# Index

A B C D E F G H I J K L M N O P Q R S T U V W X Z _
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.SnpSiftCmdAnnotateDf
  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) - 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.SnpSiftCmdAnnotateDf
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.SnpSiftCmdAnnotateDf
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) - Method in class org.snpsift.annotate.AnnotateVcfDb
  Add ID information.
annotateInfo(VcfEntry, Map) - 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.SnpSiftCmdAnnotateDf
  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) - 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
  BoolArray is a class that provides a compact representation of a boolean array using a byte array.
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.SnpSiftCmdAnnotateDf
  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.
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 is a specialized subclass of DataFrame designed to handle deletion variants.
DataFrameDel(VariantTypeCounter, VariantCategory) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameDel
DataFrameIns - Class in org.snpsift.annotate.mem.dataFrame
  DataFrameIns is a specialized subclass of DataFrame designed to handle insertion variants.
DataFrameIns(VariantTypeCounter, VariantCategory) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameIns
DataFrameMixed - Class in org.snpsift.annotate.mem.dataFrame
  DataFrameMixed is a specialized subclass of DataFrame that is designed to handle mixed data types.
DataFrameMixed(VariantTypeCounter, VariantCategory) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameMixed
DataFrameMnp - Class in org.snpsift.annotate.mem.dataFrame
  DataFrameMnp is a specialized subclass of DataFrame designed to handle multi-nucleotide polymorphisms (MNPs).
DataFrameMnp(VariantTypeCounter, VariantCategory) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameMnp
DataFrameOther - Class in org.snpsift.annotate.mem.dataFrame
  DataFrameOther is a subclass of DataFrame that is specifically tailored for handling variant type counting and categorization.
DataFrameOther(VariantTypeCounter, VariantCategory) - Constructor for class org.snpsift.annotate.mem.dataFrame.DataFrameOther
DataFrameRow - Class in org.snpsift.annotate.mem.dataFrame
  The DataFrameRow class represents a row in a DataFrame.
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
  The DataFrameSnp class extends the DataFrame class and represents a specific type of data frame that deals with single nucleotide polymorphisms (SNPs).
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
  The EnumArray class is a specialized array for storing and managing strings as enumerated values.
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
  The Fields class represents a collection of VCF (Variant Call Format) header information fields.
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, 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, 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, Set) - 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
getFieldValue(VcfHeaderInfo, VariantVcfEntry) - Static method in class org.snpsift.annotate.mem.Fields
  Get a field value from a VCF entry
getFieldValueString(String, VcfEntry) - Static method in class org.snpsift.annotate.mem.Fields
  Get a field value (string) from a VCF entry
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.SnpSiftCmdAnnotateDf
  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, 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.SnpSiftCmdAnnotateDf
  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, 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, 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) - Method in class org.snpsift.pedigree.PedigreeDraw
  Move if the object is located to the left of posX
moveIfRight(int, int, Set) - 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) - 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.SnpSiftCmdAnnotateDf
  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
  The PosIndex class is designed to manage and index chromosome positions efficiently converting chromosome positions to zero-based indices.
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) - 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) - Method in class org.snpsift.util.RandomUtil
randEnumOrNull(ArrayList) - 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.SnpSiftCmdAnnotateDf
  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.SnpSiftCmdAnnotateDf
  Run annotations
run(boolean) - Method in class org.snpsift.SnpSiftCmdCaseControl
  Run
run(boolean) - Method in class org.snpsift.SnpSiftCmdDbNsfp
  Run annotation algorithm
run(boolean) - Method in class org.snpsift.SnpSiftCmdExtractFields
run(boolean) - Method in class org.snpsift.SnpSiftCmdFilter
  Run filter
run(boolean) - Method in class org.snpsift.SnpSiftCmdFilterChrPos
  Run filter
run(boolean) - Method in class org.snpsift.SnpSiftCmdFilterGt
  Run filter
run(boolean) - Method in class org.snpsift.SnpSiftCmdGeneSets
run(boolean) - Method in class org.snpsift.SnpSiftCmdGwasCatalog
run(boolean) - Method in class org.snpsift.SnpSiftCmdIntervals
  Load a file compare calls
run(boolean) - Method in class org.snpsift.SnpSiftCmdPhastCons
  Run annotations
run(boolean) - Method in class org.snpsift.SnpSiftCmdPrivate
  Run annotations.
run(boolean) - Method in class org.snpsift.SnpSiftCmdSort
run(boolean) - Method in class org.snpsift.SnpSiftCmdVcfOperator
  Run filter

## S

sanityCheck(VcfEntry, VcfEntry) - Method in class org.snpsift.VcfLd
  Return an error message if any problem is found or empty string if it is OK.
save(DataOutputStream) - Method in class org.snpsift.annotate.VcfIndexTree
  Save to output stream
save(String) - Method in class org.snpsift.annotate.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
saveCurrentDataFrame() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
saveDataTypesCache(String) - Method in class org.snpsift.fileIterator.DbNsfp
  Save data types to cache file
saveFields() - Method in class org.snpsift.annotate.mem.database.VariantDatabase
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) - 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) - 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) - 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
SnpSiftCmdAnnotateDf - Class in org.snpsift
  Annotate a VCF file from another VCF file (database) by creating "DataFrames" for each chromosome.
SnpSiftCmdAnnotateDf() - Constructor for class org.snpsift.SnpSiftCmdAnnotateDf
SnpSiftCmdAnnotateDf(String[]) - Constructor for class org.snpsift.SnpSiftCmdAnnotateDf
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
  The StringArray class implements a memory-efficient array of strings.
StringArray(int, int) - Constructor for class org.snpsift.annotate.mem.arrays.StringArray
  Constructor
StringArrayBase - Class in org.snpsift.annotate.mem.arrays
  Abstract base class for a string array that supports iteration and serialization.
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.
  Use `SnpSiftLexer.VOCABULARY` instead.
tokenNames - Static variable in class org.snpsift.antlr.SnpSiftParser
  Deprecated.
  Use `SnpSiftParser.VOCABULARY` instead.
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) - 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) - 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) - 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.SnpSiftCmdAnnotateDf
  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
  The `VariantCategory` enum represents different categories of genetic variants.
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
  VariantTypeCounter is a class that counts the number of variants in a VCF (Variant Call Format) file.
VariantTypeCounter(Fields) - Constructor for class org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter
VariantTypeCounters - Class in org.snpsift.annotate.mem.variantTypeCounter
  The VariantTypeCounters class is responsible for counting the number of variants in VCF (Variant Call Format) files.
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_COLUMN_FIELD_NAMES - Static variable in class org.snpsift.annotate.mem.Fields
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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