Constructor
EnumArray(String[]) - Constructor for class org.snpsift.annotate.mem.arrays.EnumArray
Constructor for using an array of strings
EOF() - Method in class org.snpsift.antlr.SnpSiftParser.CompilationUnitContext
 
eq(int, int, String, String) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
Does the entry at possition 'idx' match the given (pos, ref, alt) values?
eq(int, int, String, String) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameSnp
Does the entry at possition 'idx' match the given (pos, ref, alt) values?
Eq - Class in org.snpsift.lang.expression
Equal
Eq(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Eq
 
equals(Object) - Method in class org.snpsift.lang.Value
 
errCount - Variable in class org.snpsift.annotate.AnnotateVcfDb
 
errCount - Variable in class org.snpsift.SnpSift
 
error(Throwable, String) - Method in class org.snpsift.SnpSift
Show an error (if not 'quiet' mode)
error(Throwable, String) - Method in class org.snpsift.SnpSiftCmdTsTv
Show an error (if not 'quiet' mode)
eval(VcfEntry) - Method in class org.snpsift.lang.expression.And
 
eval(VcfEntry) - Method in class org.snpsift.lang.expression.Expression
Evaluate expression using VcfEntry
eval(VcfEntry) - Method in class org.snpsift.lang.expression.ExpressionBinary
 
eval(VcfEntry) - Method in class org.snpsift.lang.expression.ExpressionUnary
 
eval(VcfEntry) - Method in class org.snpsift.lang.expression.Field
 
eval(VcfEntry) - Method in class org.snpsift.lang.expression.FieldConstantFloat
 
eval(VcfEntry) - Method in class org.snpsift.lang.expression.Literal
 
eval(VcfEntry) - Method in class org.snpsift.lang.expression.Or
 
eval(VcfEntry) - Method in class org.snpsift.lang.function.CountHet
 
eval(VcfEntry) - Method in class org.snpsift.lang.function.CountHom
 
eval(VcfEntry) - Method in class org.snpsift.lang.function.CountRef
 
eval(VcfEntry) - Method in class org.snpsift.lang.function.CountVariant
 
eval(VcfEntry) - Method in class org.snpsift.lang.function.In
 
eval(VcfEntry) - Method in class org.snpsift.lang.function.IsHet
 
eval(VcfEntry) - Method in class org.snpsift.lang.function.IsHom
 
eval(VcfEntry) - Method in class org.snpsift.lang.function.IsRef
 
eval(VcfEntry) - Method in class org.snpsift.lang.function.IsVariant
 
eval(VcfGenotype) - Method in class org.snpsift.lang.expression.Expression
Evaluate expression using genotype
eval(VcfGenotype) - Method in class org.snpsift.lang.expression.ExpressionBinary
 
eval(VcfGenotype) - Method in class org.snpsift.lang.expression.ExpressionUnary
 
eval(VcfGenotype) - Method in class org.snpsift.lang.expression.Field
 
eval(VcfGenotype) - Method in class org.snpsift.lang.expression.Literal
 
eval(VcfGenotype) - Method in class org.snpsift.lang.function.CountHet
 
eval(VcfGenotype) - Method in class org.snpsift.lang.function.CountHom
 
eval(VcfGenotype) - Method in class org.snpsift.lang.function.CountRef
 
eval(VcfGenotype) - Method in class org.snpsift.lang.function.CountVariant
 
eval(VcfGenotype) - Method in class org.snpsift.lang.function.In
 
eval(VcfGenotype) - Method in class org.snpsift.lang.function.IsHet
 
eval(VcfGenotype) - Method in class org.snpsift.lang.function.IsHom
 
eval(VcfGenotype) - Method in class org.snpsift.lang.function.IsRef
 
eval(VcfGenotype) - Method in class org.snpsift.lang.function.IsVariant
 
evalGenotype(VcfEntry) - Method in class org.snpsift.lang.expression.FieldGenotype
Evaluate expressions and return VcfGenotype
evalGenotype(VcfEntry) - Method in class org.snpsift.lang.function.FunctionBoolGenotype
Evaluate index expression and obtein genotype
evalIndex(VcfEntry) - Method in class org.snpsift.lang.expression.FieldSub
Evaluate index expression
evalIndex(VcfEntry, Expression) - Method in class org.snpsift.lang.expression.FieldSub
Evaluate index expression (VCF entry)
evalIndex(VcfGenotype) - Method in class org.snpsift.lang.expression.FieldSub
Evaluate index expression (VCF genotype)
evalIndex(VcfGenotype, Expression) - Method in class org.snpsift.lang.expression.FieldSub
Evaluate index expression (VCF genotype)
evalOp(Value) - Method in class org.snpsift.lang.expression.Exists
 
evalOp(Value) - Method in class org.snpsift.lang.expression.ExpressionUnary
 
evalOp(Value) - Method in class org.snpsift.lang.expression.Not
 
evalOp(Value, Value) - Method in class org.snpsift.lang.expression.And
 
evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Div
 
evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Eq
 
evalOp(Value, Value) - Method in class org.snpsift.lang.expression.ExpressionBinary
 
evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Ge
 
evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Gt
 
evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Has
 
evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Le
 
evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Lt
 
evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Match
 
evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Minus
 
evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Mod
 
evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Or
 
evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Plus
 
evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Times
 
evalOp(Value, Value) - Method in class org.snpsift.lang.expression.Xor
 
exceptionIfNotFound - Variable in class org.snpsift.lang.expression.Field
 
Exists - Class in org.snpsift.lang.expression
Exists operator (true if a field exists)
Exists(Expression) - Constructor for class org.snpsift.lang.expression.Exists
 
existsInfoField - Variable in class org.snpsift.annotate.AnnotateVcfDb
 
existsInfoField - Variable in class org.snpsift.SnpSiftCmdAnnotate
 
exitCompilationUnit(SnpSiftParser.CompilationUnitContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Exit a parse tree produced by SnpSiftParser.compilationUnit().
exitCompilationUnit(SnpSiftParser.CompilationUnitContext) - Method in interface org.snpsift.antlr.SnpSiftListener
Exit a parse tree produced by SnpSiftParser.compilationUnit().
exitEveryRule(ParserRuleContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
exitExpressionComp(SnpSiftParser.ExpressionCompContext) - Method in class org.snpsift.antlr.SnpSiftBaseListener
Exit a parse tree produced by the expressionComp labeled alternative 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.annotate.mem.variantTypeCounter.VariantTypeCounter
 
fields - Variable in class org.snpsift.SnpSiftCmdVcfOperator
 
Fields - Class in org.snpsift.annotate.mem
 
Fields() - Constructor for class org.snpsift.annotate.mem.Fields
 
FIELDS_EXT - Static variable in class org.snpsift.annotate.mem.database.VariantDatabase
 
fieldsDescription - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
fieldsNamesToAdd - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
fieldsString - Variable in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
 
fieldsToAdd - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
fieldsType - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
FieldSub - Class in org.snpsift.lang.expression
A field that has sub fields (e.g.
FieldSub(String, Expression) - Constructor for class org.snpsift.lang.expression.FieldSub
 
fileIdx - Variable in class org.snpsift.annotate.MarkerFile
 
fileName - Variable in class org.snpsift.fileIterator.DbNsfp
 
fileSize(int, int) - Method in class org.snpsift.annotate.VcfIndexDataChromo
File size between startIdx and endIdx inclusive
fill() - Method in class org.snpsift.annotate.mem.arrays.BoolArray
 
filter(String, String, boolean) - Method in class org.snpsift.SnpSiftCmdFilter
Filter a file
filter(String, String, boolean) - Method in class org.snpsift.SnpSiftCmdFilterGt
Filter a file
filter(VcfEntry) - Method in class org.snpsift.SnpSiftCmdFilterChrPos
Filter this line?
find(int, String, String) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
Get data from a column index by searching by position, reference and alternative alleles.
find(Variant) - Method in class org.snpsift.annotate.AnnotateVcfDb
 
find(VcfEntry) - Method in class org.snpsift.annotate.AnnotateVcfDb
Find matching entries in the database
findDbExists(QueryResult) - Method in class org.snpsift.annotate.AnnotateVcfDb
Should we annotate using 'exists' field?
findDbId(Set<String>, QueryResult) - Method in class org.snpsift.annotate.AnnotateVcfDb
Find an ID for this variant and add them to idSet
findDbInfo(String, QueryResult) - Method in class org.snpsift.annotate.AnnotateVcfDb
Find all non-empty INFO fields 'infoFieldName' in results
findDbInfo(Map<String, String>, QueryResult) - Method in class org.snpsift.annotate.AnnotateVcfDb
Find INFO fields for this VCF entry
findDbInfoAlt(String, QueryResult) - Method in class org.snpsift.annotate.AnnotateVcfDb
Find the first non-empty INFO field 'infoFieldName' in results Note: ALT must match
findDbInfoRef(Map<String, String>, Set<VcfEntry>) - Method in class org.snpsift.annotate.AnnotateVcfDb
Fill values for INFO fields requiring 'REF' value
findSpouses(Individual) - Method in class org.snpsift.pedigree.PedigreeDraw
 
firstAuthor - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
FIXED_STEP_FIELD - Static variable in class org.snpsift.SnpSiftCmdPhastCons
 
FLOAT_LITERAL - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
FLOAT_LITERAL - Static variable in class org.snpsift.antlr.SnpSiftParser
 
FLOAT_LITERAL() - Method in class org.snpsift.antlr.SnpSiftParser.LiteralFloatContext
 
forceMissingTypesAsString() - Method in class org.snpsift.fileIterator.DbNsfp
Force missing types as string
formatBytes(long) - Static method in class org.snpsift.util.FormatUtil
Format bytes as a human readable string
FormatUtil - Class in org.snpsift.util
 
FormatUtil() - Constructor for class org.snpsift.util.FormatUtil
 
formatVersion - Static variable in class org.snpsift.caseControl.SnpSiftCmdCaseControlSummary
 
Function - Class in org.snpsift.lang.function
A function that returns an expression (i.e.
Function(String) - Constructor for class org.snpsift.lang.function.Function
 
FunctionBoolGenotype - Class in org.snpsift.lang.function
A function that returns a bool type (i.e.
FunctionBoolGenotype(String, Expression) - Constructor for class org.snpsift.lang.function.FunctionBoolGenotype
 
functionBoolGenotypeFactory(ParseTree) - Method in class org.snpsift.lang.LangFactory
Create FunctionBoolGenotype from AST
FunctionCallContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.FunctionCallContext
 
functionFactory(ParseTree) - Method in class org.snpsift.lang.LangFactory
Create function
functionVcfEntryFactory(ParseTree) - Method in class org.snpsift.lang.LangFactory
Create Functions from tree Note: These functions that are calculated on the whole VcfEntry.

G

Ge - Class in org.snpsift.lang.expression
Greater equal
Ge(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Ge
 
genome - Variable in class org.snpsift.fileIterator.DbNsfp
 
genomeVersion - Variable in class org.snpsift.SnpSift
 
GENOTYPE - Enum constant in enum class org.snpsift.lang.expression.FieldIterator.IteratorType
 
GENOTYPE_VAR - Enum constant in enum class org.snpsift.lang.expression.FieldIterator.IteratorType
 
get() - Static method in class org.snpsift.lang.expression.FieldIterator
 
get(int) - Method in class org.snpsift.annotate.mem.arrays.EnumArray
Get the string at array index 'i'
get(int) - Method in class org.snpsift.annotate.mem.arrays.PosIndex
Get position at index 'i'
get(int) - Method in class org.snpsift.annotate.mem.arrays.StringArray
Get the string at array index 'i'
get(int) - Method in class org.snpsift.annotate.mem.arrays.StringArrayBase
Get the string at array index 'i'
get(int) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
Get value at index i, considering null data
get(String) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
Get the database for a chromosome
get(String) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
 
get(String) - Method in class org.snpsift.annotate.mem.Fields
 
get(String) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
 
get(String) - Method in class org.snpsift.gwasCatalog.GwasCatalog
 
get(String) - Method in class org.snpsift.pedigree.PedigreeDraw
 
get(String, int) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
Get data from a column by searching by position, reference and alternative alleles.
get(String, int) - Method in class org.snpsift.gwasCatalog.GwasCatalog
Get all entries at a given chromosome invalid input: '&' position Note: Position is zero based.
get(FieldIterator.IteratorType) - Method in class org.snpsift.lang.expression.FieldIterator
Set 'max' parameter for an iterator
getAffected() - Method in class org.snpsift.pedigree.Individual
 
getAlt() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
 
getAlt() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameSnp
 
getAltIdx() - Method in class org.snpsift.fileIterator.DbNsfp
 
getArgs() - Method in class org.snpsift.SnpSift
 
getArgs() - Method in class org.snpsift.SnpSiftCmdVcfOperator
 
getATN() - Method in class org.snpsift.antlr.SnpSiftLexer
 
getATN() - Method in class org.snpsift.antlr.SnpSiftParser
 
getByRs(String) - Method in class org.snpsift.gwasCatalog.GwasCatalog
Get an entry based on 'RS' number
getChannelNames() - Method in class org.snpsift.antlr.SnpSiftLexer
 
getChilds() - Method in class org.snpsift.pedigree.Individual
 
getChilds(Individual) - Method in class org.snpsift.pedigree.Individual
Get only childs from this spouse
getChromosome() - Method in class org.snpsift.annotate.VcfIndexDataChromo
 
getChromosome() - Method in class org.snpsift.annotate.VcfIndexTree
 
getChromosome(String) - Method in class org.snpsift.fileIterator.DbNsfp
Find chromosome 'chromoName'.
getChromosomeIdx() - Method in class org.snpsift.fileIterator.DbNsfp
 
getChrPosRefAltIdx() - Method in class org.snpsift.fileIterator.DbNsfp
 
getColor() - Method in class org.snpsift.pedigree.Individual
 
getColumn(String) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
Get a column
getConcordance() - Method in class org.snpsift.SnpSiftCmdConcordance
 
getConcordanceBySample() - Method in class org.snpsift.SnpSiftCmdConcordance
 
getConfig() - Method in class org.snpsift.SnpSift
 
getConfigFile() - Method in class org.snpsift.SnpSift
 
getCount(VariantCategory) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
 
getCountByCategory() - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
 
getCountEntries() - Method in class org.snpsift.SnpSiftCmdConcordance
 
getD() - Method in class org.snpsift.VcfLd
 
getData() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnString
Get the data, used for testing
getData(int) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
 
getData(int) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnBool
 
getData(int) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnChar
 
getData(int) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnDouble
 
getData(int) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnInt
 
getData(int) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnLong
 
getData(int) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnString
 
getDatabaseVcfFileName() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
 
getDataFrameByCategory(VariantCategory) - Method in class org.snpsift.annotate.mem.database.VariantDataFrame
 
getDataFrameByVariantType(Variant) - Method in class org.snpsift.annotate.mem.database.VariantDataFrame
Select the appropirate data set for a variant
getDataFrameValue(String) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
Get data single column value from the data frame
getDataFrameValues() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
Return all data for this row from the data frame
getDbDir() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
 
getDepth() - Method in class org.snpsift.pedigree.Individual
 
getDmax() - Method in class org.snpsift.VcfLd
 
getDmin() - Method in class org.snpsift.VcfLd
 
getDprime() - Method in class org.snpsift.VcfLd
 
getEnd(int) - Method in class org.snpsift.annotate.VcfIndexDataChromo
 
getFamilyId() - Method in class org.snpsift.pedigree.Individual
 
getFather() - Method in class org.snpsift.pedigree.Individual
 
getFieldCount() - Method in class org.snpsift.fileIterator.DbNsfp
 
getFieldFloat(VcfEntry) - Method in class org.snpsift.lang.expression.FieldConstantFloat
 
getFieldName(int) - Method in class org.snpsift.fileIterator.DbNsfp
 
getFieldNames() - Method in class org.snpsift.fileIterator.DbNsfp
 
getFieldNamesSorted() - Method in class org.snpsift.fileIterator.DbNsfp
 
getFields() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
 
getFields() - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
 
getFields() - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
 
getFieldString(VcfEntry) - Method in class org.snpsift.lang.expression.FieldEff
Get a field from VcfEntry
getFieldString(VcfEntry) - Method in class org.snpsift.lang.expression.FieldGenotype
Get a field from VcfEntry
getFieldString(VcfEntry) - Method in class org.snpsift.lang.expression.FieldGenotypeSub
Get a field from VcfEntry
getFieldString(VcfEntry) - Method in class org.snpsift.lang.expression.FieldLof
Get a field from VcfEntry
getFieldString(VcfEntry) - Method in class org.snpsift.lang.expression.FieldSub
Get a field from VcfEntry
getFieldString(VcfGenotype) - Method in class org.snpsift.lang.expression.Field
 
getFieldString(VcfGenotype) - Method in class org.snpsift.lang.expression.FieldGenotype
Get a field (as a Float) from VcfEntry
getFieldString(VcfGenotype) - Method in class org.snpsift.lang.expression.FieldGenotypeSub
Get a field from VcfGenotype
getFieldString(VcfGenotype) - Method in class org.snpsift.lang.expression.FieldSub
Get a field from VcfEntry
getFieldsType() - Method in class org.snpsift.SnpSiftCmdDbNsfp
 
getFileIdx() - Method in class org.snpsift.annotate.MarkerFile
 
getFileNames() - Method in class org.snpsift.SnpSiftCmdSplit
Names of files created when splitting
getFilePosEnd(int) - Method in class org.snpsift.annotate.VcfIndexDataChromo
 
getFilePosStart(int) - Method in class org.snpsift.annotate.VcfIndexDataChromo
 
getGenome() - Method in class org.snpsift.annotate.VcfIndex
 
getGenotype(int) - Method in class org.snpsift.caseControl.VariantCounter
 
getGrammarFileName() - Method in class org.snpsift.antlr.SnpSiftLexer
 
getGrammarFileName() - Method in class org.snpsift.antlr.SnpSiftParser
 
getId() - Method in class org.snpsift.pedigree.Individual
 
getIdx() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
 
getIndex(String) - Method in class org.snpsift.fileIterator.DbNsfp
 
getIndividuals() - Method in class org.snpsift.pedigree.PedigreeDraw
 
getIntervals() - Method in class org.snpsift.annotate.VcfIndexTree
 
getLabel() - Method in class org.snpsift.pedigree.Individual
 
getModeNames() - Method in class org.snpsift.antlr.SnpSiftLexer
 
getMother() - Method in class org.snpsift.pedigree.Individual
 
getName() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
 
getName() - Method in class org.snpsift.lang.expression.Field
 
getName() - Method in class org.snpsift.lang.expression.FieldEff
 
getName() - Method in class org.snpsift.lang.expression.FieldLof
 
getNames() - Method in class org.snpsift.annotate.mem.Fields
 
getNames2index() - Method in class org.snpsift.fileIterator.DbNsfp
 
getOffset() - Method in class org.snpsift.annotate.mem.arrays.StringArray
 
getOrCreate(String) - Method in class org.snpsift.annotate.VcfIndex
Get IntervalFileChromo by chromosome name.
getOrd(int) - Method in class org.snpsift.annotate.mem.arrays.EnumArray
Get the ordinal at array index 'i'
getOrder() - Method in class org.snpsift.pedigree.Individual
 
getOutput() - Method in class org.snpsift.SnpSift
 
getOutput() - Method in class org.snpsift.SnpSiftCmdGt
 
getpA() - Method in class org.snpsift.VcfLd
 
getpB() - Method in class org.snpsift.VcfLd
 
getPos() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
 
getPosition() - Method in class org.snpsift.pedigree.Individual
 
getQa() - Method in class org.snpsift.VcfLd
 
getQb() - Method in class org.snpsift.VcfLd
 
getRef() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
 
getRefIdx() - Method in class org.snpsift.fileIterator.DbNsfp
 
getReturnType(VcfEntry) - Method in class org.snpsift.lang.expression.FieldEff
 
getReturnType(VcfEntry) - Method in class org.snpsift.lang.expression.FieldLof
 
getReturnType(VcfGenotype) - Method in class org.snpsift.lang.expression.Field
 
getRow(int, String, String) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
Get a 'row' from the data frame.
getrSquare() - Method in class org.snpsift.VcfLd
 
getRuleIndex() - Method in class org.snpsift.antlr.SnpSiftParser.CompilationUnitContext
 
getRuleIndex() - Method in class org.snpsift.antlr.SnpSiftParser.ExpressionContext
 
getRuleNames() - Method in class org.snpsift.antlr.SnpSiftLexer
 
getRuleNames() - Method in class org.snpsift.antlr.SnpSiftParser
 
getSampleNum(VcfEntry, String) - Method in class org.snpsift.lang.expression.Field
 
getSerializedATN() - Method in class org.snpsift.antlr.SnpSiftLexer
 
getSerializedATN() - Method in class org.snpsift.antlr.SnpSiftParser
 
getSex() - Method in class org.snpsift.pedigree.Individual
 
getSize(VariantCategory, String) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
Get total size (in bytes) of a field (only string fields)
getSizesByField() - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
 
getSizeX() - Method in class org.snpsift.pedigree.PedigreeDraw
 
getSizeY() - Method in class org.snpsift.pedigree.PedigreeDraw
 
getStart(int) - Method in class org.snpsift.annotate.VcfIndexDataChromo
 
getStartIdx() - Method in class org.snpsift.fileIterator.DbNsfp
 
getTokenNames() - Method in class org.snpsift.antlr.SnpSiftLexer
Deprecated.
getTokenNames() - Method in class org.snpsift.antlr.SnpSiftParser
Deprecated.
getTraitCode() - Method in class org.snpsift.gwasCatalog.GwasCatalogEntry
Trait as a 'code' (only alpha-num chars)
getTree(String) - Method in class org.snpsift.annotate.VcfIndex
 
getType() - Method in enum class org.snpsift.lang.expression.FieldConstant.FieldConstantNames
 
getType() - Method in class org.snpsift.lang.expression.FieldIterator
 
getTypes() - Method in class org.snpsift.fileIterator.DbNsfp
 
getValues() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
 
getValues(VcfEntry) - Method in class org.snpsift.SnpSiftCmdVcfOperator
 
getValues(VcfEntry, String) - Method in class org.snpsift.SnpSiftCmdVcfOperator
Parse an INFO field (can be multiple valued) and return a list of Double
getVariantTypeCounters() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
 
getVcf() - Method in class org.snpsift.annotate.VcfIndex
 
getVcfHeader() - Method in class org.snpsift.annotate.DbVcf
 
getVcfIndexChromo(String) - Method in class org.snpsift.annotate.VcfIndex
 
getVcfInfo(String) - Method in class org.snpsift.fileIterator.DbNsfpEntry
Get data in a VCF INFO field compatible format
getVocabulary() - Method in class org.snpsift.antlr.SnpSiftLexer
 
getVocabulary() - Method in class org.snpsift.antlr.SnpSiftParser
 
groups - Variable in class org.snpsift.SnpSiftCmdCaseControl
 
Gt - Class in org.snpsift.lang.expression
Greater equal
Gt(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Gt
 
gtFieldNotFound(VcfGenotype) - Method in class org.snpsift.lang.expression.Field
 
guessDataType(String) - Method in class org.snpsift.fileIterator.DbNsfp
Guess value type
guessDataTypes() - Method in class org.snpsift.fileIterator.DbNsfp
Guess data types from file
GWAS_CATALOG - Variable in class org.snpsift.SnpSiftCmdGwasCatalog
 
GwasCatalog - Class in org.snpsift.gwasCatalog
GWAS catalog table.
GwasCatalog(String) - Constructor for class org.snpsift.gwasCatalog.GwasCatalog
 
GwasCatalogEntry - Class in org.snpsift.gwasCatalog
Entry from a GWAS-catalog References: http://www.genome.gov/gwastudies/#download http://www.genome.gov/Pages/About/OD/OPG/GWAS%20Catalog/Tab_delimited_column_descriptions_09_27.pdf
GwasCatalogEntry() - Constructor for class org.snpsift.gwasCatalog.GwasCatalogEntry
 
GwasCatalogFileIterator - Class in org.snpsift.gwasCatalog
Iterate on each line of a GWAS catalog (TXT, tab separated format)
GwasCatalogFileIterator(String) - Constructor for class org.snpsift.gwasCatalog.GwasCatalogFileIterator
 

H

Has - Class in org.snpsift.lang.expression
Equal
Has(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Has
 
hasEntry(int, String, String) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
Get data from a column by searching by position, reference and alternative alleles.
hasField(String) - Method in class org.snpsift.fileIterator.DbNsfp
Do we have a column 'colName'?
hashCode() - Method in class org.snpsift.lang.Value
 
hasNext() - Method in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
 
hasNext() - Method in class org.snpsift.lang.expression.FieldIterator
Is there a 'next'
hasOrder() - Method in class org.snpsift.pedigree.Individual
 
hasPosition() - Method in class org.snpsift.pedigree.Individual
 
hasValues(String) - Method in class org.snpsift.fileIterator.DbNsfpEntry
Do we have values for this allele
hasVcfInfoPerAlleleRef - Variable in class org.snpsift.annotate.AnnotateVcfDb
 
HEADER_PREFIX - Static variable in class org.snpsift.fileIterator.DbNsfp
 
headers() - Method in class org.snpsift.hwe.SnpSiftCmdHwe
 
headers() - Method in class org.snpsift.SnpSift
Headers to add
headers() - Method in class org.snpsift.SnpSiftCmdAnnotate
Build headers to add
headers() - Method in class org.snpsift.SnpSiftCmdAnnotateMem
Build headers to add
headers() - Method in class org.snpsift.SnpSiftCmdCaseControl
Lines to be added to VCF header
headers() - Method in class org.snpsift.SnpSiftCmdFilter
 
headers() - Method in class org.snpsift.SnpSiftCmdFilterGt
 
headers() - Method in class org.snpsift.SnpSiftCmdGeneSets
 
headers() - Method in class org.snpsift.SnpSiftCmdGt
 
headers() - Method in class org.snpsift.SnpSiftCmdGwasCatalog
 
headers() - Method in class org.snpsift.SnpSiftCmdVarType
 
headers() - Method in class org.snpsift.SnpSiftCmdVcfOperator
 
help - Variable in class org.snpsift.SnpSift
 
hwe(VcfEntry, boolean) - Method in class org.snpsift.hwe.VcfHwe
Calculate Hardy-Weimberg equilibrium and add data to vcfEntry (INFO fields)
hweLogPn12(int, int, int) - Method in class org.snpsift.hwe.VcfHwe
Calculate exact log of "P[ n12 | n1, n2]" References: "Principles of population genetics", Hartl invalid input: '&' Clark, page 58 (formula 2.5) "A Note on Exact test of Hardy Weinbeg Equilibrium", G.
hweP(int, int, int) - Method in class org.snpsift.hwe.VcfHwe
Calculate goodness of fit for n1, n2 combination.
hwePchi2(int, int, int) - Method in class org.snpsift.hwe.VcfHwe
Calculate goodness of fit using Chi square approximation
hwePn12(int, int, int) - Method in class org.snpsift.hwe.VcfHwe
Calculate exact probability of "P[ n12 | n1, n2]" References: "Principles of population genetics", Hartl invalid input: '&' Clark, page 58 (formula 2.5) "A Note on Exact test of Hardy Weinbeg Equilibrium", G.

I

ID - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
ID - Static variable in class org.snpsift.antlr.SnpSiftParser
 
ID() - Method in class org.snpsift.antlr.SnpSiftParser.FunctionCallContext
 
ID() - Method in class org.snpsift.antlr.SnpSiftParser.VarReferenceContext
 
idx - Variable in class org.snpsift.antlr.SnpSiftParser.LiteralIndexContext
 
In - Class in org.snpsift.lang.function
Is an expression in a set?
In(ArrayList<HashSet<String>>, Expression, Expression) - Constructor for class org.snpsift.lang.function.In
 
incGenotype(int) - Method in class org.snpsift.caseControl.VariantCounter
 
incGenotype(int, int) - Method in class org.snpsift.caseControl.VariantCounter
 
index() - Method in class org.snpsift.annotate.VcfIndex
Load or create index
INDEX_EXT - Static variable in class org.snpsift.annotate.VcfIndex
 
INDEX_FORMAT_VERSION - Static variable in class org.snpsift.annotate.VcfIndex
 
index2offset - Variable in class org.snpsift.annotate.mem.arrays.StringArray
 
indexOf(int) - Method in class org.snpsift.annotate.mem.arrays.PosIndex
Find the index of a position using binary search
indexOfSlow(int) - Method in class org.snpsift.annotate.mem.arrays.PosIndex
Find the index of a position using a (slow) linear search Used for testing
indexStr(int) - Method in class org.snpsift.lang.expression.Field
Convert and index to a string
Individual - Class in org.snpsift.pedigree
An individual in the pedigree Individuals are like TfamEntries but have drawing info (coordinates, color, etc.)
Individual(TfamEntry) - Constructor for class org.snpsift.pedigree.Individual
 
Inf - Enum constant in enum class org.snpsift.lang.expression.FieldConstant.FieldConstantNames
 
INFO_GENE_SETS - Static variable in class org.snpsift.SnpSiftCmdGeneSets
 
infoFields - Variable in class org.snpsift.annotate.AnnotateVcfDb
 
infoFields - Variable in class org.snpsift.SnpSiftCmdAnnotate
 
infoFields - Variable in class org.snpsift.SnpSiftCmdVcfOperator
 
init() - Method in class org.snpsift.lang.expression.FieldLof
 
init() - Method in class org.snpsift.lang.expression.FieldNmd
 
init() - Method in class org.snpsift.SnpSift
Initialize default values
init() - Method in class org.snpsift.SnpSiftCmdAnnotate
Initialize default values
init() - Method in class org.snpsift.SnpSiftCmdAnnotateMem
Initialize
init() - Method in class org.snpsift.SnpSiftCmdCaseControl
 
init() - Method in class org.snpsift.SnpSiftCmdConcordance
 
init() - Method in class org.snpsift.SnpSiftCmdDbNsfp
Initialize default values
init() - Method in class org.snpsift.SnpSiftCmdExtractFields
 
init() - Method in class org.snpsift.SnpSiftCmdFilter
Initialize default values
init() - Method in class org.snpsift.SnpSiftCmdFilterGt
Initialize default values
init() - Method in class org.snpsift.SnpSiftCmdGwasCatalog
Initialize default values
init() - Method in class org.snpsift.SnpSiftCmdIntervals
Initialize default values
init() - Method in class org.snpsift.SnpSiftCmdIntervalsIndex
 
init() - Method in class org.snpsift.SnpSiftCmdJoin
 
init() - Method in class org.snpsift.SnpSiftCmdPhastCons
 
init() - Method in class org.snpsift.SnpSiftCmdVcf2Tped
Default parameters
INITIAL_CAPACITY - Static variable in class org.snpsift.annotate.VcfIndexDataChromo
 
INITIAL_CAPACITY - Static variable in class org.snpsift.annotate.VcfIndexTree
 
initialSampleSize - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
initialValue() - Method in class org.snpsift.SnpSiftCmdVcfOperator
 
initTabix(String) - Method in class org.snpsift.annotate.DbVcfTabix
Initialize tabix reader
initTabix(String) - Method in class org.snpsift.fileIterator.DbNsfp
Initialize tabix reader
INS - Enum constant in enum class org.snpsift.annotate.mem.VariantCategory
 
INT_LITERAL - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
INT_LITERAL - Static variable in class org.snpsift.antlr.SnpSiftParser
 
INT_LITERAL() - Method in class org.snpsift.antlr.SnpSiftParser.LiteralIntContext
 
intergenic - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
intersects(int, int) - Method in class org.snpsift.annotate.VcfIndexDataChromo
Does interval at position 'idx' intersect positions 'pos'?
intersects(int, Marker) - Method in class org.snpsift.annotate.VcfIndexDataChromo
Does interval at position 'idx' intersect 'marker'?
inverseFieldSelection - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
is(int) - Method in class org.snpsift.annotate.mem.arrays.BoolArray
Is the data value is index i set?
isBool() - Method in class org.snpsift.lang.Value
 
isConstantField(String) - Static method in class org.snpsift.lang.expression.FieldConstant
Is this string a constant's name?
isDescendant(Individual) - Method in class org.snpsift.pedigree.Individual
Is 'this' descendant from 'ind' (e.g.
isEmpty() - Method in class org.snpsift.annotate.VcfIndexTree
 
isFemale() - Method in class org.snpsift.pedigree.Individual
 
isFloat() - Method in class org.snpsift.lang.Value
 
IsHet - Class in org.snpsift.lang.function
Is 'genotypeNum' heterozygous?
IsHet(Expression) - Constructor for class org.snpsift.lang.function.IsHet
 
IsHom - Class in org.snpsift.lang.function
Is 'genotypeNum' homozygous?
IsHom(Expression) - Constructor for class org.snpsift.lang.function.IsHom
 
isInSync() - Method in class org.snpsift.annotate.VcfIndexTree
 
isInt() - Method in class org.snpsift.lang.Value
 
isMale() - Method in class org.snpsift.pedigree.Individual
 
isNull() - Method in class org.snpsift.lang.Value
 
isNull(int) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
Is the data at index i null?
isNUllData - Variable in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
 
isOpt(String) - Method in class org.snpsift.SnpSift
Is this a command line option (e.g.
IsRef - Class in org.snpsift.lang.function
Is 'genotypeNum' reference?
IsRef(Expression) - Constructor for class org.snpsift.lang.function.IsRef
 
isRoot() - Method in class org.snpsift.pedigree.Individual
Is this a root node?
isSampleName(VcfEntry, String) - Method in class org.snpsift.lang.expression.Field
 
isString() - Method in class org.snpsift.lang.Value
 
isSub() - Method in class org.snpsift.lang.expression.Field
 
isSub() - Method in class org.snpsift.lang.expression.FieldGenotype
 
isSub() - Method in class org.snpsift.lang.expression.FieldGenotypeSub
 
isSub() - Method in class org.snpsift.lang.expression.FieldSub
 
IsVariant - Class in org.snpsift.lang.function
Is 'genotypeNum' reference?
IsVariant(Expression) - Constructor for class org.snpsift.lang.function.IsVariant
 
iterator() - Method in class org.snpsift.annotate.mem.arrays.StringArrayBase
 
iterator() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
 
iterator() - Method in class org.snpsift.annotate.mem.Fields
 
iterator() - Method in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
 
iterator() - Method in class org.snpsift.annotate.VcfIndexTree
 
iterator() - Method in class org.snpsift.gwasCatalog.GwasCatalog
 

J

join(boolean) - Method in class org.snpsift.SnpSiftCmdSplit
Join files
journal - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 

K

key(String, int) - Method in class org.snpsift.gwasCatalog.GwasCatalog
Create a 'key' string
key(GwasCatalogEntry) - Method in class org.snpsift.gwasCatalog.GwasCatalog
Create a 'key' string

L

label(Point, String) - Method in class org.snpsift.pedigree.PedigreeDraw
 
LangFactory - Class in org.snpsift.lang
Creates objects from an AST
LangFactory() - Constructor for class org.snpsift.lang.LangFactory
 
LangFactory(ArrayList<HashSet<String>>, EffFormatVersion, boolean) - Constructor for class org.snpsift.lang.LangFactory
 
latestResults - Variable in class org.snpsift.fileIterator.DbNsfp
 
latestResultsInterval - Variable in class org.snpsift.fileIterator.DbNsfp
 
latestVcfEntry - Variable in class org.snpsift.SnpSiftCmdConcordance
 
ld() - Method in class org.snpsift.VcfLd
Calculate linkage disequilibrium parameters
ld(VcfEntry, VcfEntry) - Method in class org.snpsift.VcfLd
Calculate linkage disequilibrium parameter
Le - Class in org.snpsift.lang.expression
Less or equal than
Le(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Le
 
left - Variable in class org.snpsift.lang.expression.ExpressionBinary
 
length() - Method in class org.snpsift.annotate.mem.arrays.StringArrayBase
Number of ellements in the array
line(Point, Point) - Method in class org.snpsift.pedigree.PedigreeDraw
 
line(Point, Point, String) - Method in class org.snpsift.pedigree.PedigreeDraw
 
line(Individual, Individual, Individual) - Method in class org.snpsift.pedigree.PedigreeDraw
Line between Mother-Father and Child
lineDashed(Point, Point, String) - Method in class org.snpsift.pedigree.PedigreeDraw
 
lines2SortedVariantsVcfIterator(String) - Static method in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
Create a VcfFileIterator from a string containig VCF lines
link - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
Literal - Class in org.snpsift.lang.expression
 
Literal(long) - Constructor for class org.snpsift.lang.expression.Literal
 
Literal(Boolean) - Constructor for class org.snpsift.lang.expression.Literal
 
Literal(Double) - Constructor for class org.snpsift.lang.expression.Literal
 
Literal(String) - Constructor for class org.snpsift.lang.expression.Literal
 
LiteralBoolContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.LiteralBoolContext
 
LiteralFloatContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.LiteralFloatContext
 
LiteralIndexContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.LiteralIndexContext
 
LiteralIntContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.LiteralIntContext
 
LiteralStringContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.LiteralStringContext
 
load() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
 
load(DataInputStream) - Method in class org.snpsift.annotate.VcfIndexTree
Read data from input stream
load(String) - Static method in class org.snpsift.annotate.mem.Fields
 
load(String) - Static method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
Load from file
load(String) - Method in class org.snpsift.gwasCatalog.GwasCatalog
Load data from file
load(String, boolean) - Static method in class org.snpsift.annotate.mem.database.VariantDataFrame
 
load(String, Genome) - Method in class org.snpsift.annotate.VcfIndexTree
 
loadConfig() - Method in class org.snpsift.SnpSift
Read config file
loadIndex(String) - Method in class org.snpsift.annotate.VcfIndex
Load index form a file
loadIntervals() - Method in class org.snpsift.SnpSiftCmdIntervalsIndex
Load all BED files
loadVcfFiles() - Method in class org.snpsift.SnpSiftCmdSort
Load VCF files
LOF - Enum constant in enum class org.snpsift.lang.expression.FieldIterator.IteratorType
 
log - Variable in class org.snpsift.SnpSift
 
Lt - Class in org.snpsift.lang.expression
Greater equal
Lt(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Lt
 

M

main(String[]) - Static method in class org.snpsift.annotate.mem.Zzz
Main
main(String[]) - Static method in class org.snpsift.hwe.SnpSiftCmdHwe
Main
main(String[]) - Static method in class org.snpsift.SnpSift
Main
main(String[]) - Static method in class org.snpsift.util.FastaSample
Main
male(Individual) - Method in class org.snpsift.pedigree.PedigreeDraw
 
mappedGene - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
mappedTrait - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
mappedTraitUri - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
marker(int) - Method in class org.snpsift.annotate.VcfIndexDataChromo
Create a marker form data at position 'idx'
MarkerFile - Class in org.snpsift.annotate
Represents a marker in a file (located at 'fileIdx' bytes since the beginning of the file)
MarkerFile(Marker, int, int, long) - Constructor for class org.snpsift.annotate.MarkerFile
 
match(Variant, VariantVcfEntry) - Method in class org.snpsift.annotate.AnnotateVcfDb
Does database entry 'dbVcfEntry' match 'variant'?
match(Variant, DbNsfpEntry) - Method in class org.snpsift.fileIterator.DbNsfp
Does database entry 'DbNsfpEntry' match 'variant'?
Match - Class in org.snpsift.lang.expression
Match a regular expression (string)
Match(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Match
 
MAX - Enum constant in enum class org.snpsift.SnpSiftCmdVcfOperator.Operator
 
MAX_DIFF_COLLAPSE - Static variable in class org.snpsift.annotate.VcfIndexTree
 
MAX_ERRORS - Static variable in class org.snpsift.annotate.AnnotateVcfDb
 
MAX_NUM_STRING_TO_SHOW - Static variable in class org.snpsift.annotate.mem.arrays.EnumArray
 
MAX_NUM_STRING_TO_SHOW - Static variable in class org.snpsift.annotate.mem.arrays.StringArray
 
MAX_NUMBER_OF_ELEMENTS_TO_SHOW - Static variable in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
 
MAX_NUMBER_OF_ENUM_VALUES - Static variable in class org.snpsift.annotate.mem.arrays.EnumArray
 
MAX_ROWS_TO_SHOW - Static variable in class org.snpsift.annotate.mem.dataFrame.DataFrame
 
maxBlockSize - Variable in class org.snpsift.SnpSiftCmdAnnotate
 
maxChrPosRefAltIdx - Variable in class org.snpsift.fileIterator.DbNsfp
 
mean() - Method in class org.snpsift.SnpSiftCmdCovarianceMatrix
Calculate mean
merged - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
method - Variable in class org.snpsift.SnpSiftCmdAnnotate
 
MIN - Enum constant in enum class org.snpsift.SnpSiftCmdVcfOperator.Operator
 
MIN_JUMP - Static variable in class org.snpsift.SnpSiftCmdDbNsfp
 
Minus - Class in org.snpsift.lang.expression
And expression
Minus(Expression) - Constructor for class org.snpsift.lang.expression.Minus
 
Minus(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Minus
 
MISSING - Enum constant in enum class org.snpsift.SnpSiftCmdVcf2Tped.UseMissing
 
MISSING_ENTRY - Static variable in class org.snpsift.SnpSiftCmdConcordance
 
MISSING_GENOTYPE - Static variable in class org.snpsift.SnpSiftCmdConcordance
 
MIXED - Enum constant in enum class org.snpsift.annotate.mem.VariantCategory
 
MNP - Enum constant in enum class org.snpsift.annotate.mem.VariantCategory
 
Mod - Class in org.snpsift.lang.expression
And expression
Mod(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Mod
 
modeNames - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
moveIfLeft(int, int, Set<Individual>) - Method in class org.snpsift.pedigree.PedigreeDraw
Move if the object is located to the left of posX
moveIfRight(int, int, Set<Individual>) - Method in class org.snpsift.pedigree.PedigreeDraw
Move if the object is located to the right of posX
multipleValues - Variable in class org.snpsift.fileIterator.DbNsfp
 

N

Na - Class in org.snpsift.lang.expression
Exists operator (true if a field exists)
Na(Expression) - Constructor for class org.snpsift.lang.expression.Na
 
name - Variable in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
 
name - Variable in class org.snpsift.lang.expression.Field
 
names2index - Variable in class org.snpsift.fileIterator.DbNsfp
 
NaN - Enum constant in enum class org.snpsift.lang.expression.FieldConstant.FieldConstantNames
 
needsConfig - Variable in class org.snpsift.SnpSift
 
needsDb - Variable in class org.snpsift.SnpSift
 
needsGenome - Variable in class org.snpsift.SnpSift
 
negated - Variable in class org.snpsift.lang.expression.Expression
 
Neq - Class in org.snpsift.lang.expression
Not equal
Neq(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Neq
 
next() - Method in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
 
next() - Method in class org.snpsift.lang.expression.FieldIterator
Next in iteration
NMD - Enum constant in enum class org.snpsift.lang.expression.FieldIterator.IteratorType
 
Not - Class in org.snpsift.lang.expression
Not expression
Not(Expression) - Constructor for class org.snpsift.lang.expression.Not
 
NotMatch - Class in org.snpsift.lang.expression
Match a regular expression (string)
NotMatch(Expression, Expression) - Constructor for class org.snpsift.lang.expression.NotMatch
 
NULL - Static variable in class org.snpsift.lang.Value
 
number - Variable in class org.snpsift.lang.expression.Field
 
numEnums() - Method in class org.snpsift.annotate.mem.arrays.EnumArray
Number of enums in the array
numWorkers - Variable in class org.snpsift.SnpSift
 

O

of(String[]) - Static method in class org.snpsift.annotate.mem.arrays.StringArray
Create a StringArray from an array of strings
of(String, String[]) - Static method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnString
Create a StringColumn from an array of strings
of(Collection<String>) - Static method in class org.snpsift.annotate.mem.arrays.StringArray
Create a StringArray from a collection of strings
of(Variant) - Static method in enum class org.snpsift.annotate.mem.VariantCategory
 
offset - Variable in class org.snpsift.annotate.mem.arrays.StringArray
 
op - Variable in class org.snpsift.antlr.SnpSiftParser.ExpressionCompContext
 
op - Variable in class org.snpsift.antlr.SnpSiftParser.ExpressionExistsContext
 
op - Variable in class org.snpsift.antlr.SnpSiftParser.ExpressionLogicContext
 
op - Variable in class org.snpsift.antlr.SnpSiftParser.ExpressionPlusContext
 
op - Variable in class org.snpsift.antlr.SnpSiftParser.ExpressionTimesContext
 
op - Variable in class org.snpsift.antlr.SnpSiftParser.ExpressionUnaryContext
 
open() - Method in class org.snpsift.annotate.AnnotateVcfDb
 
open() - Method in interface org.snpsift.annotate.DbMarker
Open database (load index in memory if required)
open() - Method in class org.snpsift.annotate.DbVcf
 
open() - Method in class org.snpsift.annotate.DbVcfMem
Open database annotation file
open() - Method in class org.snpsift.annotate.DbVcfSorted
Open VCF database annotation file
open() - Method in class org.snpsift.annotate.DbVcfTabix
Open database annotation file
open() - Method in class org.snpsift.annotate.VcfIndex
Open file
open() - Method in class org.snpsift.fileIterator.DbNsfp
 
openVcfInputFile() - Method in class org.snpsift.SnpSift
Open VCF input file
operator - Variable in class org.snpsift.lang.expression.Expression
 
operator - Variable in class org.snpsift.SnpSiftCmdVcfOperator
 
Or - Class in org.snpsift.lang.expression
Or expression
Or(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Or
 
orBeta - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
ord2enum - Variable in class org.snpsift.annotate.mem.arrays.EnumArray
 
org.snpsift - package org.snpsift
 
org.snpsift.annotate - package org.snpsift.annotate
 
org.snpsift.annotate.mem - package org.snpsift.annotate.mem
 
org.snpsift.annotate.mem.arrays - package org.snpsift.annotate.mem.arrays
 
org.snpsift.annotate.mem.database - package org.snpsift.annotate.mem.database
 
org.snpsift.annotate.mem.dataFrame - package org.snpsift.annotate.mem.dataFrame
 
org.snpsift.annotate.mem.dataFrame.dataFrameColumn - package org.snpsift.annotate.mem.dataFrame.dataFrameColumn
 
org.snpsift.annotate.mem.variantTypeCounter - package org.snpsift.annotate.mem.variantTypeCounter
 
org.snpsift.antlr - package org.snpsift.antlr
 
org.snpsift.caseControl - package org.snpsift.caseControl
 
org.snpsift.fileIterator - package org.snpsift.fileIterator
 
org.snpsift.gwasCatalog - package org.snpsift.gwasCatalog
 
org.snpsift.hwe - package org.snpsift.hwe
 
org.snpsift.lang - package org.snpsift.lang
 
org.snpsift.lang.expression - package org.snpsift.lang.expression
 
org.snpsift.lang.function - package org.snpsift.lang.function
 
org.snpsift.pedigree - package org.snpsift.pedigree
 
org.snpsift.phatsCons - package org.snpsift.phatsCons
 
org.snpsift.util - package org.snpsift.util
 
OTHER - Enum constant in enum class org.snpsift.annotate.mem.VariantCategory
 
outField - Variable in class org.snpsift.SnpSiftCmdVcfOperator
 
output - Variable in class org.snpsift.SnpSift
 

P

pAllelic(int[], int[], double) - Method in class org.snpsift.SnpSiftCmdCaseControl
Allelic model: Count number of SNPs
parseArgs(String[]) - Method in class org.snpsift.caseControl.SnpSiftCmdCaseControlSummary
 
parseArgs(String[]) - Method in class org.snpsift.hwe.SnpSiftCmdHwe
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSift
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdAlleleMatrix
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdAnnotate
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdAnnotateMem
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdCaseControl
 
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdConcordance
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdCovarianceMatrix
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdDbNsfp
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdExtractFields
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdFilter
Parse command line options
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdFilterChrPos
Parse command line options
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdFilterGt
Parse command line options
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdGeneSets
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdGt
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdGwasCatalog
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdIntersect
 
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdIntervals
 
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdIntervalsIndex
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdJoin
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdPedShow
 
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdPhastCons
 
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdPrivate
 
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdRemoveReferenceGenotypes
 
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdRmInfo
 
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdSort
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdSplit
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdTsTv
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdVarType
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdVcf2Tped
 
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdVcfCheck
Parse command line arguments
parseArgs(String[]) - Method in class org.snpsift.SnpSiftCmdVcfOperator
 
parseChrPosRefAlt() - Method in class org.snpsift.fileIterator.DbNsfpEntry
Parse dbSNFP 'Chr, pos, ref, alt' values from a single line
parseExpression(String) - Method in class org.snpsift.SnpSiftCmdFilter
Parse expression
parseExpression(String) - Method in class org.snpsift.SnpSiftCmdFilterGt
Parse expression
parseGenotypes(VcfEntry) - Method in class org.snpsift.caseControl.VariantCounter
Update genotype counts
parseKeyValues() - Method in class org.snpsift.fileIterator.DbNsfpEntry
Parse dbSNFP ALL values from a single line and store them in 'values' hash
parsePosition(String) - Method in class org.snpsift.fileIterator.DbNsfpEntry
Parse a string as a 'position'.
parseVcfHeaderFields(String) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
Read VCF header and get columns data types
parseVcfHeaderFields(VcfFileIterator) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
Read VCF header and get columns data types
pDominant(int[], int[], double) - Method in class org.snpsift.SnpSiftCmdCaseControl
Dominant model: Either a/A or A/A causes the disease
pedigree - Variable in class org.snpsift.SnpSiftCmdCaseControl
 
PedigreeDraw - Class in org.snpsift.pedigree
Draws a pedigree using SVG
PedigreeDraw(String) - Constructor for class org.snpsift.pedigree.PedigreeDraw
 
PedigreeDraw(PedPedigree) - Constructor for class org.snpsift.pedigree.PedigreeDraw
 
pGenotypic(int[], int[]) - Method in class org.snpsift.SnpSiftCmdCaseControl
Genotypic model (Chi Square)
PhastCons - Class in org.snpsift.phatsCons
Conservation score
PhastCons() - Constructor for class org.snpsift.phatsCons.PhastCons
 
platform - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
Plus - Class in org.snpsift.lang.expression
And expression
Plus(Expression) - Constructor for class org.snpsift.lang.expression.Plus
 
Plus(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Plus
 
PLUS - Enum constant in enum class org.snpsift.SnpSiftCmdVcfOperator.Operator
 
PosIndex - Class in org.snpsift.annotate.mem.arrays
An index by possition
PosIndex(int) - Constructor for class org.snpsift.annotate.mem.arrays.PosIndex
 
pRecessive(int[], int[], double) - Method in class org.snpsift.SnpSiftCmdCaseControl
Recessive model: Only A/A causes the disease
prependInfoFieldName - Variable in class org.snpsift.annotate.AnnotateVcfDb
 
prependInfoFieldName - Variable in class org.snpsift.SnpSiftCmdAnnotate
 
prependInfoName(String) - Method in class org.snpsift.annotate.AnnotateVcfDb
Prepend 'prependInfoFieldName' to all info fields
processStr(VcfEntry, StringBuilder) - Method in class org.snpsift.SnpSiftCmdAlleleMatrix
Process a VCF entry and return a string (tab separated values)
processVcfHeader(VcfFileIterator) - Method in class org.snpsift.SnpSift
Process VCF header related issues
processVcfHeader(VcfFileIterator) - Method in class org.snpsift.SnpSiftCmdCaseControl
 
PRODUCT - Enum constant in enum class org.snpsift.SnpSiftCmdVcfOperator.Operator
 
pTrend(int[], int[]) - Method in class org.snpsift.SnpSiftCmdCaseControl
Trend model
pubmedId - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
pValue - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
pValueMlog - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
pValueText - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
pvalueThreshold - Variable in class org.snpsift.SnpSiftCmdCaseControl
 

Q

query(Interval) - Method in class org.snpsift.annotate.VcfIndexTree
Query index to find all VCF entries intersecting 'marker' Store VCF entries in 'results'
query(Interval, int, Markers) - Method in class org.snpsift.annotate.VcfIndexTree
Query index to find all VCF entries intersecting 'marker', starting from node 'idx' Store VCF entries in 'results'
query(Marker) - Method in class org.snpsift.annotate.VcfIndex
Query interval forest
query(Variant) - Method in class org.snpsift.annotate.AnnotateVcfDb
Query database and find results matching 'variant'
query(Variant) - Method in class org.snpsift.annotate.DbVcf
Find matching entries in the database
query(Variant) - Method in class org.snpsift.annotate.DbVcfMem
 
query(Variant) - Method in class org.snpsift.annotate.DbVcfSorted
 
query(Variant) - Method in class org.snpsift.annotate.DbVcfTabix
 
query(Variant) - Method in class org.snpsift.fileIterator.DbNsfp
Query tabix file to get dbNsfp entries (or cached entries from latest results)
query(Q) - Method in interface org.snpsift.annotate.DbMarker
Find matching entries in the database
queryIntersects(Interval, int, Markers) - Method in class org.snpsift.annotate.VcfIndexTree
Query VCF entries intersecting 'marker' at node 'idx'
QueryResult - Class in org.snpsift.annotate
A database query and a result.
QueryResult(Variant, Collection<VariantVcfEntry>) - Constructor for class org.snpsift.annotate.QueryResult
 
quiet - Variable in class org.snpsift.SnpSift
 

R

rand() - Method in class org.snpsift.util.RandomUtil
 
randAcgt() - Method in class org.snpsift.util.RandomUtil
 
randBase(String) - Method in class org.snpsift.util.RandomUtil
 
randBases(int) - Method in class org.snpsift.util.RandomUtil
 
randBases(int, String) - Method in class org.snpsift.util.RandomUtil
 
randBool() - Method in class org.snpsift.util.RandomUtil
 
randBoolOrNull() - Method in class org.snpsift.util.RandomUtil
 
randChar() - Method in class org.snpsift.util.RandomUtil
 
randCharOrNull() - Method in class org.snpsift.util.RandomUtil
 
randDouble(double) - Method in class org.snpsift.util.RandomUtil
 
randDoubleOrNull() - Method in class org.snpsift.util.RandomUtil
 
randEnum(ArrayList<String>) - Method in class org.snpsift.util.RandomUtil
 
randEnumOrNull(ArrayList<String>) - Method in class org.snpsift.util.RandomUtil
 
randInt() - Method in class org.snpsift.util.RandomUtil
 
randInt(int) - Method in class org.snpsift.util.RandomUtil
 
randIntOrNull() - Method in class org.snpsift.util.RandomUtil
 
randIntOrNull(int) - Method in class org.snpsift.util.RandomUtil
 
randLong() - Method in class org.snpsift.util.RandomUtil
 
randLong(long) - Method in class org.snpsift.util.RandomUtil
 
randLongOrNull() - Method in class org.snpsift.util.RandomUtil
 
randLongOrNull(long) - Method in class org.snpsift.util.RandomUtil
 
RandomUtil - Class in org.snpsift.util
 
RandomUtil() - Constructor for class org.snpsift.util.RandomUtil
 
RandomUtil(int) - Constructor for class org.snpsift.util.RandomUtil
 
randString(int) - Method in class org.snpsift.util.RandomUtil
 
randStringOrNull() - Method in class org.snpsift.util.RandomUtil
 
randStringOrNull(int) - Method in class org.snpsift.util.RandomUtil
 
randVariant(VariantCategory) - Method in class org.snpsift.util.RandomUtil
 
randVariantAlt(VariantCategory, String) - Method in class org.snpsift.util.RandomUtil
 
randVariantRef(VariantCategory) - Method in class org.snpsift.util.RandomUtil
 
read(long) - Method in class org.snpsift.annotate.VcfIndex
Read a VcfEntry at position 'fileIdx'
read(MarkerFile) - Method in class org.snpsift.annotate.VcfIndex
Read a VcfEntry referenced by 'markerFile'
readDb() - Method in class org.snpsift.SnpSiftCmdGwasCatalog
Read database
REF - Static variable in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
 
REF_NAME - Static variable in class org.snpsift.fileIterator.DbNsfp
 
REFERENCE - Enum constant in enum class org.snpsift.SnpSiftCmdVcf2Tped.UseMissing
 
refIdx - Variable in class org.snpsift.fileIterator.DbNsfp
 
region - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
removeChild(Individual) - Method in class org.snpsift.pedigree.Individual
 
replicationSampleSize - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
reportedGene - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
reset() - Method in class org.snpsift.annotate.mem.arrays.BoolArray
 
reset() - Method in class org.snpsift.lang.expression.FieldIterator
Reset all counters
reset() - Method in class org.snpsift.util.RandomUtil
 
resize() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
Resize and memory optimize the data
resize() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
Resize and memory optimize the data
resize() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnString
Resize and memory optimize the data
results - Variable in class org.snpsift.annotate.QueryResult
 
returnType - Variable in class org.snpsift.lang.expression.Field
 
returnType(VcfEntry) - Method in class org.snpsift.lang.expression.Field
 
returnType(VcfGenotype) - Method in class org.snpsift.lang.expression.Field
 
REVISION - Static variable in class org.snpsift.SnpSift
 
right - Variable in class org.snpsift.lang.expression.ExpressionBinary
 
riskAllele - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
riskAlleleFrequency - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
RULE_compilationUnit - Static variable in class org.snpsift.antlr.SnpSiftParser
 
RULE_expression - Static variable in class org.snpsift.antlr.SnpSiftParser
 
ruleNames - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
ruleNames - Static variable in class org.snpsift.antlr.SnpSiftParser
 
run() - Method in class org.snpsift.caseControl.SnpSiftCmdCaseControlSummary
Run summary
run() - Method in class org.snpsift.hwe.SnpSiftCmdHwe
Analyze the file (run multi-thread mode)
run() - Method in class org.snpsift.SnpSift
 
run() - Method in class org.snpsift.SnpSiftCmdAlleleMatrix
Process the whole VCF file
run() - Method in class org.snpsift.SnpSiftCmdAnnotate
Annotate each entry of a VCF file
run() - Method in class org.snpsift.SnpSiftCmdAnnotateMem
Annotate each entry of a VCF file
run() - Method in class org.snpsift.SnpSiftCmdCaseControl
Load a file compare calls
run() - Method in class org.snpsift.SnpSiftCmdConcordance
 
run() - Method in class org.snpsift.SnpSiftCmdCovarianceMatrix
Process the whole file
run() - Method in class org.snpsift.SnpSiftCmdDbNsfp
 
run() - Method in class org.snpsift.SnpSiftCmdExtractFields
Run main algorithm
run() - Method in class org.snpsift.SnpSiftCmdFilter
 
run() - Method in class org.snpsift.SnpSiftCmdFilterChrPos
 
run() - Method in class org.snpsift.SnpSiftCmdFilterGt
 
run() - Method in class org.snpsift.SnpSiftCmdGeneSets
Annotate entries
run() - Method in class org.snpsift.SnpSiftCmdGt
Process a VCF entry and return a string (tab separated values)
run() - Method in class org.snpsift.SnpSiftCmdGwasCatalog
Annotate entries
run() - Method in class org.snpsift.SnpSiftCmdIntersect
Run annotations
run() - Method in class org.snpsift.SnpSiftCmdIntervals
 
run() - Method in class org.snpsift.SnpSiftCmdIntervalsIndex
Load a file compare calls
run() - Method in class org.snpsift.SnpSiftCmdJoin
Run algorithm
run() - Method in class org.snpsift.SnpSiftCmdPedShow
Run: Main method
run() - Method in class org.snpsift.SnpSiftCmdPhastCons
Run
run() - Method in class org.snpsift.SnpSiftCmdPrivate
Run annotations
run() - Method in class org.snpsift.SnpSiftCmdRemoveReferenceGenotypes
Analyze the file
run() - Method in class org.snpsift.SnpSiftCmdRmInfo
Analyze the file
run() - Method in class org.snpsift.SnpSiftCmdSort
Run
run() - Method in class org.snpsift.SnpSiftCmdSplit
Run
run() - Method in class org.snpsift.SnpSiftCmdTsTv
Analyze the file
run() - Method in class org.snpsift.SnpSiftCmdVarType
Annotate entries
run() - Method in class org.snpsift.SnpSiftCmdVcf2Tped
Run annotations
run() - Method in class org.snpsift.SnpSiftCmdVcfCheck
Process the whole VCF file
run() - Method in class org.snpsift.SnpSiftCmdVcfOperator
Annotate
run() - Method in class org.snpsift.util.FastaSample
 
run(boolean) - Method in class org.snpsift.SnpSiftCmdAnnotate
Run annotations
run(boolean) - Method in class org.snpsift.SnpSiftCmdAnnotateMem
Run annotations
run(boolean) - Method in class org.snpsift.SnpSiftCmdCaseControl
Run
run(boolean) - Method in class org.snpsift.SnpSiftCmdDbNsfp
Run annotation algorithm
run(boolean) - Method in class org.snpsift.SnpSiftCmdExtractFields
 
run(boolean) - Method in class org.snpsift.SnpSiftCmdFilter
Run filter
run(boolean) - Method in class org.snpsift.SnpSiftCmdFilterChrPos
Run filter
run(boolean) - Method in class org.snpsift.SnpSiftCmdFilterGt
Run filter
run(boolean) - Method in class org.snpsift.SnpSiftCmdGeneSets
 
run(boolean) - Method in class org.snpsift.SnpSiftCmdGwasCatalog
 
run(boolean) - Method in class org.snpsift.SnpSiftCmdIntervals
Load a file compare calls
run(boolean) - Method in class org.snpsift.SnpSiftCmdPhastCons
Run annotations
run(boolean) - Method in class org.snpsift.SnpSiftCmdPrivate
Run annotations.
run(boolean) - Method in class org.snpsift.SnpSiftCmdSort
 
run(boolean) - Method in class org.snpsift.SnpSiftCmdVcfOperator
Run filter

S

sanityCheck(VcfEntry, VcfEntry) - Method in class org.snpsift.VcfLd
Return an error message if any problem is found or empty string if it is OK.
save() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
 
save(DataOutputStream) - Method in class org.snpsift.annotate.VcfIndexTree
Save to output stream
save(String) - Method in class org.snpsift.annotate.mem.Fields
Save to file
save(String) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
 
save(String) - Method in class org.snpsift.annotate.VcfIndex
Save index file
saveDataTypesCache(String) - Method in class org.snpsift.fileIterator.DbNsfp
Save data types to cache file
saveOutput - Variable in class org.snpsift.SnpSift
 
sempred(RuleContext, int, int) - Method in class org.snpsift.antlr.SnpSiftParser
 
SEP - Static variable in class org.snpsift.SnpSiftCmdConcordance
 
SEP_GT - Static variable in class org.snpsift.SnpSiftCmdConcordance
 
SEPARATOR - Static variable in class org.snpsift.SnpSiftCmdAlleleMatrix
 
set(int) - Method in class org.snpsift.annotate.mem.arrays.BoolArray
Set data to null
set(int, boolean) - Method in class org.snpsift.annotate.mem.arrays.BoolArray
 
set(int, int) - Method in class org.snpsift.annotate.mem.arrays.PosIndex
Set position to entry number 'i'
set(int, Object) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
Set value at index i, consideting null data
set(int, String) - Method in class org.snpsift.annotate.mem.arrays.EnumArray
Add a string to the array WARNING: Typically you use either 'add' or 'set', but not both
set(int, String) - Method in class org.snpsift.annotate.mem.arrays.StringArray
Add a string to the array WARNING: Typically you use either 'add' or 'set', but not both
set(int, String) - Method in class org.snpsift.annotate.mem.arrays.StringArrayBase
Add a string to the array Return the index of the next element
set(String, int, Object) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
Set data in a column
set(String, Object) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
 
setAddFilterField(String) - Method in class org.snpsift.SnpSiftCmdFilter
 
setAffected(Boolean) - Method in class org.snpsift.pedigree.Individual
 
setAnnotateEmpty(boolean) - Method in class org.snpsift.annotate.AnnotateVcfDb
 
setAnnotateEmpty(boolean) - Method in class org.snpsift.SnpSiftCmdAnnotate
 
setColor(String) - Method in class org.snpsift.pedigree.Individual
 
setCommand(Class) - Method in class org.snpsift.SnpSift
 
setCommand(String) - Method in class org.snpsift.SnpSift
 
setConfig(Config) - Method in class org.snpsift.SnpSift
 
setConfigFile(String) - Method in class org.snpsift.SnpSift
 
setCount(int, int, int, int, int, int, int, int) - Method in class org.snpsift.VcfLd
Set counters in order to calculate LD parameters
setData(int, Object) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
Set data at index i
setData(int, Object) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnBool
 
setData(int, Object) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnChar
 
setData(int, Object) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnDouble
 
setData(int, Object) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnInt
 
setData(int, Object) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnLong
 
setData(int, Object) - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnString
 
setDataFrame() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
Populate row in DataFrame with the values in this row
setDataFrame(String) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
Set the data frame with a value from this row
setDataFrame(String, Object) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
Set the data frame with a specific value
setDbDir(String) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
 
setDbFileName(String) - Method in class org.snpsift.SnpSift
 
setDebug(boolean) - Method in class org.snpsift.annotate.AnnotateVcfDb
 
setDebug(boolean) - Method in interface org.snpsift.annotate.DbMarker
 
setDebug(boolean) - Method in class org.snpsift.annotate.DbVcf
 
setDebug(boolean) - Method in class org.snpsift.annotate.VcfIndex
 
setDebug(boolean) - Method in class org.snpsift.annotate.VcfIndexTree
 
setDebug(boolean) - Method in class org.snpsift.fileIterator.DbNsfp
 
setDebug(boolean) - Method in class org.snpsift.SnpSift
 
setDepth(int) - Method in class org.snpsift.pedigree.Individual
 
setExceptionIfNotFound(boolean) - Method in class org.snpsift.lang.expression.Field
 
setExceptionIfNotFound(boolean) - Method in class org.snpsift.SnpSiftCmdFilter
 
setExistsInfoField(String) - Method in class org.snpsift.annotate.AnnotateVcfDb
 
setExpression(String) - Method in class org.snpsift.SnpSiftCmdFilter
 
setFather(Individual) - Method in class org.snpsift.pedigree.Individual
 
setFieldNamesAnnotate(String[]) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
 
setFieldsNamesToAdd(String) - Method in class org.snpsift.SnpSiftCmdDbNsfp
 
setFilePosEnd(long) - Method in class org.snpsift.annotate.VcfIndexDataChromo
 
setFilterId(String) - Method in class org.snpsift.SnpSiftCmdFilter
 
setFormatVersion(EffFormatVersion) - Method in class org.snpsift.SnpSiftCmdFilter
 
setGenotype(int, int) - Method in class org.snpsift.caseControl.VariantCounter
 
setId(String) - Method in class org.snpsift.pedigree.Individual
 
setIdx(int) - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
 
setInfoFields(boolean, Collection<String>) - Method in class org.snpsift.annotate.AnnotateVcfDb
 
setInOffset(int) - Method in class org.snpsift.SnpSiftCmdIntervalsIndex
 
setInverse(boolean) - Method in class org.snpsift.SnpSiftCmdFilter
 
setLabel(String) - Method in class org.snpsift.pedigree.Individual
 
setMax(FieldIterator.IteratorType, int) - Method in class org.snpsift.lang.expression.FieldIterator
Set 'max' parameter for an iterator
setMaxBlockSize(int) - Method in class org.snpsift.annotate.DbVcfSorted
 
setMaxBlockSize(int) - Method in class org.snpsift.annotate.VcfIndex
 
setMaxBlockSize(int) - Method in class org.snpsift.annotate.VcfIndexTree
 
setMother(Individual) - Method in class org.snpsift.pedigree.Individual
 
setMsigdb(String) - Method in class org.snpsift.SnpSiftCmdGeneSets
 
setNegated(boolean) - Method in class org.snpsift.lang.expression.Expression
 
setNullRatio(double) - Method in class org.snpsift.util.RandomUtil
 
setOrder(int) - Method in class org.snpsift.pedigree.Individual
 
setPrefix(String) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
 
setPrefix(String) - Method in class org.snpsift.annotate.mem.database.VariantDataFrame
 
setPrependInfoFieldName(String) - Method in class org.snpsift.annotate.AnnotateVcfDb
 
setQuiet(boolean) - Method in class org.snpsift.SnpSift
 
setRand(Random) - Method in class org.snpsift.util.RandomUtil
 
setRmFilterField(String) - Method in class org.snpsift.SnpSiftCmdFilter
 
setSaveOutput(boolean) - Method in class org.snpsift.SnpSift
 
setSeed(long) - Method in class org.snpsift.util.RandomUtil
 
setSets(ArrayList<HashSet<String>>) - Method in class org.snpsift.SnpSiftCmdFilter
 
setSex(Sex) - Method in class org.snpsift.pedigree.Individual
 
setShowVcfHeader(boolean) - Method in class org.snpsift.SnpSift
 
setShowVersion(boolean) - Method in class org.snpsift.SnpSift
 
setSuppressOutput(boolean) - Method in class org.snpsift.SnpSift
 
setTabixCheck(boolean) - Method in class org.snpsift.SnpSiftCmdDbNsfp
 
setType(int) - Method in class org.snpsift.lang.expression.FieldIterator
 
setUseId(boolean) - Method in class org.snpsift.annotate.AnnotateVcfDb
 
setUsePassField(boolean) - Method in class org.snpsift.SnpSiftCmdFilter
 
setUseRefAlt(boolean) - Method in class org.snpsift.annotate.AnnotateVcfDb
 
setVcf(VcfFileIterator) - Method in class org.snpsift.annotate.VcfIndexTree
 
setVcfHeaderAddProgramVersion(boolean) - Method in class org.snpsift.SnpSift
 
setVerbose(boolean) - Method in class org.snpsift.annotate.AnnotateVcfDb
 
setVerbose(boolean) - Method in interface org.snpsift.annotate.DbMarker
 
setVerbose(boolean) - Method in class org.snpsift.annotate.DbVcf
 
setVerbose(boolean) - Method in class org.snpsift.annotate.mem.database.VariantDatabase
 
setVerbose(boolean) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
 
setVerbose(boolean) - Method in class org.snpsift.annotate.VcfIndex
 
setVerbose(boolean) - Method in class org.snpsift.annotate.VcfIndexTree
 
setVerbose(boolean) - Method in class org.snpsift.fileIterator.DbNsfp
 
setVerbose(boolean) - Method in class org.snpsift.SnpSift
 
setWriteBySampleFile(boolean) - Method in class org.snpsift.SnpSiftCmdConcordance
 
setWriteSummaryFile(boolean) - Method in class org.snpsift.SnpSiftCmdConcordance
 
shiftArgs - Variable in class org.snpsift.SnpSift
 
SHORT_VARIANT_LEN - Static variable in class org.snpsift.util.RandomUtil
 
SHOW - Static variable in class org.snpsift.annotate.DbVcfMem
 
SHOW - Static variable in class org.snpsift.SnpSiftCmdAnnotate
 
SHOW - Static variable in class org.snpsift.SnpSiftCmdExtractFields
 
SHOW - Static variable in class org.snpsift.SnpSiftCmdGeneSets
 
SHOW - Static variable in class org.snpsift.SnpSiftCmdGwasCatalog
 
SHOW - Static variable in class org.snpsift.SnpSiftCmdSort
 
SHOW - Static variable in class org.snpsift.SnpSiftCmdSplit
 
SHOW - Static variable in class org.snpsift.SnpSiftCmdVarType
 
SHOW_EVERY - Static variable in class org.snpsift.annotate.VcfIndex
 
SHOW_EVERY - Static variable in class org.snpsift.hwe.SnpSiftCmdHwe
 
SHOW_EVERY - Static variable in class org.snpsift.SnpSiftCmdAlleleMatrix
 
SHOW_EVERY - Static variable in class org.snpsift.SnpSiftCmdCaseControl
 
SHOW_EVERY - Static variable in class org.snpsift.SnpSiftCmdConcordance
 
SHOW_EVERY - Static variable in class org.snpsift.SnpSiftCmdCovarianceMatrix
 
SHOW_EVERY - Static variable in class org.snpsift.SnpSiftCmdDbNsfp
 
SHOW_EVERY - Static variable in class org.snpsift.SnpSiftCmdGt
 
SHOW_EVERY - Static variable in class org.snpsift.SnpSiftCmdPhastCons
 
SHOW_EVERY - Static variable in class org.snpsift.SnpSiftCmdRemoveReferenceGenotypes
 
SHOW_EVERY - Static variable in class org.snpsift.SnpSiftCmdTsTv
 
SHOW_EVERY - Static variable in class org.snpsift.util.ShowProgress
 
SHOW_EVERY_LINE - Static variable in class org.snpsift.util.ShowProgress
 
SHOW_EVERY_NL - Static variable in class org.snpsift.SnpSiftCmdRemoveReferenceGenotypes
 
SHOW_EVERY_NL - Static variable in class org.snpsift.SnpSiftCmdTsTv
 
SHOW_EVERY_VCFLINES - Static variable in class org.snpsift.SnpSift
 
SHOW_LINES - Static variable in class org.snpsift.annotate.DbVcfMem
 
SHOW_LINES - Static variable in class org.snpsift.SnpSiftCmdGeneSets
 
SHOW_LINES - Static variable in class org.snpsift.SnpSiftCmdGwasCatalog
 
SHOW_LINES - Static variable in class org.snpsift.SnpSiftCmdSort
 
SHOW_LINES - Static variable in class org.snpsift.SnpSiftCmdSplit
 
SHOW_LINES - Static variable in class org.snpsift.SnpSiftCmdVarType
 
showCmd() - Method in class org.snpsift.SnpSift
Show command line
ShowProgress - Class in org.snpsift.util
 
ShowProgress() - Constructor for class org.snpsift.util.ShowProgress
 
ShowProgress(int, int) - Constructor for class org.snpsift.util.ShowProgress
 
showVcfHeader - Variable in class org.snpsift.SnpSift
 
showVersion - Variable in class org.snpsift.SnpSift
 
showVersion() - Method in class org.snpsift.SnpSift
Show version number
size() - Method in class org.snpsift.annotate.mem.arrays.BoolArray
 
size() - Method in class org.snpsift.annotate.mem.arrays.EnumArray
Size of the data array (capacity of number of bytes)
size() - Method in class org.snpsift.annotate.mem.arrays.PosIndex
Number of entries in use
size() - Method in class org.snpsift.annotate.mem.arrays.StringArray
Size of the data array (capacity of number of bytes)
size() - Method in class org.snpsift.annotate.mem.arrays.StringArrayBase
Number of different strings in the array
size() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
Number of elements in this DataColumn
size() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnBool
 
size() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnChar
 
size() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnDouble
 
size() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnInt
 
size() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnLong
 
size() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnString
 
size() - Static method in enum class org.snpsift.annotate.mem.VariantCategory
 
size() - Method in class org.snpsift.annotate.VcfIndexDataChromo
 
size() - Method in class org.snpsift.annotate.VcfIndexTree
 
sizeByDepth(int[]) - Method in class org.snpsift.pedigree.Individual
Size by depth
sizeBytes() - Method in class org.snpsift.annotate.mem.arrays.BoolArray
 
sizeBytes() - Method in class org.snpsift.annotate.mem.arrays.EnumArray
Memory size of this object (approximate size in bytes)
sizeBytes() - Method in class org.snpsift.annotate.mem.arrays.PosIndex
Memory size of this object (approximate size in bytes)
sizeBytes() - Method in class org.snpsift.annotate.mem.arrays.StringArray
Memory size of this object (approximate size in bytes)
sizeBytes() - Method in class org.snpsift.annotate.mem.arrays.StringArrayBase
Memory size of this object (approximate size in bytes)
sizeBytes() - Method in class org.snpsift.annotate.mem.database.VariantDataFrame
 
sizeBytes() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
Memory size of this object
sizeBytes() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
Memory size of this object (approximate size in bytes)
sizeBytes() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnBool
Memory size of this object (approximate size in bytes)
sizeBytes() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnChar
Memory size of this object (approximate size in bytes)
sizeBytes() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnDouble
Memory size of this object (approximate size in bytes)
sizeBytes() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnInt
Memory size of this object (approximate size in bytes)
sizeBytes() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnLong
Memory size of this object (approximate size in bytes)
sizeBytes() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnString
Memory size of this object (approximate size in bytes)
sizeOf(String) - Static method in class org.snpsift.annotate.mem.arrays.StringArray
Calculate the size of a string in memory
sizeOf(String[]) - Static method in class org.snpsift.annotate.mem.arrays.StringArray
 
sizeOf(Collection<String>) - Static method in class org.snpsift.annotate.mem.arrays.StringArray
 
sizesByField - Variable in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
 
SNP_A - Enum constant in enum class org.snpsift.annotate.mem.VariantCategory
 
SNP_C - Enum constant in enum class org.snpsift.annotate.mem.VariantCategory
 
SNP_G - Enum constant in enum class org.snpsift.annotate.mem.VariantCategory
 
SNP_T - Enum constant in enum class org.snpsift.annotate.mem.VariantCategory
 
snpGeneIds - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
snpIdCurrent - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
snps - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
SnpSift - Class in org.snpsift
Generic SnpSift tool caller
SnpSift() - Constructor for class org.snpsift.SnpSift
 
SnpSift(String[]) - Constructor for class org.snpsift.SnpSift
 
SnpSiftBaseListener - Class in org.snpsift.antlr
This class provides an empty implementation of SnpSiftListener, which can be extended to create a listener which only needs to handle a subset of the available methods.
SnpSiftBaseListener() - Constructor for class org.snpsift.antlr.SnpSiftBaseListener
 
SnpSiftBaseVisitor<T> - Class in org.snpsift.antlr
This class provides an empty implementation of SnpSiftVisitor, which can be extended to create a visitor which only needs to handle a subset of the available methods.
SnpSiftBaseVisitor() - Constructor for class org.snpsift.antlr.SnpSiftBaseVisitor
 
SnpSiftCmdAlleleMatrix - Class in org.snpsift
Convert VCf file to allele matrix Note: Only use SNPs Note: Only variants with two possible alleles.
SnpSiftCmdAlleleMatrix() - Constructor for class org.snpsift.SnpSiftCmdAlleleMatrix
 
SnpSiftCmdAnnotate - Class in org.snpsift
Annotate a VCF file with ID from another VCF file (database)
SnpSiftCmdAnnotate() - Constructor for class org.snpsift.SnpSiftCmdAnnotate
 
SnpSiftCmdAnnotate(String[]) - Constructor for class org.snpsift.SnpSiftCmdAnnotate
 
SnpSiftCmdAnnotateMem - Class in org.snpsift
Annotate a VCF file from another VCF file (database) The database file is loaded into memory.
SnpSiftCmdAnnotateMem() - Constructor for class org.snpsift.SnpSiftCmdAnnotateMem
 
SnpSiftCmdAnnotateMem(String[]) - Constructor for class org.snpsift.SnpSiftCmdAnnotateMem
 
SnpSiftCmdCaseControl - Class in org.snpsift
Count number of cases and controls
SnpSiftCmdCaseControl() - Constructor for class org.snpsift.SnpSiftCmdCaseControl
 
SnpSiftCmdCaseControl(String[]) - Constructor for class org.snpsift.SnpSiftCmdCaseControl
 
SnpSiftCmdCaseControlSummary - Class in org.snpsift.caseControl
Summarize a VCF annotated file
SnpSiftCmdCaseControlSummary() - Constructor for class org.snpsift.caseControl.SnpSiftCmdCaseControlSummary
 
SnpSiftCmdCaseControlSummary(String[]) - Constructor for class org.snpsift.caseControl.SnpSiftCmdCaseControlSummary
 
SnpSiftCmdConcordance - Class in org.snpsift
Calculate genotyping concordance between two VCF files.
SnpSiftCmdConcordance() - Constructor for class org.snpsift.SnpSiftCmdConcordance
 
SnpSiftCmdConcordance(String[]) - Constructor for class org.snpsift.SnpSiftCmdConcordance
 
SnpSiftCmdCovarianceMatrix - Class in org.snpsift
Convert allele 'matrix' file into Covariance matrix Note: Only variants with two possible alleles.
SnpSiftCmdCovarianceMatrix() - Constructor for class org.snpsift.SnpSiftCmdCovarianceMatrix
 
SnpSiftCmdCovarianceMatrix(String[]) - Constructor for class org.snpsift.SnpSiftCmdCovarianceMatrix
 
SnpSiftCmdDbNsfp - Class in org.snpsift
Annotate a VCF file with dbNSFP.
SnpSiftCmdDbNsfp() - Constructor for class org.snpsift.SnpSiftCmdDbNsfp
 
SnpSiftCmdDbNsfp(String[]) - Constructor for class org.snpsift.SnpSiftCmdDbNsfp
 
SnpSiftCmdExtractFields - Class in org.snpsift
Extract fields from VCF file to a TXT (tab separated) format
SnpSiftCmdExtractFields() - Constructor for class org.snpsift.SnpSiftCmdExtractFields
 
SnpSiftCmdExtractFields(String[]) - Constructor for class org.snpsift.SnpSiftCmdExtractFields
 
SnpSiftCmdFilter - Class in org.snpsift
Generic SnpSift filter Filter out data based on VCF attributes: - Chromosome, Position, etc.
SnpSiftCmdFilter() - Constructor for class org.snpsift.SnpSiftCmdFilter
 
SnpSiftCmdFilter(String[]) - Constructor for class org.snpsift.SnpSiftCmdFilter
 
SnpSiftCmdFilterChrPos - Class in org.snpsift
Filter using CHROM:POS only
SnpSiftCmdFilterChrPos() - Constructor for class org.snpsift.SnpSiftCmdFilterChrPos
 
SnpSiftCmdFilterChrPos(String[]) - Constructor for class org.snpsift.SnpSiftCmdFilterChrPos
 
SnpSiftCmdFilterGt - Class in org.snpsift
Generic SnpSift genotype filter Removes genotypes matching the filter: e.g.
SnpSiftCmdFilterGt() - Constructor for class org.snpsift.SnpSiftCmdFilterGt
 
SnpSiftCmdFilterGt(String[]) - Constructor for class org.snpsift.SnpSiftCmdFilterGt
 
SnpSiftCmdGeneSets - Class in org.snpsift
Annotate a VCF file using Gene sets (MSigDb) or gene ontology (GO)
SnpSiftCmdGeneSets() - Constructor for class org.snpsift.SnpSiftCmdGeneSets
 
SnpSiftCmdGeneSets(String[]) - Constructor for class org.snpsift.SnpSiftCmdGeneSets
 
SnpSiftCmdGt - Class in org.snpsift
Add genotype information to INFO fields
SnpSiftCmdGt() - Constructor for class org.snpsift.SnpSiftCmdGt
 
SnpSiftCmdGt(String[]) - Constructor for class org.snpsift.SnpSiftCmdGt
 
SnpSiftCmdGwasCatalog - Class in org.snpsift
Annotate a VCF file using GWAS catalog database Loads GWAS catalog in memory, thus it makes no assumption about order.
SnpSiftCmdGwasCatalog() - Constructor for class org.snpsift.SnpSiftCmdGwasCatalog
 
SnpSiftCmdGwasCatalog(String[]) - Constructor for class org.snpsift.SnpSiftCmdGwasCatalog
 
SnpSiftCmdHwe - Class in org.snpsift.hwe
Calculate Hardy-Weinberg equilibrium and goodness of fit for each entry in a VCF file
SnpSiftCmdHwe() - Constructor for class org.snpsift.hwe.SnpSiftCmdHwe
 
SnpSiftCmdHwe(String[]) - Constructor for class org.snpsift.hwe.SnpSiftCmdHwe
 
SnpSiftCmdIntersect - Class in org.snpsift
Intersect intervals
SnpSiftCmdIntersect() - Constructor for class org.snpsift.SnpSiftCmdIntersect
 
SnpSiftCmdIntersect(String[]) - Constructor for class org.snpsift.SnpSiftCmdIntersect
 
SnpSiftCmdIntervals - Class in org.snpsift
Filter variants that hit intervals
SnpSiftCmdIntervals() - Constructor for class org.snpsift.SnpSiftCmdIntervals
 
SnpSiftCmdIntervals(String[]) - Constructor for class org.snpsift.SnpSiftCmdIntervals
 
SnpSiftCmdIntervalsIndex - Class in org.snpsift
Filter variants that hit intervals Use an indexed VCF file.
SnpSiftCmdIntervalsIndex() - Constructor for class org.snpsift.SnpSiftCmdIntervalsIndex
 
SnpSiftCmdIntervalsIndex(String[]) - Constructor for class org.snpsift.SnpSiftCmdIntervalsIndex
 
SnpSiftCmdJoin - Class in org.snpsift
Annotate a VCF file with ID from another VCF file (database)
SnpSiftCmdJoin() - Constructor for class org.snpsift.SnpSiftCmdJoin
 
SnpSiftCmdJoin(String[]) - Constructor for class org.snpsift.SnpSiftCmdJoin
 
SnpSiftCmdPedShow - Class in org.snpsift
Draws a pedigree using SVG according to a VCF file
SnpSiftCmdPedShow() - Constructor for class org.snpsift.SnpSiftCmdPedShow
 
SnpSiftCmdPedShow(String[]) - Constructor for class org.snpsift.SnpSiftCmdPedShow
 
SnpSiftCmdPhastCons - Class in org.snpsift
Annotate using PhastCons score files
SnpSiftCmdPhastCons() - Constructor for class org.snpsift.SnpSiftCmdPhastCons
 
SnpSiftCmdPhastCons(String[]) - Constructor for class org.snpsift.SnpSiftCmdPhastCons
 
SnpSiftCmdPrivate - Class in org.snpsift
Annotate if a variant is 'private'.
SnpSiftCmdPrivate() - Constructor for class org.snpsift.SnpSiftCmdPrivate
 
SnpSiftCmdPrivate(String[]) - Constructor for class org.snpsift.SnpSiftCmdPrivate
 
SnpSiftCmdRemoveReferenceGenotypes - Class in org.snpsift
Removes reference genotypes.
SnpSiftCmdRemoveReferenceGenotypes() - Constructor for class org.snpsift.SnpSiftCmdRemoveReferenceGenotypes
 
SnpSiftCmdRemoveReferenceGenotypes(String[]) - Constructor for class org.snpsift.SnpSiftCmdRemoveReferenceGenotypes
 
SnpSiftCmdRmInfo - Class in org.snpsift
Removes INFO fields
SnpSiftCmdRmInfo() - Constructor for class org.snpsift.SnpSiftCmdRmInfo
 
SnpSiftCmdRmInfo(String[]) - Constructor for class org.snpsift.SnpSiftCmdRmInfo
 
SnpSiftCmdSort - Class in org.snpsift
Sort VCF file/s by chromosome invalid input: '&' position
SnpSiftCmdSort() - Constructor for class org.snpsift.SnpSiftCmdSort
 
SnpSiftCmdSort(String[]) - Constructor for class org.snpsift.SnpSiftCmdSort
 
SnpSiftCmdSplit - Class in org.snpsift
Split a large VCF file by chromosome or bby number of lines
SnpSiftCmdSplit() - Constructor for class org.snpsift.SnpSiftCmdSplit
 
SnpSiftCmdSplit(String[]) - Constructor for class org.snpsift.SnpSiftCmdSplit
 
SnpSiftCmdTsTv - Class in org.snpsift
Calculate Ts/Tv rations per sample (transitions vs transversions)
SnpSiftCmdTsTv() - Constructor for class org.snpsift.SnpSiftCmdTsTv
 
SnpSiftCmdTsTv(String[]) - Constructor for class org.snpsift.SnpSiftCmdTsTv
 
SnpSiftCmdVarType - Class in org.snpsift
Annotate a VCF file with variant type
SnpSiftCmdVarType() - Constructor for class org.snpsift.SnpSiftCmdVarType
 
SnpSiftCmdVarType(String[]) - Constructor for class org.snpsift.SnpSiftCmdVarType
 
SnpSiftCmdVcf2Tped - Class in org.snpsift
Transform a VCF to a TPED file
SnpSiftCmdVcf2Tped() - Constructor for class org.snpsift.SnpSiftCmdVcf2Tped
 
SnpSiftCmdVcf2Tped(String[]) - Constructor for class org.snpsift.SnpSiftCmdVcf2Tped
 
SnpSiftCmdVcf2Tped.UseMissing - Enum Class in org.snpsift
 
SnpSiftCmdVcfCheck - Class in org.snpsift
Check VCF files (run some simple checks)
SnpSiftCmdVcfCheck() - Constructor for class org.snpsift.SnpSiftCmdVcfCheck
 
SnpSiftCmdVcfCheck(String[]) - Constructor for class org.snpsift.SnpSiftCmdVcfCheck
 
SnpSiftCmdVcfOperator - Class in org.snpsift
Annotate a field based on an operation (max, min, etc.) of other VCF fields
SnpSiftCmdVcfOperator() - Constructor for class org.snpsift.SnpSiftCmdVcfOperator
 
SnpSiftCmdVcfOperator(String[]) - Constructor for class org.snpsift.SnpSiftCmdVcfOperator
 
SnpSiftCmdVcfOperator.Operator - Enum Class in org.snpsift
 
SnpSiftLexer - Class in org.snpsift.antlr
 
SnpSiftLexer(CharStream) - Constructor for class org.snpsift.antlr.SnpSiftLexer
 
SnpSiftListener - Interface in org.snpsift.antlr
This interface defines a complete listener for a parse tree produced by SnpSiftParser.
SnpSiftParser - Class in org.snpsift.antlr
 
SnpSiftParser(TokenStream) - Constructor for class org.snpsift.antlr.SnpSiftParser
 
SnpSiftParser.CompilationUnitContext - Class in org.snpsift.antlr
 
SnpSiftParser.ExpressionCompContext - Class in org.snpsift.antlr
 
SnpSiftParser.ExpressionCondContext - Class in org.snpsift.antlr
 
SnpSiftParser.ExpressionContext - Class in org.snpsift.antlr
 
SnpSiftParser.ExpressionExistsContext - Class in org.snpsift.antlr
 
SnpSiftParser.ExpressionLogicContext - Class in org.snpsift.antlr
 
SnpSiftParser.ExpressionParenContext - Class in org.snpsift.antlr
 
SnpSiftParser.ExpressionPlusContext - Class in org.snpsift.antlr
 
SnpSiftParser.ExpressionSetContext - Class in org.snpsift.antlr
 
SnpSiftParser.ExpressionTimesContext - Class in org.snpsift.antlr
 
SnpSiftParser.ExpressionUnaryContext - Class in org.snpsift.antlr
 
SnpSiftParser.FunctionCallContext - Class in org.snpsift.antlr
 
SnpSiftParser.LiteralBoolContext - Class in org.snpsift.antlr
 
SnpSiftParser.LiteralFloatContext - Class in org.snpsift.antlr
 
SnpSiftParser.LiteralIndexContext - Class in org.snpsift.antlr
 
SnpSiftParser.LiteralIntContext - Class in org.snpsift.antlr
 
SnpSiftParser.LiteralStringContext - Class in org.snpsift.antlr
 
SnpSiftParser.VarReferenceContext - Class in org.snpsift.antlr
 
SnpSiftParser.VarReferenceListContext - Class in org.snpsift.antlr
 
SnpSiftParser.VarReferenceListSubContext - Class in org.snpsift.antlr
 
SnpSiftVisitor<T> - Interface in org.snpsift.antlr
This interface defines a complete generic visitor for a parse tree produced by SnpSiftParser.
SOFTWARE_NAME - Static variable in class org.snpsift.SnpSift
 
SortedVariantsVcfIterator - Class in org.snpsift.annotate.mem
This is a class that reads a VCF file and returns the variants in sorted order.
SortedVariantsVcfIterator(BufferedReader) - Constructor for class org.snpsift.annotate.mem.SortedVariantsVcfIterator
 
SortedVariantsVcfIterator(String) - Constructor for class org.snpsift.annotate.mem.SortedVariantsVcfIterator
 
SPLIT_REGEX - Static variable in class org.snpsift.lang.expression.Has
 
splitValuesField(String) - Static method in class org.snpsift.fileIterator.DbNsfpEntry
 
square(int, int, int, int, String, int, String) - Method in class org.snpsift.pedigree.PedigreeDraw
 
stab(int) - Method in class org.snpsift.annotate.VcfIndexTree
 
START_FIELD - Static variable in class org.snpsift.SnpSiftCmdPhastCons
 
startIdx - Variable in class org.snpsift.fileIterator.DbNsfp
 
STRING_LITERAL - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
STRING_LITERAL - Static variable in class org.snpsift.antlr.SnpSiftParser
 
STRING_LITERAL() - Method in class org.snpsift.antlr.SnpSiftParser.LiteralStringContext
 
StringArray - Class in org.snpsift.annotate.mem.arrays
Implement a memory efficient array of strings It only stores bytes (i.e.
StringArray(int, int) - Constructor for class org.snpsift.annotate.mem.arrays.StringArray
Constructor
StringArrayBase - Class in org.snpsift.annotate.mem.arrays
Implement a memory efficient array of strings It only stores bytes (i.e.
StringArrayBase() - Constructor for class org.snpsift.annotate.mem.arrays.StringArrayBase
Constructor
study - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
SUBFIELD_SEPARATOR - Static variable in class org.snpsift.fileIterator.DbNsfp
 
SUBFIELD_SEPARATOR_2 - Static variable in class org.snpsift.fileIterator.DbNsfp
 
SUBFIELD_SEPARATOR_CHAR - Static variable in class org.snpsift.fileIterator.DbNsfp
 
SUBFIELD_SEPARATOR_CHAR_2 - Static variable in class org.snpsift.fileIterator.DbNsfp
 
Summary - Class in org.snpsift.caseControl
Summarize a VCF annotated file
Summary() - Constructor for class org.snpsift.caseControl.Summary
 
suppressOutput - Variable in class org.snpsift.SnpSift
 
swapMinorAllele(int[], int[]) - Method in class org.snpsift.SnpSiftCmdCaseControl
Swap counts if REF is minor allele (instead of ALT)

T

T__0 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__0 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__1 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__1 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__10 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__10 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__11 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__11 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__12 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__12 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__13 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__13 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__14 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__14 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__15 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__15 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__16 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__16 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__17 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__17 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__18 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__18 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__19 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__19 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__2 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__2 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__20 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__20 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__21 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__21 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__22 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__22 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__23 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__23 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__24 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__24 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__25 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__25 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__26 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__26 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__27 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__27 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__28 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__28 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__29 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__29 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__3 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__3 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__30 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__30 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__31 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__31 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__32 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__32 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__33 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__33 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__34 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__34 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__4 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__4 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__5 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__5 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__6 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__6 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__7 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__7 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__8 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__8 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
T__9 - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
T__9 - Static variable in class org.snpsift.antlr.SnpSiftParser
 
tabixCheck - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
tabixReader - Variable in class org.snpsift.annotate.DbVcfTabix
 
tabixReader - Variable in class org.snpsift.fileIterator.DbNsfp
 
tfamFile - Variable in class org.snpsift.SnpSiftCmdCaseControl
 
tick(int) - Method in class org.snpsift.util.ShowProgress
 
tick(int, VariantVcfEntry) - Method in class org.snpsift.util.ShowProgress
 
tick(int, VcfEntry) - Method in class org.snpsift.util.ShowProgress
Call this method every iteration
Times - Class in org.snpsift.lang.expression
And expression
Times(Expression, Expression) - Constructor for class org.snpsift.lang.expression.Times
 
tokenNames - Static variable in class org.snpsift.antlr.SnpSiftLexer
Deprecated.
tokenNames - Static variable in class org.snpsift.antlr.SnpSiftParser
Deprecated.
toString() - Method in class org.snpsift.annotate.AnnotateVcfDb
 
toString() - Method in class org.snpsift.annotate.MarkerFile
 
toString() - Method in class org.snpsift.annotate.mem.arrays.EnumArray
 
toString() - Method in class org.snpsift.annotate.mem.arrays.StringArray
 
toString() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
 
toString() - Method in class org.snpsift.annotate.mem.database.VariantDataFrame
 
toString() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrame
 
toString() - Method in class org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn
 
toString() - Method in class org.snpsift.annotate.mem.dataFrame.DataFrameRow
 
toString() - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
 
toString() - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
 
toString() - Method in class org.snpsift.annotate.QueryResult
 
toString() - Method in class org.snpsift.annotate.VcfIndex
 
toString() - Method in class org.snpsift.annotate.VcfIndexDataChromo
 
toString() - Method in class org.snpsift.annotate.VcfIndexTree
 
toString() - Method in class org.snpsift.caseControl.VariantCounter
 
toString() - Method in class org.snpsift.fileIterator.DbNsfpEntry
 
toString() - Method in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
toString() - Method in class org.snpsift.lang.expression.ExpressionBinary
 
toString() - Method in class org.snpsift.lang.expression.ExpressionUnary
 
toString() - Method in class org.snpsift.lang.expression.Field
 
toString() - Method in class org.snpsift.lang.expression.FieldEff
 
toString() - Method in class org.snpsift.lang.expression.FieldGenotype
 
toString() - Method in class org.snpsift.lang.expression.FieldGenotypeSub
 
toString() - Method in class org.snpsift.lang.expression.FieldIterator
 
toString() - Method in class org.snpsift.lang.expression.FieldLof
 
toString() - Method in class org.snpsift.lang.expression.FieldSub
 
toString() - Method in class org.snpsift.lang.expression.Literal
 
toString() - Method in class org.snpsift.lang.function.Function
 
toString() - Method in class org.snpsift.lang.function.FunctionBoolGenotype
 
toString() - Method in class org.snpsift.lang.function.In
 
toString() - Method in class org.snpsift.lang.Value
 
toString() - Method in class org.snpsift.pedigree.Individual
 
toString() - Method in class org.snpsift.SnpSiftCmdCovarianceMatrix
 
toString(int) - Method in class org.snpsift.annotate.VcfIndexTree
 
toString(List<String>) - Method in class org.snpsift.caseControl.Summary
 
toStringAll() - Method in class org.snpsift.annotate.VcfIndex
Show all entries
toStringAll() - Method in class org.snpsift.annotate.VcfIndexTree
 
toStringTitle(List<String>) - Method in class org.snpsift.caseControl.Summary
 
toStringTree() - Method in class org.snpsift.pedigree.Individual
 
trait - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
TRUE - Static variable in class org.snpsift.lang.Value
 
type() - Method in class org.snpsift.lang.Value
 
TYPE_ALL - Static variable in class org.snpsift.lang.expression.Field
 
TYPE_ANY - Static variable in class org.snpsift.lang.expression.Field
 
types - Variable in class org.snpsift.fileIterator.DbNsfp
 

U

uniqueIds(Set<String>, String) - Method in class org.snpsift.annotate.AnnotateVcfDb
IDs from database not present in VCF
unknown(Individual) - Method in class org.snpsift.pedigree.PedigreeDraw
 
unSanitize(String) - Method in class org.snpsift.SnpSift
Convert a sanitized expression (from Galaxy) back to the original string References: http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg00530.html
updateSizes(VariantCategory, String, String) - Method in class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
Update sizes for a field
upstreamGeneDistance - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
upstreamGeneId - Variable in class org.snpsift.gwasCatalog.GwasCatalogEntry
 
usage(String) - Method in class org.snpsift.caseControl.SnpSiftCmdCaseControlSummary
Show usage message
usage(String) - Method in class org.snpsift.hwe.SnpSiftCmdHwe
Show usage and exit
usage(String) - Method in class org.snpsift.SnpSift
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdAlleleMatrix
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdAnnotate
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdAnnotateMem
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdCaseControl
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdConcordance
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdCovarianceMatrix
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdDbNsfp
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdExtractFields
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdFilter
Usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdFilterChrPos
Usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdFilterGt
Usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdGeneSets
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdGt
 
usage(String) - Method in class org.snpsift.SnpSiftCmdGwasCatalog
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdIntersect
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdIntervals
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdIntervalsIndex
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdJoin
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdPedShow
 
usage(String) - Method in class org.snpsift.SnpSiftCmdPhastCons
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdPrivate
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdRemoveReferenceGenotypes
Show usage and exit
usage(String) - Method in class org.snpsift.SnpSiftCmdRmInfo
Show usage and exit
usage(String) - Method in class org.snpsift.SnpSiftCmdSort
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdSplit
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdTsTv
Show usage and exit
usage(String) - Method in class org.snpsift.SnpSiftCmdVarType
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdVcf2Tped
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdVcfCheck
Show usage message
usage(String) - Method in class org.snpsift.SnpSiftCmdVcfOperator
 
usageGenericAndDb() - Method in class org.snpsift.SnpSift
Options common to all commands
useAllInfoFields - Variable in class org.snpsift.annotate.AnnotateVcfDb
 
useChiSquare - Variable in class org.snpsift.SnpSiftCmdCaseControl
 
useId - Variable in class org.snpsift.annotate.AnnotateVcfDb
 
useId - Variable in class org.snpsift.SnpSiftCmdAnnotate
 
useInfoField - Variable in class org.snpsift.SnpSiftCmdAnnotate
 
useInfoFields - Variable in class org.snpsift.annotate.AnnotateVcfDb
 
useRefAlt - Variable in class org.snpsift.annotate.AnnotateVcfDb
 
useRefAlt - Variable in class org.snpsift.SnpSiftCmdAnnotate
 

V

Value - Class in org.snpsift.lang
 
Value(Object) - Constructor for class org.snpsift.lang.Value
 
valueOf(String) - Static method in enum class org.snpsift.annotate.mem.VariantCategory
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpsift.lang.expression.FieldConstant.FieldConstantNames
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpsift.lang.expression.FieldIterator.IteratorType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpsift.SnpSiftCmdVcf2Tped.UseMissing
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.snpsift.SnpSiftCmdVcfOperator.Operator
Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.snpsift.annotate.mem.VariantCategory
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpsift.lang.expression.FieldConstant.FieldConstantNames
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpsift.lang.expression.FieldIterator.IteratorType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpsift.SnpSiftCmdVcf2Tped.UseMissing
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.snpsift.SnpSiftCmdVcfOperator.Operator
Returns an array containing the constants of this enum class, in the order they are declared.
VAR - Enum constant in enum class org.snpsift.lang.expression.FieldIterator.IteratorType
 
variant - Variable in class org.snpsift.annotate.QueryResult
 
VARIANT_DATABASE_EXT - Static variable in class org.snpsift.annotate.mem.database.VariantDatabase
 
VARIANT_DATAFRAME_EXT - Static variable in class org.snpsift.annotate.mem.database.VariantDatabase
 
VariantCategory - Enum Class in org.snpsift.annotate.mem
 
VariantCounter - Class in org.snpsift.caseControl
A counnter for genotypes
VariantCounter(int) - Constructor for class org.snpsift.caseControl.VariantCounter
 
VariantDatabase - Class in org.snpsift.annotate.mem.database
A database of variant's data used to annotate a VCF file (i.e.
VariantDatabase() - Constructor for class org.snpsift.annotate.mem.database.VariantDatabase
 
VariantDatabase(String, String, String[]) - Constructor for class org.snpsift.annotate.mem.database.VariantDatabase
Constructor used to create a database
VariantDatabase(String, String, String[], String, boolean) - Constructor for class org.snpsift.annotate.mem.database.VariantDatabase
Constructor used to annotate a database
VariantDataFrame - Class in org.snpsift.annotate.mem.database
A DataFrame of variant's data that is indexed "variant type AND chromosome possition".
VariantDataFrame(VariantTypeCounter) - Constructor for class org.snpsift.annotate.mem.database.VariantDataFrame
 
variantsMinHeap - Variable in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
 
VariantTypeCounter - Class in org.snpsift.annotate.mem.variantTypeCounter
Count different types of variants These statistics are used to create data sets
VariantTypeCounter(Fields) - Constructor for class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
 
VariantTypeCounters - Class in org.snpsift.annotate.mem.variantTypeCounter
Variant type counters for each chromosome
VariantTypeCounters(boolean) - Constructor for class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
 
VariantTypeCounters(Fields, boolean) - Constructor for class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
 
VarReferenceContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.VarReferenceContext
 
VarReferenceListContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.VarReferenceListContext
 
VarReferenceListSubContext(SnpSiftParser.ExpressionContext) - Constructor for class org.snpsift.antlr.SnpSiftParser.VarReferenceListSubContext
 
VARTYPE - Static variable in class org.snpsift.SnpSiftCmdVarType
 
vcf - Variable in class org.snpsift.annotate.DbVcfTabix
 
VCF_INFO_CASE - Static variable in class org.snpsift.SnpSiftCmdCaseControl
 
VCF_INFO_CC_ALL - Static variable in class org.snpsift.SnpSiftCmdCaseControl
 
VCF_INFO_CC_DOM - Static variable in class org.snpsift.SnpSiftCmdCaseControl
 
VCF_INFO_CC_GENO - Static variable in class org.snpsift.SnpSiftCmdCaseControl
 
VCF_INFO_CC_REC - Static variable in class org.snpsift.SnpSiftCmdCaseControl
 
VCF_INFO_CC_TREND - Static variable in class org.snpsift.SnpSiftCmdCaseControl
 
VCF_INFO_CONTROL - Static variable in class org.snpsift.SnpSiftCmdCaseControl
 
VCF_INFO_FILTER_DELETED - Static variable in class org.snpsift.SnpSiftCmdFilter
 
VCF_INFO_PHASTCONS_FIELD - Static variable in class org.snpsift.SnpSiftCmdPhastCons
 
vcf2Tped(String, String, String, String) - Method in class org.snpsift.SnpSiftCmdVcf2Tped
Convert a VCF to a TPED file
vcfChr - Variable in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
 
vcfDbFile - Variable in class org.snpsift.annotate.AnnotateVcfDb
 
vcfEntryPending - Variable in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
 
vcfFile - Variable in class org.snpsift.SnpSiftCmdAnnotate
 
vcfFile - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
vcfFileIterator - Variable in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
 
vcfFileName - Variable in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
 
vcfFileName - Variable in class org.snpsift.SnpSiftCmdDbNsfp
 
vcfHeader - Variable in class org.snpsift.annotate.DbVcf
 
vcfHeaderAddProgramVersion - Variable in class org.snpsift.SnpSift
 
vcfHeaderProcessed - Variable in class org.snpsift.SnpSift
 
vcfHeaders() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
 
vcfHeaders(String) - Method in class org.snpsift.annotate.mem.Fields
Get VCF headers
VcfHwe - Class in org.snpsift.hwe
Calculate Hardy-Weimberg equilibrium and goodness of fit.
VcfHwe() - Constructor for class org.snpsift.hwe.VcfHwe
 
VcfIndex - Class in org.snpsift.annotate
An index for a VCF file
VcfIndex(String) - Constructor for class org.snpsift.annotate.VcfIndex
 
VcfIndexDataChromo - Class in org.snpsift.annotate
Represents a set of VCF entries stored in an (uncompressed) file All entries belong to the same chromosome
VcfIndexDataChromo(Genome) - Constructor for class org.snpsift.annotate.VcfIndexDataChromo
 
VcfIndexDataChromo(Genome, String) - Constructor for class org.snpsift.annotate.VcfIndexDataChromo
 
VcfIndexTree - Class in org.snpsift.annotate
Interval tree structure for an 'VcfIndexChromo' The whole tree is stored in a single class as a set of arrays.
VcfIndexTree() - Constructor for class org.snpsift.annotate.VcfIndexTree
 
VcfIndexTree(VcfFileIterator, VcfIndexDataChromo) - Constructor for class org.snpsift.annotate.VcfIndexTree
 
vcfInfo - Variable in class org.snpsift.lang.expression.Field
 
vcfInfoNumber - Variable in class org.snpsift.lang.expression.Field
 
vcfInfoPerAllele - Variable in class org.snpsift.annotate.AnnotateVcfDb
 
vcfInfoPerAlleleRef - Variable in class org.snpsift.annotate.AnnotateVcfDb
 
vcfInputFile - Variable in class org.snpsift.SnpSift
 
VcfLd - Class in org.snpsift
Calculate Linkage Disequilibrium Reference: "Principles of population genetics (4th edition)" Hartl invalid input: '&' Clark, pages 73 to 81 Note: I try to follow the same notation as the book.
VcfLd() - Constructor for class org.snpsift.VcfLd
 
vcfPos - Variable in class org.snpsift.annotate.mem.SortedVariantsVcfIterator
 
verbose - Variable in class org.snpsift.annotate.AnnotateVcfDb
 
verbose - Variable in class org.snpsift.annotate.DbVcf
 
verbose - Variable in class org.snpsift.fileIterator.DbNsfp
 
verbose - Variable in class org.snpsift.SnpSift
 
VERSION - Static variable in class org.snpsift.SnpSift
 
VERSION_MAJOR - Static variable in class org.snpsift.SnpSift
 
VERSION_NO_NAME - Static variable in class org.snpsift.SnpSift
 
VERSION_SHORT - Static variable in class org.snpsift.SnpSift
 
visitCompilationUnit(SnpSiftParser.CompilationUnitContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
Visit a parse tree produced by SnpSiftParser.compilationUnit().
visitCompilationUnit(SnpSiftParser.CompilationUnitContext) - Method in interface org.snpsift.antlr.SnpSiftVisitor
Visit a parse tree produced by SnpSiftParser.compilationUnit().
visitErrorNode(ErrorNode) - Method in class org.snpsift.antlr.SnpSiftBaseListener
visitExpressionComp(SnpSiftParser.ExpressionCompContext) - Method in class org.snpsift.antlr.SnpSiftBaseVisitor
Visit a parse tree produced by the expressionComp labeled alternative 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
 

Z

Zzz - Class in org.snpsift.annotate.mem
Test: This class loaads a "database" VCF file and then annotates another VCF file.
Zzz() - Constructor for class org.snpsift.annotate.mem.Zzz
 

_

_ATN - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
_ATN - Static variable in class org.snpsift.antlr.SnpSiftParser
 
_decisionToDFA - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
_decisionToDFA - Static variable in class org.snpsift.antlr.SnpSiftParser
 
_serializedATN - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
_serializedATN - Static variable in class org.snpsift.antlr.SnpSiftParser
 
_sharedContextCache - Static variable in class org.snpsift.antlr.SnpSiftLexer
 
_sharedContextCache - Static variable in class org.snpsift.antlr.SnpSiftParser
 
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