A B C D E F G H I J K L M N O P Q R S T U V W Z

A

ABGenotypeFilter - Class in org.mulinlab.varnote.filters.query.gt

ABGenotypeFilter(GenotypeQC) - Constructor for class org.mulinlab.varnote.filters.query.gt.ABGenotypeFilter

AbstractDatababseAnnoParser - Class in org.mulinlab.varnote.config.anno.databse.anno

AbstractDatababseAnnoParser(ExtractConfig, boolean, AnnoOutFormat) - Constructor for class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

AbstractDatabaseFilter - Class in org.mulinlab.varnote.config.anno.databse.filter

AbstractDatabaseFilter() - Constructor for class org.mulinlab.varnote.config.anno.databse.filter.AbstractDatabaseFilter

AbstractDBReader - Class in org.mulinlab.varnote.operations.readers.db

AbstractDBReader(Database) - Constructor for class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

AbstractDBReader(Database, boolean) - Constructor for class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

AbstractDBReader.Iterator - Interface in org.mulinlab.varnote.operations.readers.db

AbstractFileReader - Class in org.mulinlab.varnote.operations.readers.query

AbstractFileReader() - Constructor for class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

AbstractFileReader(QueryReaderItf, Format) - Constructor for class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

AbstractFileReader(String, Format) - Constructor for class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

AbstractFileReader(String, FileType, Format) - Constructor for class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

AbstractMapper<T> - Class in org.mulinlab.varnote.operations.mapper

AbstractMapper(RunConfig, int) - Constructor for class org.mulinlab.varnote.operations.mapper.AbstractMapper

AbstractQuery - Class in org.mulinlab.varnote.operations.query

AbstractQuery(List<Database>, boolean) - Constructor for class org.mulinlab.varnote.operations.query.AbstractQuery

AbstractQueryParser - Class in org.mulinlab.varnote.config.anno.query

AbstractQueryParser(Format) - Constructor for class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

AbstractQueryReader<T> - Class in org.mulinlab.varnote.cmdline.txtreader.abs

AbstractQueryReader() - Constructor for class org.mulinlab.varnote.cmdline.txtreader.abs.AbstractQueryReader

AbstractReaderStack - Class in org.mulinlab.varnote.operations.stack

AbstractReaderStack(ProcessResult) - Constructor for class org.mulinlab.varnote.operations.stack.AbstractReaderStack

ABVariantFilter - Class in org.mulinlab.varnote.filters.query.vc

ABVariantFilter(VairantQC) - Constructor for class org.mulinlab.varnote.filters.query.vc.ABVariantFilter

accession(String) - Method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation.Builder

addBin(SROB) - Method in class org.mulinlab.varnote.operations.index.IndexWriter

addDBVal(String) - Method in class org.mulinlab.varnote.config.anno.NormalField

addDBValByAlt(String, int, String[]) - Method in class org.mulinlab.varnote.config.anno.InfoField

addGenotypeFilters(GenotypeFilter) - Method in class org.mulinlab.varnote.config.param.FilterParam

addLineFilters(LineFilter) - Method in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

addLVCount() - Method in class org.mulinlab.varnote.utils.TimeMetric

addMapper(Mapper<M>) - Method in interface org.mulinlab.varnote.utils.mapreduce.MapReduce

addMapper(Mapper<M>) - Method in class org.mulinlab.varnote.utils.mapreduce.SimpleMapReduce

addPrintter(String, Integer) - Method in class org.mulinlab.varnote.config.io.temp.FlatPrintter

addPrintter(String, Integer) - Method in class org.mulinlab.varnote.config.io.temp.Printter

addPrintter(String, Integer) - Method in class org.mulinlab.varnote.config.io.temp.ZipPrintter

addRecord() - Method in class org.mulinlab.varnote.utils.TimeMetric

addRecord(long) - Method in class org.mulinlab.varnote.utils.TimeMetric

addSeqsName(String) - Method in class org.mulinlab.varnote.operations.index.IndexWriter

addTranscriptModel(TranscriptModel) - Method in class org.mulinlab.varnote.utils.jannovar.GeneBuilder

addVariantFilters(VariantFilter) - Method in class org.mulinlab.varnote.config.param.FilterParam

addVCFHeader(VCFHeader) - Method in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

addVCFHeader(VCFHeader) - Method in class org.mulinlab.varnote.config.anno.databse.anno.DatabaseAnnoVCFParser

adjustCol(int) - Static method in class org.mulinlab.varnote.utils.VannoUtils

adjustPos() - Method in class org.mulinlab.varnote.utils.stream.BZIP2InputStream

ADOutFeature - Class in org.mulinlab.varnote.config.parser.output

ADOutFeature(LocFeature) - Constructor for class org.mulinlab.varnote.config.parser.output.ADOutFeature

AdvancedBZip2CompressorInputStream - Class in org.mulinlab.varnote.utils.stream

An input stream that decompresses from the BZip2 format to be read as any other stream.

AdvancedBZip2CompressorInputStream(InputStream) - Constructor for class org.mulinlab.varnote.utils.stream.AdvancedBZip2CompressorInputStream

Constructs a new BZip2CompressorInputStream which decompresses bytes read from the specified stream.

affectedsAreCompatible(GenotypesContext) - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceXRFilter

affectsCodingRegion(VariantEffect) - Static method in class org.mulinlab.varnote.utils.jannovar.VariantEffectUtility

AFSource - Enum in org.mulinlab.varnote.utils.enumset

ajustEND(String) - Method in class org.mulinlab.varnote.operations.decode.VCFLocCodec

ajustPos() - Method in class org.mulinlab.varnote.utils.stream.GZInputStream

ajustSVTYPE(String) - Method in class org.mulinlab.varnote.operations.decode.VCFLocCodec

ALLELE - Static variable in class org.mulinlab.varnote.config.anno.FieldFormat

ALLELE_INDENTIFIER - Static variable in class org.mulinlab.varnote.config.anno.FieldFormat

ALLELE_LENGTH - Static variable in class org.mulinlab.varnote.config.anno.FieldFormat

AllelePosition - Class in org.mulinlab.varnote.utils.jannovar

Class for computing and holding minimised single allele variant coordinates.

ALLOW_LARGE_VARIANTS - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

allValues() - Static method in enum org.mulinlab.varnote.utils.enumset.FormatType

alt(String) - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation.Builder

alt - Variable in class org.mulinlab.varnote.utils.node.LocFeature

altPositionColumn - Variable in class org.mulinlab.varnote.utils.format.Format

ANNO_CONFIG - Static variable in class org.mulinlab.varnote.cmdline.txtreader.run.AnnoRunReader

ANNO_CONFIG_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

ANNO_CONFIG_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

ANNO_CONFIG_SUFFIX - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

ANNO_FO_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

ANNO_FO_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

ANNO_FORMAT - Static variable in class org.mulinlab.varnote.cmdline.txtreader.run.AnnoRunReader

ANNO_OF_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

ANNO_OF_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

ANNO_RESULT_SUFFIX - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

ANNO_VH_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

ANNO_VH_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

AnnoConfigArgumentCollection - Class in org.mulinlab.varnote.cmdline.collection

AnnoConfigArgumentCollection() - Constructor for class org.mulinlab.varnote.cmdline.collection.AnnoConfigArgumentCollection

AnnoConfigReader<T> - Class in org.mulinlab.varnote.cmdline.txtreader.anno

AnnoConfigReader() - Constructor for class org.mulinlab.varnote.cmdline.txtreader.anno.AnnoConfigReader

AnnoMapper - Class in org.mulinlab.varnote.operations.mapper

AnnoMapper(OverlapRunConfig, int) - Constructor for class org.mulinlab.varnote.operations.mapper.AnnoMapper

AnnoOut - Class in org.mulinlab.varnote.config.parser.output

AnnoOut(LocFeature) - Constructor for class org.mulinlab.varnote.config.parser.output.AnnoOut

annoOutFormat - Variable in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

AnnoOutFormat - Enum in org.mulinlab.varnote.utils.enumset

AnnoOutParam - Class in org.mulinlab.varnote.config.param.output

AnnoOutParam() - Constructor for class org.mulinlab.varnote.config.param.output.AnnoOutParam

AnnoOutParam(String) - Constructor for class org.mulinlab.varnote.config.param.output.AnnoOutParam

AnnoOutputArgumentCollection - Class in org.mulinlab.varnote.cmdline.collection

AnnoOutputArgumentCollection() - Constructor for class org.mulinlab.varnote.cmdline.collection.AnnoOutputArgumentCollection

AnnoParser - Class in org.mulinlab.varnote.config.parser

AnnoParser(AnnoRunConfig, Map<String, ExtractConfig>, int) - Constructor for class org.mulinlab.varnote.config.parser.AnnoParser

AnnoProgramGroup - Class in org.mulinlab.varnote.cmdline.programgroups

Tools that manipulate read data in SAM, BAM or CRAM format

AnnoProgramGroup() - Constructor for class org.mulinlab.varnote.cmdline.programgroups.AnnoProgramGroup

annoRecord(LocFeature, Map<String, LocFeature[]>, int) - Method in class org.mulinlab.varnote.config.run.AnnoRunConfig

AnnoRunConfig - Class in org.mulinlab.varnote.config.run

AnnoRunConfig() - Constructor for class org.mulinlab.varnote.config.run.AnnoRunConfig

AnnoRunConfig(String) - Constructor for class org.mulinlab.varnote.config.run.AnnoRunConfig

AnnoRunConfig(String, String[]) - Constructor for class org.mulinlab.varnote.config.run.AnnoRunConfig

AnnoRunConfig(QueryFileParam, List<DBParam>) - Constructor for class org.mulinlab.varnote.config.run.AnnoRunConfig

AnnoRunConfig(String, String[], String, AnnoOutParam, int) - Constructor for class org.mulinlab.varnote.config.run.AnnoRunConfig

AnnoRunConfig(QueryFileParam, List<DBParam>, String, AnnoOutParam, int) - Constructor for class org.mulinlab.varnote.config.run.AnnoRunConfig

AnnoRunReader<T> - Class in org.mulinlab.varnote.cmdline.txtreader.run

AnnoRunReader() - Constructor for class org.mulinlab.varnote.cmdline.txtreader.run.AnnoRunReader

annotate(String, int, String, String) - Method in class org.mulinlab.varnote.utils.jannovar.JannovarVariantAnnotator

Given a single allele from a multi-positional site, incoming variants might not be fully trimmed.

annotate(String, int, String, String) - Method in interface org.mulinlab.varnote.utils.jannovar.VariantAnnotator

annotate(LocFeature) - Method in class org.mulinlab.varnote.utils.JannovarUtils

annotate(String, Integer, String, String) - Method in class org.mulinlab.varnote.utils.JannovarUtils

annotateVariant(String, int, String, String) - Method in class org.mulinlab.varnote.utils.jannovar.JannovarAnnotationService

Takes VCF (forward-strand, one-based) style variants and returns a set of Jannovar VariantAnnotations.

Annotation - Class in org.mulinlab.varnote.cmdline.tools

Annotation() - Constructor for class org.mulinlab.varnote.cmdline.tools.Annotation

AnnotationConfig - Class in org.mulinlab.varnote.cmdline.tools.config

AnnotationConfig() - Constructor for class org.mulinlab.varnote.cmdline.tools.config.AnnotationConfig

AnnotationIntersectFile - Class in org.mulinlab.varnote.cmdline.tools

AnnotationIntersectFile() - Constructor for class org.mulinlab.varnote.cmdline.tools.AnnotationIntersectFile

annotations(List<TranscriptAnnotation>) - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation.Builder

areInSameOrAdjacentBlocks(long, long) - Static method in class org.mulinlab.varnote.utils.gz.BlockCompressedFilePointerUtil

Arguments - Class in org.mulinlab.varnote.cmdline.constant

Arguments() - Constructor for class org.mulinlab.varnote.cmdline.constant.Arguments

argValue - Variable in class org.mulinlab.varnote.cmdline.collection.TagArgument

assertOutputIsValid(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

asString(long) - Static method in class org.mulinlab.varnote.utils.gz.BlockCompressedFilePointerUtil

available() - Method in class org.mulinlab.varnote.utils.stream.LimitInputStream

B

BED_FIELD - Static variable in class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

BEDFileReader - Class in org.mulinlab.varnote.operations.readers.query

BEDFileReader(QueryReaderItf, Format) - Constructor for class org.mulinlab.varnote.operations.readers.query.BEDFileReader

BEDFileReader(String) - Constructor for class org.mulinlab.varnote.operations.readers.query.BEDFileReader

BEDFileReader(String, Format) - Constructor for class org.mulinlab.varnote.operations.readers.query.BEDFileReader

BEDFileReader(String, FileType, Format) - Constructor for class org.mulinlab.varnote.operations.readers.query.BEDFileReader

BEDHeaderLineFilter - Class in org.mulinlab.varnote.filters.query.line

BEDHeaderLineFilter(Format) - Constructor for class org.mulinlab.varnote.filters.query.line.BEDHeaderLineFilter

BEDLocCodec - Class in org.mulinlab.varnote.operations.decode

BEDLocCodec(boolean) - Constructor for class org.mulinlab.varnote.operations.decode.BEDLocCodec

BEDLocCodec(Format, boolean) - Constructor for class org.mulinlab.varnote.operations.decode.BEDLocCodec

beg - Variable in class org.mulinlab.varnote.utils.node.LocFeature

BEGIN - Static variable in class org.mulinlab.varnote.cmdline.txtreader.anno.FormatReader

BEGIN - Static variable in class org.mulinlab.varnote.cmdline.txtreader.anno.VcfInfoReader

BGZReader - Class in org.mulinlab.varnote.operations.readers.itf

BGZReader(String) - Constructor for class org.mulinlab.varnote.operations.readers.itf.BGZReader

BGZReader - Class in org.mulinlab.varnote.utils.gz

BGZReader() - Constructor for class org.mulinlab.varnote.utils.gz.BGZReader

BGZReader(String, int) - Constructor for class org.mulinlab.varnote.utils.gz.BGZReader

bgzStr - Variable in class org.mulinlab.varnote.utils.node.LocFeature

BIN_GENOMIC_SPAN - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

block - Variable in class org.mulinlab.varnote.operations.readers.db.VannoReader.VannoIteratorImpl

BLOCK_ADDRESS - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

BLOCK_START_WITH_END_BTYE - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

BLOCK_START_WITH_END_INT - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

BLOCK_START_WITH_END_SHORT - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

BLOCK_START_WO_END - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

blockAddress - Variable in class org.mulinlab.varnote.utils.node.NodeWithFilePointer

BlockBean(long) - Constructor for class org.mulinlab.varnote.operations.index.IndexWriter.BlockBean

BlockCompressedFilePointerUtil - Class in org.mulinlab.varnote.utils.gz

BlockCompressedFilePointerUtil() - Constructor for class org.mulinlab.varnote.utils.gz.BlockCompressedFilePointerUtil

BlockFeature - Class in org.mulinlab.varnote.utils.block

BlockFeature() - Constructor for class org.mulinlab.varnote.utils.block.BlockFeature

BlockFeature.VannoFeature - Class in org.mulinlab.varnote.utils.block

blockOffset - Variable in class org.mulinlab.varnote.utils.node.NodeWithFilePointer

buf - Variable in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

buf - Variable in class org.mulinlab.varnote.operations.readers.db.VannoReader

buf - Variable in class org.mulinlab.varnote.utils.database.index.Index

BUFFER_SIZE - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

build() - Method in class org.mulinlab.varnote.utils.jannovar.GeneBuilder

build() - Method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation.Builder

build() - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation.Builder

build() - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual.Builder

builder() - Static method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation

Builder() - Constructor for class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation.Builder

builder() - Static method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation

Builder() - Constructor for class org.mulinlab.varnote.utils.jannovar.VariantAnnotation.Builder

builder() - Static method in class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual

Builder() - Constructor for class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual.Builder

ByteInputStream - Class in org.mulinlab.varnote.utils.stream

ByteInputStream(File, int, char) - Constructor for class org.mulinlab.varnote.utils.stream.ByteInputStream

BZip2Constants - Class in org.mulinlab.varnote.utils.stream

BZip2Constants() - Constructor for class org.mulinlab.varnote.utils.stream.BZip2Constants

BZIP2InputStream - Class in org.mulinlab.varnote.utils.stream

BZIP2InputStream(String, int) - Constructor for class org.mulinlab.varnote.utils.stream.BZIP2InputStream

BZIP2InputStream.Spider - Class in org.mulinlab.varnote.utils.stream

C

canDecode(String) - Method in class org.mulinlab.varnote.operations.decode.LocCodec

CellMark - Enum in org.mulinlab.varnote.utils.enumset

CellType - Enum in org.mulinlab.varnote.utils.enumset

checkAutoThread() - Method in class org.mulinlab.varnote.config.param.RunParam

checkChr() - Method in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

checkCount(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

checkDataIsValid(Format, String[]) - Static method in class org.mulinlab.varnote.utils.headerparser.HeaderFormatReader

checkDB() - Method in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

checkFileType(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

checkFormat(String, Format) - Static method in class org.mulinlab.varnote.utils.GenomicRegionUtils

checkIndexFile() - Method in class org.mulinlab.varnote.utils.database.Database

checkIndexFile() - Method in class org.mulinlab.varnote.utils.database.TbiDatabase

checkIndexFile() - Method in class org.mulinlab.varnote.utils.database.VannoDatabase

checkIndexType(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

checkIntersectType(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

checkLoc() - Method in class org.mulinlab.varnote.utils.format.Format

checkMissing(OptionSet, String[]) - Static method in class org.mulinlab.varnote.utils.VannoUtils

checkMode(int) - Static method in class org.mulinlab.varnote.utils.VannoUtils

checkOutFormat(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

checkParam() - Method in class org.mulinlab.varnote.config.param.DBParam

checkParam() - Method in class org.mulinlab.varnote.config.param.IndexParam

checkParam() - Method in class org.mulinlab.varnote.config.param.output.AnnoOutParam

checkParam() - Method in class org.mulinlab.varnote.config.param.output.IntersetOutParam

checkParam() - Method in class org.mulinlab.varnote.config.param.output.OutParam

checkParam() - Method in class org.mulinlab.varnote.config.param.Param

checkParam() - Method in class org.mulinlab.varnote.config.param.RunParam

checkQueryFormat(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

checkThreadNum(int) - Method in class org.mulinlab.varnote.config.param.RunParam

checkType(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

checkValidBGZ(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

chr - Variable in class org.mulinlab.varnote.utils.node.LocFeature

chr2tid(String) - Method in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

chr2tid(String) - Method in class org.mulinlab.varnote.utils.database.index.Index

return chromosome ID or -1 if it is unknown

CHR_START - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

ChromosomalRegion - Interface in org.mulinlab.varnote.utils.jannovar

ChromosomalRegionIndex<T extends ChromosomalRegion> - Class in org.mulinlab.varnote.utils.jannovar

Interval tree-backed index for chromosomal regions.

chromosome(int) - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation.Builder

chromosomeName(String) - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation.Builder

ChromosomeType - Enum in org.mulinlab.varnote.utils.enumset

chrToTypeMap - Static variable in class org.mulinlab.varnote.utils.VannoUtils

clear() - Method in class org.mulinlab.varnote.operations.readers.db.VannoMixReader.MixVannoIteratorImpl

clear() - Method in class org.mulinlab.varnote.utils.block.SROB

clear() - Method in class org.mulinlab.varnote.utils.node.LocFeature

clearST() - Method in class org.mulinlab.varnote.operations.stack.AbstractReaderStack

clearST() - Method in class org.mulinlab.varnote.operations.stack.ExactStack

clearST() - Method in class org.mulinlab.varnote.operations.stack.IntervalStack

clone() - Method in class org.mulinlab.varnote.config.anno.databse.VCFParser

clone() - Method in class org.mulinlab.varnote.config.param.FilterParam

clone() - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceADFilter

clone() - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceARFilter

clone() - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceFilter

clone() - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceXDFilter

clone() - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceXRFilter

clone() - Method in class org.mulinlab.varnote.filters.query.gt.ABGenotypeFilter

clone() - Method in class org.mulinlab.varnote.filters.query.gt.DepthFilter

clone() - Method in interface org.mulinlab.varnote.filters.query.gt.GenotypeFilter

clone() - Method in class org.mulinlab.varnote.filters.query.gt.GenotypeQualityFilter

clone() - Method in interface org.mulinlab.varnote.filters.query.VariantFilter

clone() - Method in class org.mulinlab.varnote.filters.query.vc.ABVariantFilter

clone() - Method in class org.mulinlab.varnote.filters.query.vc.QDFilter

clone() - Method in class org.mulinlab.varnote.filters.RegionFilter

clone() - Method in class org.mulinlab.varnote.operations.decode.BEDLocCodec

clone() - Method in class org.mulinlab.varnote.operations.decode.LocCodec

clone() - Method in class org.mulinlab.varnote.operations.decode.RSIDLocCodec

clone() - Method in class org.mulinlab.varnote.operations.decode.TABLocCodec

clone() - Method in class org.mulinlab.varnote.operations.decode.VCFLocCodec

clone() - Method in class org.mulinlab.varnote.utils.database.Database

clone() - Method in class org.mulinlab.varnote.utils.database.TbiDatabase

clone() - Method in class org.mulinlab.varnote.utils.database.VannoDatabase

clone() - Method in class org.mulinlab.varnote.utils.node.LocFeature

clone() - Method in class org.mulinlab.varnote.utils.node.NodeWithFilePointer

close() - Method in class org.mulinlab.varnote.config.io.PrintGZ

close() - Method in class org.mulinlab.varnote.filters.iterator.LineFilterIterator

close() - Method in class org.mulinlab.varnote.filters.iterator.NoFilterIterator

close() - Method in class org.mulinlab.varnote.filters.iterator.VCFFilterIterator

close() - Method in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

close() - Method in class org.mulinlab.varnote.operations.readers.db.VannoReader

close() - Method in class org.mulinlab.varnote.utils.gz.BGZReader

close() - Method in class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

close() must be called in order to flush any remaining buffered bytes.

close(long) - Method in class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

close(long) - Method in class org.mulinlab.varnote.utils.gz.MyEndianOutputStream

close() - Method in class org.mulinlab.varnote.utils.stream.AdvancedBZip2CompressorInputStream

close() - Method in class org.mulinlab.varnote.utils.stream.GZInputStream

close() - Method in class org.mulinlab.varnote.utils.stream.GZInputStream.GZReader

closeFP() - Method in class org.mulinlab.varnote.utils.gz.BGZReader

closeInputStream() - Method in class org.mulinlab.varnote.utils.stream.BZIP2InputStream.Spider

closeReader() - Method in class org.mulinlab.varnote.operations.readers.itf.BGZReader

closeReader() - Method in class org.mulinlab.varnote.operations.readers.itf.GZIPReader

closeReader() - Method in class org.mulinlab.varnote.operations.readers.itf.LongLineReader

closeReader() - Method in interface org.mulinlab.varnote.operations.readers.itf.QueryReaderItf

closeReader() - Method in class org.mulinlab.varnote.operations.readers.itf.thread.GZIPThreadReader

closeReader() - Method in class org.mulinlab.varnote.operations.readers.itf.thread.SpiderReader

CMDProgram - Class in org.mulinlab.varnote.cmdline.abstractclass

CMDProgram() - Constructor for class org.mulinlab.varnote.cmdline.abstractclass.CMDProgram

codec - Variable in class org.mulinlab.varnote.operations.readers.db.TbiReader

COL - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

COLOR_STATUS - Static variable in class org.mulinlab.varnote.cmdline.constant.CommandLineDefaults

colsToExtract - Variable in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

COLUMNS - Static variable in class org.mulinlab.varnote.cmdline.txtreader.anno.AnnoConfigReader

COMMA - Variable in class org.mulinlab.varnote.config.anno.NormalField

COMMA - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

CommandLineDefaults - Class in org.mulinlab.varnote.cmdline.constant

CommandLineDefaults() - Constructor for class org.mulinlab.varnote.cmdline.constant.CommandLineDefaults

COMMENT - Static variable in class org.mulinlab.varnote.cmdline.txtreader.anno.FormatReader

COMMENT - Static variable in class org.mulinlab.varnote.cmdline.txtreader.anno.VcfInfoReader

COMMENT_LINE - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.AbstractQueryReader

COMMENT_LINE - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

commentIndicator - Variable in class org.mulinlab.varnote.config.param.postDB.PostDBParam

commentIndicator - Variable in class org.mulinlab.varnote.utils.database.index.vannoIndex.VannoIndex

COMMNT_INDICATOR - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

COMMNT_INDICATOR - Static variable in class org.mulinlab.varnote.cmdline.txtreader.anno.AnnoConfigReader

compare(long, long) - Static method in class org.mulinlab.varnote.utils.gz.BlockCompressedFilePointerUtil

compareTo(ChromosomalRegion) - Method in interface org.mulinlab.varnote.utils.jannovar.ChromosomalRegion

CompressorInputStream - Class in org.mulinlab.varnote.utils.stream

CompressorInputStream() - Constructor for class org.mulinlab.varnote.utils.stream.CompressorInputStream

compute(List<Integer>) - Method in class org.mulinlab.varnote.config.anno.FieldFormat

config - Variable in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

config - Variable in class org.mulinlab.varnote.operations.mapper.AbstractMapper

config - Variable in class org.mulinlab.varnote.utils.database.Database

configArguments - Variable in class org.mulinlab.varnote.cmdline.tools.Annotation

configArguments - Variable in class org.mulinlab.varnote.cmdline.tools.AnnotationIntersectFile

configFile - Variable in class org.mulinlab.varnote.cmdline.abstractclass.ConfigProgram

ConfigProgram - Class in org.mulinlab.varnote.cmdline.abstractclass

ConfigProgram() - Constructor for class org.mulinlab.varnote.cmdline.abstractclass.ConfigProgram

ConfigProgramGroup - Class in org.mulinlab.varnote.cmdline.programgroups

Tools that manipulate read data in SAM, BAM or CRAM format

ConfigProgramGroup() - Constructor for class org.mulinlab.varnote.cmdline.programgroups.ConfigProgramGroup

containsId(String) - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree

convertList(Map<String, List<LocFeature>>) - Static method in class org.mulinlab.varnote.utils.RunFactory

convertToJannovarPedigree(Pedigree) - Static method in class org.mulinlab.varnote.utils.pedigree.PedigreeConverter

Count - Class in org.mulinlab.varnote.cmdline.tools

Count() - Constructor for class org.mulinlab.varnote.cmdline.tools.Count

COUNT - Static variable in class org.mulinlab.varnote.cmdline.txtreader.anno.VcfInfoReader

count - Variable in class org.mulinlab.varnote.filters.iterator.LineFilterIterator

count(int) - Method in class org.mulinlab.varnote.utils.stream.CompressorInputStream

Increments the counter of already read bytes.

count(long) - Method in class org.mulinlab.varnote.utils.stream.CompressorInputStream

Increments the counter of already read bytes.

count - Variable in class org.mulinlab.varnote.utils.TimeMetric

COUNT_RESULT_SUFFIX - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

CounterMapper - Class in org.mulinlab.varnote.operations.mapper

CounterMapper(CountRunConfig, int) - Constructor for class org.mulinlab.varnote.operations.mapper.CounterMapper

CountResultProcess - Class in org.mulinlab.varnote.operations.process

CountResultProcess() - Constructor for class org.mulinlab.varnote.operations.process.CountResultProcess

CountRunConfig - Class in org.mulinlab.varnote.config.run

CountRunConfig() - Constructor for class org.mulinlab.varnote.config.run.CountRunConfig

CountRunConfig(String, String[]) - Constructor for class org.mulinlab.varnote.config.run.CountRunConfig

CountRunConfig(QueryFileParam, List<DBParam>) - Constructor for class org.mulinlab.varnote.config.run.CountRunConfig

CountRunConfig(String, String[], int) - Constructor for class org.mulinlab.varnote.config.run.CountRunConfig

CountRunConfig(QueryFileParam, List<DBParam>, int) - Constructor for class org.mulinlab.varnote.config.run.CountRunConfig

CRC - Class in org.mulinlab.varnote.utils.stream

createReader() - Method in class org.mulinlab.varnote.utils.stream.GZInputStream

creatSpider() - Method in class org.mulinlab.varnote.utils.stream.BZIP2InputStream

currentTid - Variable in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

customCommandLineValidation() - Method in class org.mulinlab.varnote.cmdline.abstractclass.CMDProgram

D

DatababseFilter - Interface in org.mulinlab.varnote.config.anno.databse.filter

Database - Class in org.mulinlab.varnote.utils.database

Database(DBParam) - Constructor for class org.mulinlab.varnote.utils.database.Database

DatabaseAnnoBEDParser - Class in org.mulinlab.varnote.config.anno.databse.anno

DatabaseAnnoBEDParser(ExtractConfig, boolean, AnnoOutFormat) - Constructor for class org.mulinlab.varnote.config.anno.databse.anno.DatabaseAnnoBEDParser

DatabaseAnnoVCFParser - Class in org.mulinlab.varnote.config.anno.databse.anno

DatabaseAnnoVCFParser(ExtractConfig, boolean, AnnoOutFormat) - Constructor for class org.mulinlab.varnote.config.anno.databse.anno.DatabaseAnnoVCFParser

DatabaseBEDFilter - Class in org.mulinlab.varnote.config.anno.databse.filter

DatabaseBEDFilter() - Constructor for class org.mulinlab.varnote.config.anno.databse.filter.DatabaseBEDFilter

DatabaseFactory - Class in org.mulinlab.varnote.utils.database

DatabaseFactory() - Constructor for class org.mulinlab.varnote.utils.database.DatabaseFactory

DatabaseVCFFilter - Class in org.mulinlab.varnote.config.anno.databse.filter

DatabaseVCFFilter(List<VariantFilter>, VCFParser) - Constructor for class org.mulinlab.varnote.config.anno.databse.filter.DatabaseVCFFilter

databses - Variable in class org.mulinlab.varnote.config.run.RunConfig

db - Variable in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

db - Variable in class org.mulinlab.varnote.utils.database.Database

DB_BEGIN - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

DB_DOC - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

DB_INDEX_TYPE - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

DB_INPUT_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

DB_INPUT_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

DB_LABEL - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

DB_MODE - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

DB_PATH - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

DBAnnoParam - Class in org.mulinlab.varnote.config.param.postDB

DBAnnoParam(String) - Constructor for class org.mulinlab.varnote.config.param.postDB.DBAnnoParam

DBArgumentCollection - Class in org.mulinlab.varnote.cmdline.collection

DBArgumentCollection() - Constructor for class org.mulinlab.varnote.cmdline.collection.DBArgumentCollection

dbArguments - Variable in class org.mulinlab.varnote.cmdline.abstractclass.QueryProgram

dbArguments - Variable in class org.mulinlab.varnote.cmdline.tools.RandomAccess

dbFiles - Variable in class org.mulinlab.varnote.cmdline.collection.DBArgumentCollection

DBFilterParam - Class in org.mulinlab.varnote.config.param.postDB

DBFilterParam() - Constructor for class org.mulinlab.varnote.config.param.postDB.DBFilterParam

dbIndexPath - Variable in class org.mulinlab.varnote.utils.database.Database

dbName - Variable in class org.mulinlab.varnote.utils.database.Database

DBParam - Class in org.mulinlab.varnote.config.param

DBParam(String) - Constructor for class org.mulinlab.varnote.config.param.DBParam

DBParam(File) - Constructor for class org.mulinlab.varnote.config.param.DBParam

DBParam(String, IndexType) - Constructor for class org.mulinlab.varnote.config.param.DBParam

DBParam(String, String, IntersectType, IndexType) - Constructor for class org.mulinlab.varnote.config.param.DBParam

DBParam(String, String, String, String) - Constructor for class org.mulinlab.varnote.config.param.DBParam

dbParams - Variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

dbParams - Variable in class org.mulinlab.varnote.config.run.RunConfig

dbs - Variable in class org.mulinlab.varnote.operations.query.AbstractQuery

dbValues - Variable in class org.mulinlab.varnote.config.anno.NormalField

decode(String) - Method in class org.mulinlab.varnote.operations.decode.BEDLocCodec

decode(String) - Method in class org.mulinlab.varnote.operations.decode.LocCodec

decode(String) - Method in class org.mulinlab.varnote.operations.decode.RSIDLocCodec

decode(String) - Method in class org.mulinlab.varnote.operations.decode.TABLocCodec

decode(String) - Method in class org.mulinlab.varnote.operations.decode.VCFLocCodec

decode(String) - Method in class org.mulinlab.varnote.utils.database.Database

decodeFull - Variable in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

DEFALT_OUT_MODE - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFALT_OUT_MODE_VAL - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_ALLOW_MAX_VIRANTS - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_COL - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_COMMENT_INDICATOR - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_COMMENT_INDICATOR - Static variable in class org.mulinlab.varnote.utils.format.Format

DEFAULT_DISPLAY_LABEL - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_FORCE_OVERLAP - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_GZIP - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_HAS_HEADER - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_INTERSECT - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_IS_COUNT - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_IS_GZIP - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_LOG - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_LOJ - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_MAX_LENGTH - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_MODE - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_REMOVE_COMMENT - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_RSID_COL - Static variable in class org.mulinlab.varnote.utils.format.Format

DEFAULT_SKIP - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_THREAD - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_USE_JDK - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

DEFAULT_ZERO_BASED - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

defaultBuild() - Static method in enum org.mulinlab.varnote.utils.enumset.GenomeAssembly

defaultFormat(String, boolean) - Static method in class org.mulinlab.varnote.utils.format.Format

defaultParam(String) - Static method in class org.mulinlab.varnote.config.param.postDB.DBAnnoParam

defaultVal() - Static method in enum org.mulinlab.varnote.utils.enumset.GenomeAssembly

defaultVal() - Static method in enum org.mulinlab.varnote.utils.enumset.TranscriptSource

defaultVCFParser(Format, String, FileType) - Static method in class org.mulinlab.varnote.config.anno.databse.VCFParser

DELETION - Static variable in class org.mulinlab.varnote.utils.VannoUtils

Delimiter - Enum in org.mulinlab.varnote.utils.enumset

DepthFilter - Class in org.mulinlab.varnote.filters.query.gt

DepthFilter(int) - Constructor for class org.mulinlab.varnote.filters.query.gt.DepthFilter

DESC - Static variable in class org.mulinlab.varnote.cmdline.txtreader.anno.VcfInfoReader

determineFileType(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

distanceFromNearestGene(int) - Method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation.Builder

doEnd() - Method in class org.mulinlab.varnote.cmdline.txtreader.abs.AbstractQueryReader

doEnd() - Method in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

doEnd() - Method in interface org.mulinlab.varnote.cmdline.txtreader.abs.RunReaderInterface

doEnd() - Method in class org.mulinlab.varnote.cmdline.txtreader.anno.AnnoConfigReader

doEnd() - Method in class org.mulinlab.varnote.cmdline.txtreader.anno.FormatReader

doEnd() - Method in class org.mulinlab.varnote.cmdline.txtreader.anno.OverlapHeaderReader

doEnd() - Method in class org.mulinlab.varnote.cmdline.txtreader.anno.VcfInfoReader

doEnd() - Method in class org.mulinlab.varnote.cmdline.txtreader.run.AnnoRunReader

doEnd() - Method in class org.mulinlab.varnote.cmdline.txtreader.run.FileQueryReader

doEnd() - Method in class org.mulinlab.varnote.cmdline.txtreader.run.IntersectRunReader

doEnd() - Method in class org.mulinlab.varnote.config.io.temp.Printter

doEnd() - Method in class org.mulinlab.varnote.utils.TimeMetric

doEnd(long) - Method in class org.mulinlab.varnote.utils.TimeMetric

doInit() - Method in class org.mulinlab.varnote.cmdline.txtreader.abs.AbstractQueryReader

doInit() - Method in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

doInit() - Method in interface org.mulinlab.varnote.cmdline.txtreader.abs.RunReaderInterface

doInit() - Method in class org.mulinlab.varnote.cmdline.txtreader.anno.AnnoConfigReader

doMap() - Method in class org.mulinlab.varnote.operations.mapper.AbstractMapper

doMap() - Method in interface org.mulinlab.varnote.utils.mapreduce.Mapper

doProcess(LocFeature) - Method in class org.mulinlab.varnote.operations.process.CountResultProcess

doProcess(List<NodeWithFilePointer>) - Method in interface org.mulinlab.varnote.operations.process.ProcessBlock

doProcess(LocFeature) - Method in interface org.mulinlab.varnote.operations.process.ProcessResult

doProcess(LocFeature) - Method in class org.mulinlab.varnote.operations.process.TabixResultProcess

doProcess(LocFeature) - Method in class org.mulinlab.varnote.operations.process.VannoResultProcess

doQuery(LocFeature) - Method in class org.mulinlab.varnote.operations.mapper.AbstractMapper

doQuery(LocFeature) - Method in class org.mulinlab.varnote.operations.mapper.AnnoMapper

doQuery(LocFeature) - Method in class org.mulinlab.varnote.operations.mapper.CounterMapper

doQuery(LocFeature) - Method in class org.mulinlab.varnote.operations.mapper.IntersetMapper

doQuery(LocFeature) - Method in class org.mulinlab.varnote.operations.query.AbstractQuery

doQuery(String) - Method in class org.mulinlab.varnote.operations.query.AbstractQuery

doQuery(LocFeature) - Method in interface org.mulinlab.varnote.operations.query.Query

doQuery(LocFeature) - Method in class org.mulinlab.varnote.operations.query.TabixQuery

doReducer(List<V>) - Method in interface org.mulinlab.varnote.utils.mapreduce.Reducer

DOUBLE_HYPHEN - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

doWork() - Method in class org.mulinlab.varnote.cmdline.abstractclass.CMDProgram

doWork() - Method in class org.mulinlab.varnote.cmdline.index.Index

doWork() - Method in class org.mulinlab.varnote.cmdline.index.IndexInfo

doWork() - Method in class org.mulinlab.varnote.cmdline.tools.Annotation

doWork() - Method in class org.mulinlab.varnote.cmdline.tools.AnnotationIntersectFile

doWork() - Method in class org.mulinlab.varnote.cmdline.tools.config.AnnotationConfig

doWork() - Method in class org.mulinlab.varnote.cmdline.tools.config.IntersectConfig

doWork() - Method in class org.mulinlab.varnote.cmdline.tools.Count

doWork() - Method in class org.mulinlab.varnote.cmdline.tools.Intersect

doWork() - Method in class org.mulinlab.varnote.cmdline.tools.RandomAccess

E

empty() - Static method in class org.mulinlab.varnote.utils.jannovar.ChromosomalRegionIndex

Returns an empty index.

empty() - Static method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation

empty() - Static method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation

empty() - Static method in class org.mulinlab.varnote.utils.pedigree.Pedigree

END - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.AbstractQueryReader

END - Static variable in class org.mulinlab.varnote.operations.readers.db.VannoReader

end - Variable in class org.mulinlab.varnote.utils.node.LocFeature

EOF_ITERATOR - Static variable in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

iterator returned instead of null when there is no more data

equals(Object) - Method in class org.mulinlab.varnote.utils.jannovar.AllelePosition

equals(Object) - Method in class org.mulinlab.varnote.utils.jannovar.ChromosomalRegionIndex

equals(Object) - Method in class org.mulinlab.varnote.utils.jannovar.Gene

equals(Object) - Method in class org.mulinlab.varnote.utils.jannovar.RegulatoryFeature

equals(Object) - Method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation

equals(Object) - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation

equals(Object) - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree

equals(Object) - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual

evalJudgement(String) - Static method in class org.mulinlab.varnote.utils.ExpressionUtils

ExactStack - Class in org.mulinlab.varnote.operations.stack

ExactStack(ProcessResult) - Constructor for class org.mulinlab.varnote.operations.stack.ExactStack

exceedMaxLength() - Method in class org.mulinlab.varnote.operations.decode.LocCodec

EXCEPTION - Static variable in class org.mulinlab.varnote.config.anno.FieldFormat

EXCLUDE - Static variable in class org.mulinlab.varnote.config.anno.databse.anno.ExtractConfig

exists(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

ExpressionUtils - Class in org.mulinlab.varnote.utils

ExpressionUtils() - Constructor for class org.mulinlab.varnote.utils.ExpressionUtils

extHeaderFile - Variable in class org.mulinlab.varnote.cmdline.abstractclass.IndexProgram

extHeaderFile - Variable in class org.mulinlab.varnote.cmdline.collection.InputFileArgumentCollection

extractCommandLineProgram(String[], List<String>, String) - Static method in class org.mulinlab.varnote.cmdline.VarNoteCommandLine

ExtractConfig - Class in org.mulinlab.varnote.config.anno.databse.anno

ExtractConfig(DBAnnoParam, Database) - Constructor for class org.mulinlab.varnote.config.anno.databse.anno.ExtractConfig

extractDBFeature(Map<String, String>, LocFeature, int) - Method in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

extractDBFeature(Map<String, String>, LocFeature, int) - Method in class org.mulinlab.varnote.config.anno.databse.anno.DatabaseAnnoVCFParser

extractFieldsValue(LocFeature, LocFeature[]) - Method in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

extractValues(LocFeature, LocFeature[]) - Method in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

F

familyId(String) - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual.Builder

fatherId(String) - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual.Builder

fcount - Variable in class org.mulinlab.varnote.filters.iterator.LineFilterIterator

feature - Variable in class org.mulinlab.varnote.filters.iterator.LineFilterIterator

Feature(int, int, int) - Constructor for class org.mulinlab.varnote.utils.block.SROB.Feature

FieldFormat - Class in org.mulinlab.varnote.config.anno

FieldFormat(String, String, String) - Constructor for class org.mulinlab.varnote.config.anno.FieldFormat

FieldFormat.FormatVariable - Class in org.mulinlab.varnote.config.anno

FIELDS - Static variable in class org.mulinlab.varnote.cmdline.txtreader.anno.AnnoConfigReader

file - Variable in class org.mulinlab.varnote.config.io.temp.ThreadPrintter

FILE_TYPE_DOC - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

fileds - Variable in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

filedsInfoMap - Variable in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

fileName - Variable in class org.mulinlab.varnote.config.anno.NormalField

filePath - Variable in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

FileQueryReader<T> - Class in org.mulinlab.varnote.cmdline.txtreader.run

FileQueryReader() - Constructor for class org.mulinlab.varnote.cmdline.txtreader.run.FileQueryReader

fileToIndex - Variable in class org.mulinlab.varnote.cmdline.abstractclass.IndexProgram

fileType - Variable in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

FileType - Enum in org.mulinlab.varnote.utils.enumset

filterChrCount - Variable in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceFilter

filterCompatibleCount - Variable in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceFilter

FilterConfig - Class in org.mulinlab.varnote.config.anno.databse.filter

FilterConfig() - Constructor for class org.mulinlab.varnote.config.anno.databse.filter.FilterConfig

filterCount - Variable in class org.mulinlab.varnote.filters.query.gt.ABGenotypeFilter

filterCount - Variable in class org.mulinlab.varnote.filters.query.vc.ABVariantFilter

filterLine(String) - Method in class org.mulinlab.varnote.cmdline.txtreader.abs.AbstractQueryReader

filterLine(String) - Method in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

filterLine(String) - Method in interface org.mulinlab.varnote.cmdline.txtreader.abs.RunReaderInterface

filterLine(String) - Method in class org.mulinlab.varnote.cmdline.txtreader.anno.AnnoConfigReader

filterLine(String) - Method in class org.mulinlab.varnote.cmdline.txtreader.anno.FormatReader

filterLine(String) - Method in class org.mulinlab.varnote.cmdline.txtreader.anno.OverlapHeaderReader

filterLine(String) - Method in class org.mulinlab.varnote.cmdline.txtreader.anno.VcfInfoReader

FilterParam - Class in org.mulinlab.varnote.config.param

FilterParam() - Constructor for class org.mulinlab.varnote.config.param.FilterParam

FilterParam(List<VariantFilter>, List<GenotypeFilter>, MendelianInheritanceFilter, RegionFilter) - Constructor for class org.mulinlab.varnote.config.param.FilterParam

filters - Variable in class org.mulinlab.varnote.filters.iterator.LineFilterIterator

FIND - Static variable in class org.mulinlab.varnote.operations.readers.db.VannoReader

findOverlap(LocFeature) - Method in class org.mulinlab.varnote.operations.stack.AbstractReaderStack

findOverlap(LocFeature) - Method in class org.mulinlab.varnote.operations.stack.ExactStack

findOverlap(LocFeature) - Method in class org.mulinlab.varnote.operations.stack.IntervalStack

findOverlap(LocFeature) - Method in class org.mulinlab.varnote.operations.stack.IntervalStackFC

findOverlapInST(LocFeature) - Method in class org.mulinlab.varnote.operations.stack.AbstractReaderStack

findOverlapInST(LocFeature) - Method in class org.mulinlab.varnote.operations.stack.ExactStack

findOverlapInST(LocFeature) - Method in class org.mulinlab.varnote.operations.stack.IntervalStack

findOverlapInST(LocFeature) - Method in class org.mulinlab.varnote.operations.stack.IntervalStackFC

findOverlaps(List<LocFeature>) - Method in class org.mulinlab.varnote.operations.stack.AbstractReaderStack

findOverlaps(List<LocFeature>) - Method in class org.mulinlab.varnote.operations.stack.ExactStack

findOverlaps(List<LocFeature>) - Method in class org.mulinlab.varnote.operations.stack.IntervalStack

FlatPrintter - Class in org.mulinlab.varnote.config.io.temp

FlatPrintter(OutParam) - Constructor for class org.mulinlab.varnote.config.io.temp.FlatPrintter

FlatThreadPrintter - Class in org.mulinlab.varnote.config.io.temp

FlatThreadPrintter(String, int) - Constructor for class org.mulinlab.varnote.config.io.temp.FlatThreadPrintter

flush() - Method in class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

WARNING: flush() affects the output format, because it causes the current contents of uncompressedBuffer to be compressed and written, even if it isn't full.

FORCE_OVERLAP - Static variable in class org.mulinlab.varnote.cmdline.txtreader.run.AnnoRunReader

FORCE_OVERLAP - Static variable in class org.mulinlab.varnote.config.anno.NormalField

FORMAT - Static variable in class org.mulinlab.varnote.cmdline.txtreader.anno.FormatReader

format - Variable in class org.mulinlab.varnote.cmdline.txtreader.run.FileQueryReader

format - Variable in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

format - Variable in class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

format - Variable in class org.mulinlab.varnote.config.param.IndexParam

format - Variable in class org.mulinlab.varnote.operations.decode.LocCodec

format - Variable in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

format - Variable in class org.mulinlab.varnote.utils.database.Database

format - Variable in class org.mulinlab.varnote.utils.database.index.Index

Format - Class in org.mulinlab.varnote.utils.format

Format(int, int, int, int, int, String, int, int, boolean) - Constructor for class org.mulinlab.varnote.utils.format.Format

Format(int, int, int, int, int, String, int, int, boolean, FormatType) - Constructor for class org.mulinlab.varnote.utils.format.Format

FORMAT_ALT_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_BEGIN_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_BEGIN_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_CHROM_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_CHROM_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_COMMENT_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_COMMENT_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_END_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_END_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_HEADER_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_HEADER_PATH_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_HEADER_PATH_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_HEADER_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_REF_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_SKIP_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_SKIP_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_ZERO_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

FORMAT_ZERO_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

formatElapseTime(long) - Static method in class org.mulinlab.varnote.utils.TimeMetric

formatIsMatch(String, Format) - Static method in class org.mulinlab.varnote.utils.VannoUtils

FormatReader<T> - Class in org.mulinlab.varnote.cmdline.txtreader.anno

FormatReader() - Constructor for class org.mulinlab.varnote.cmdline.txtreader.anno.FormatReader

FormatType - Enum in org.mulinlab.varnote.utils.enumset

FormatVariable(String, int, String) - Constructor for class org.mulinlab.varnote.config.anno.FieldFormat.FormatVariable

fromValue(String) - Static method in enum org.mulinlab.varnote.utils.enumset.GenomeAssembly

G

Gene - Class in org.mulinlab.varnote.utils.jannovar

Gene(ReferenceDictionary, String, ImmutableList<TranscriptModel>) - Constructor for class org.mulinlab.varnote.utils.jannovar.Gene

GeneBuilder - Class in org.mulinlab.varnote.utils.jannovar

GeneBuilder(ReferenceDictionary, String) - Constructor for class org.mulinlab.varnote.utils.jannovar.GeneBuilder

geneId - Variable in class org.mulinlab.varnote.config.parser.output.ADOutFeature

geneId(String) - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation.Builder

genesToRegion(List<Gene>, int) - Static method in class org.mulinlab.varnote.utils.GenomicRegionUtils

geneSymbol - Variable in class org.mulinlab.varnote.config.parser.output.ADOutFeature

geneSymbol(String) - Method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation.Builder

geneSymbol(String) - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation.Builder

genomeAssembly - Variable in class org.mulinlab.varnote.cmdline.collection.VariantEffectArgumentCollection

GenomeAssembly - Enum in org.mulinlab.varnote.utils.enumset

genomeAssembly(GenomeAssembly) - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation.Builder

GenomeAssembly.InvalidGenomeAssemblyException - Exception in org.mulinlab.varnote.utils.enumset

GenomicRegionType - Enum in org.mulinlab.varnote.utils.enumset

GenomicRegionUtils - Class in org.mulinlab.varnote.utils

GenomicRegionUtils() - Constructor for class org.mulinlab.varnote.utils.GenomicRegionUtils

GenotypeFilter - Interface in org.mulinlab.varnote.filters.query.gt

GenotypeQC - Enum in org.mulinlab.varnote.utils.enumset

GenotypeQualityFilter - Class in org.mulinlab.varnote.filters.query.gt

GenotypeQualityFilter(int) - Constructor for class org.mulinlab.varnote.filters.query.gt.GenotypeQualityFilter

getAbsolutePath(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

getAccession() - Method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation

getAddress(SeekableStream) - Static method in class org.mulinlab.varnote.utils.VannoUtils

getAffectedFemaleParentNames() - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceXRFilter

getAffectPersonNumber(Pedigree) - Static method in class org.mulinlab.varnote.utils.VannoUtils

getAllele() - Method in class org.mulinlab.varnote.config.anno.ValWithAllele

getAllowLargeVariants() - Method in class org.mulinlab.varnote.cmdline.collection.RunArgumentCollection

getAlt() - Method in class org.mulinlab.varnote.utils.jannovar.AllelePosition

getAlt() - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation

getAlt() - Method in interface org.mulinlab.varnote.utils.jannovar.VariantCoordinates

getAlts() - Method in class org.mulinlab.varnote.utils.node.LocFeature

getAnnoOutFormat() - Method in class org.mulinlab.varnote.config.param.output.AnnoOutParam

getArgValue() - Method in class org.mulinlab.varnote.cmdline.collection.TagArgument

getAVGOffset() - Method in class org.mulinlab.varnote.utils.block.SROB

getBedAlleleFormat() - Static method in class org.mulinlab.varnote.utils.VannoUtils

getBEDDataStart(StringJoiner, LocFeature) - Method in class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

getBEDHeaderStart(StringJoiner) - Method in class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

getBeg(BlockCompressedInputStream, int) - Method in class org.mulinlab.varnote.utils.block.BlockFeature

getBeg() - Method in class org.mulinlab.varnote.utils.block.BlockFeature.VannoFeature

getBeg() - Method in class org.mulinlab.varnote.utils.block.SROB.Feature

getBGZFilePointer() - Method in class org.mulinlab.varnote.utils.block.SROB

getBins(int, int) - Method in class org.mulinlab.varnote.operations.readers.db.TbiMixReader

getBlockAddress() - Method in class org.mulinlab.varnote.operations.index.IndexWriter.BlockBean

getBlockAddress() - Method in class org.mulinlab.varnote.operations.readers.db.VannoReader.SROBListRead

getBlockAddress() - Method in class org.mulinlab.varnote.utils.block.BlockFeature

getBlockAddress(long) - Static method in class org.mulinlab.varnote.utils.gz.BlockCompressedFilePointerUtil

getBlockFeature() - Method in class org.mulinlab.varnote.utils.block.SROB

getBlockOffset() - Method in class org.mulinlab.varnote.operations.index.IndexWriter.BlockBean

getBlockOffset() - Method in class org.mulinlab.varnote.operations.index.IndexWriter.SROBListBean

getBlockOffset() - Method in class org.mulinlab.varnote.utils.block.BlockFeature.VannoFeature

getBlockOffset(long) - Static method in class org.mulinlab.varnote.utils.gz.BlockCompressedFilePointerUtil

getBlockSize100k() - Method in class org.mulinlab.varnote.utils.stream.AdvancedBZip2CompressorInputStream

getBytesRead() - Method in class org.mulinlab.varnote.utils.stream.CompressorInputStream

Returns the current number of bytes read from this stream.

getC() - Method in enum org.mulinlab.varnote.utils.enumset.Delimiter

getCellTypeIdx() - Method in enum org.mulinlab.varnote.utils.enumset.RegFunc

getChromosome() - Method in interface org.mulinlab.varnote.utils.jannovar.ChromosomalRegion

getChromosome() - Method in class org.mulinlab.varnote.utils.jannovar.RegulatoryFeature

getChromosome() - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation

getChromosome() - Method in interface org.mulinlab.varnote.utils.jannovar.VariantCoordinates

getChromosomeName() - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation

getChromosomeName() - Method in interface org.mulinlab.varnote.utils.jannovar.VariantCoordinates

getChromosomes() - Method in class org.mulinlab.varnote.utils.database.index.Index

return the chromosomes in that tabix file

getCodec() - Method in class org.mulinlab.varnote.config.anno.databse.VCFParser

getCol(String) - Method in class org.mulinlab.varnote.utils.format.Format

getCols() - Method in class org.mulinlab.varnote.config.param.postDB.DBAnnoParam

getColToExtract() - Method in class org.mulinlab.varnote.config.anno.databse.anno.ExtractConfig

getColumnName(int) - Method in class org.mulinlab.varnote.utils.format.Format

getColumnNames() - Method in class org.mulinlab.varnote.utils.database.index.Index

getColumnNames() - Method in class org.mulinlab.varnote.utils.database.index.TbiIndex

getColumnNames() - Method in class org.mulinlab.varnote.utils.database.index.vannoIndex.VannoIndex

getCommandLineParser() - Method in class org.mulinlab.varnote.cmdline.abstractclass.CMDProgram

getComment(String, String) - Method in class org.mulinlab.varnote.config.run.OverlapRunConfig

getCommentIndicator() - Method in class org.mulinlab.varnote.config.param.postDB.PostDBParam

getCommentIndicator() - Method in class org.mulinlab.varnote.utils.format.Format

getConfig() - Method in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

getConfig() - Method in class org.mulinlab.varnote.utils.database.Database

getContig() - Method in class org.mulinlab.varnote.utils.node.LocFeature

getCoordAlleleFormat() - Static method in class org.mulinlab.varnote.utils.VannoUtils

getCoordOnlyFormat() - Static method in class org.mulinlab.varnote.utils.VannoUtils

getCount() - Method in class org.mulinlab.varnote.config.run.CountRunConfig

getCount() - Method in class org.mulinlab.varnote.filters.iterator.LineFilterIterator

getCount() - Method in class org.mulinlab.varnote.filters.query.gt.ABGenotypeFilter

getCount() - Method in interface org.mulinlab.varnote.filters.query.gt.GenotypeFilter

getCount() - Method in interface org.mulinlab.varnote.filters.query.VariantFilter

getCount() - Method in class org.mulinlab.varnote.filters.query.vc.ABVariantFilter

getCount() - Method in class org.mulinlab.varnote.filters.RegionFilter

getCount() - Method in class org.mulinlab.varnote.operations.mapper.AbstractMapper

getCount() - Method in class org.mulinlab.varnote.utils.stream.CompressorInputStream

Deprecated.

this method may yield wrong results for large archives, use #getBytesRead instead

getCount() - Method in class org.mulinlab.varnote.utils.TimeMetric

getCountReducer() - Static method in class org.mulinlab.varnote.utils.ReducerFactory

getCStr() - Method in enum org.mulinlab.varnote.utils.enumset.Delimiter

getCtxValArr(VariantContext) - Method in class org.mulinlab.varnote.filters.query.vc.ABVariantFilter

getData() - Method in class org.mulinlab.varnote.utils.JannovarUtils

getDatabses() - Method in class org.mulinlab.varnote.config.run.RunConfig

getDataStr() - Method in class org.mulinlab.varnote.utils.format.Format

getDb() - Method in class org.mulinlab.varnote.config.anno.databse.anno.ExtractConfig

getDb() - Method in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

getDb() - Method in class org.mulinlab.varnote.utils.database.Database

getDbIndexPath() - Method in class org.mulinlab.varnote.utils.database.Database

getDBList() - Method in class org.mulinlab.varnote.cmdline.collection.DBArgumentCollection

getDBNames() - Method in class org.mulinlab.varnote.config.run.CountRunConfig

getDBParam() - Method in class org.mulinlab.varnote.cmdline.collection.TagArgument

getDbParams() - Method in class org.mulinlab.varnote.config.run.RunConfig

getDbParesers() - Method in class org.mulinlab.varnote.config.parser.AnnoParser

getDbPath() - Method in class org.mulinlab.varnote.config.param.DBParam

getDbPath() - Method in class org.mulinlab.varnote.utils.database.Database

getDefaultCompressionLevel() - Static method in class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

getDefaultDeflaterFactory() - Static method in class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

getDefaultLocCodec(Format, boolean, VCFHeader) - Static method in class org.mulinlab.varnote.utils.VannoUtils

getDefaultName(String) - Method in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

getDelimChar() - Method in class org.mulinlab.varnote.utils.format.Format

getDelimiter() - Method in class org.mulinlab.varnote.utils.format.Format

getDelimStr() - Method in class org.mulinlab.varnote.utils.format.Format

getDescription() - Method in class org.mulinlab.varnote.cmdline.programgroups.AnnoProgramGroup

getDescription() - Method in class org.mulinlab.varnote.cmdline.programgroups.ConfigProgramGroup

getDescription() - Method in class org.mulinlab.varnote.cmdline.programgroups.IndexProgramGroup

getDescription() - Method in class org.mulinlab.varnote.cmdline.programgroups.QueryProgramGroup

getDisplayNameForToolClass(Class<?>) - Static method in class org.mulinlab.varnote.cmdline.VarNoteCommandLine

getDisplaySummaryForTool(Class<?>, CommandLineProgramProperties) - Static method in class org.mulinlab.varnote.cmdline.VarNoteCommandLine

getDistanceFromNearestGene() - Method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation

getEnd(BlockCompressedInputStream, int) - Method in class org.mulinlab.varnote.utils.block.BlockFeature

getEnd() - Method in class org.mulinlab.varnote.utils.block.BlockFeature.VannoFeature

getEnd() - Method in class org.mulinlab.varnote.utils.block.SROB.Feature

getEnd() - Method in interface org.mulinlab.varnote.utils.jannovar.ChromosomalRegion

getEnd() - Method in class org.mulinlab.varnote.utils.jannovar.RegulatoryFeature

getEnd() - Method in class org.mulinlab.varnote.utils.node.LocFeature

getExt() - Method in enum org.mulinlab.varnote.utils.enumset.IndexType

getExtension(VannoUtils.FileExt, String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

getExtIndex() - Method in enum org.mulinlab.varnote.utils.enumset.IndexType

getFamilyId() - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual

getFatherId() - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual

getFcount() - Method in class org.mulinlab.varnote.filters.iterator.LineFilterIterator

getFeatureInAlt(LocFeature, LocFeature[]) - Static method in class org.mulinlab.varnote.utils.VannoUtils

getFeatureMatchRefAndAlt(LocFeature, LocFeature[]) - Static method in class org.mulinlab.varnote.utils.VannoUtils

getFeaturesMatchRefAndAltList(LocFeature, LocFeature[]) - Static method in class org.mulinlab.varnote.utils.VannoUtils

getFeatureType() - Method in class org.mulinlab.varnote.utils.jannovar.RegulatoryFeature

getFieldName(int) - Method in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

getFieldName() - Method in class org.mulinlab.varnote.config.anno.FieldFormat

getFields() - Method in class org.mulinlab.varnote.config.param.postDB.DBAnnoParam

getFieldValWithFormat(String) - Method in class org.mulinlab.varnote.config.anno.FieldFormat

getFile() - Method in class org.mulinlab.varnote.config.io.temp.ThreadPrintter

getFileName() - Method in class org.mulinlab.varnote.config.anno.NormalField

getFileName() - Method in class org.mulinlab.varnote.utils.stream.BZIP2InputStream

getFilePath() - Method in class org.mulinlab.varnote.operations.readers.itf.BGZReader

getFilePath() - Method in class org.mulinlab.varnote.operations.readers.itf.GZIPReader

getFilePath() - Method in class org.mulinlab.varnote.operations.readers.itf.LongLineReader

getFilePath() - Method in interface org.mulinlab.varnote.operations.readers.itf.QueryReaderItf

getFilePath() - Method in class org.mulinlab.varnote.operations.readers.itf.thread.GZIPThreadReader

getFilePath() - Method in class org.mulinlab.varnote.operations.readers.itf.thread.SpiderReader

getFilePath() - Method in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

getFilePath() - Method in class org.mulinlab.varnote.utils.stream.BZIP2InputStream.Spider

getFilePath() - Method in class org.mulinlab.varnote.utils.stream.GZInputStream.GZReader

getFilePointer() - Method in class org.mulinlab.varnote.operations.index.IndexWriter.BlockBean

getFilePointer() - Method in class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

Encode virtual file pointer Upper 48 bits is the byte offset into the compressed stream of a block.

getFileType() - Method in class org.mulinlab.varnote.config.param.query.QueryFileParam

getFileType() - Method in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

getFilterChrCount() - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceFilter

getFilterCompatibleCount() - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceFilter

getFilterCount() - Method in class org.mulinlab.varnote.filters.query.gt.ABGenotypeFilter

getFilterIterator() - Method in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

getFilterIterator() - Method in class org.mulinlab.varnote.operations.readers.query.BEDFileReader

getFilterIterator() - Method in class org.mulinlab.varnote.operations.readers.query.TABFileReader

getFilterIterator() - Method in class org.mulinlab.varnote.operations.readers.query.VCFFileReader

getFilterParam() - Method in class org.mulinlab.varnote.operations.readers.query.VCFFileReader

getFlag(int) - Method in class org.mulinlab.varnote.operations.index.IndexWriter

getFlags() - Method in class org.mulinlab.varnote.utils.format.Format

getFormat() - Method in class org.mulinlab.varnote.cmdline.abstractclass.QueryFileProgram

getFormat(String, boolean) - Method in class org.mulinlab.varnote.cmdline.collection.InputFileArgumentCollection

getFormat(boolean) - Method in class org.mulinlab.varnote.cmdline.collection.TagArgument

getFormat() - Method in class org.mulinlab.varnote.cmdline.tools.Count

getFormat() - Method in class org.mulinlab.varnote.config.anno.databse.anno.ExtractConfig

getFormat() - Method in class org.mulinlab.varnote.config.param.IndexParam

getFormat() - Method in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

getFormat() - Method in class org.mulinlab.varnote.utils.database.Database

getFormat() - Method in class org.mulinlab.varnote.utils.database.index.Index

getGeneId() - Method in interface org.mulinlab.varnote.utils.jannovar.Variant

getGeneId() - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation

getGeneList(List<String>) - Method in class org.mulinlab.varnote.utils.JannovarUtils

getGeneSymbol() - Method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation

getGeneSymbol() - Method in interface org.mulinlab.varnote.utils.jannovar.Variant

getGeneSymbol() - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation

getGenome() - Method in class org.mulinlab.varnote.utils.JannovarUtils

getGenomeAssembly() - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation

getGenomeAssembly() - Method in interface org.mulinlab.varnote.utils.jannovar.VariantCoordinates

getGenotypeFilters() - Method in class org.mulinlab.varnote.config.param.FilterParam

getGzOut() - Method in class org.mulinlab.varnote.config.io.PrintGZ

getHeader(StringJoiner) - Method in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

getHeader(StringJoiner) - Method in class org.mulinlab.varnote.config.anno.databse.anno.DatabaseAnnoVCFParser

getHeader() - Method in class org.mulinlab.varnote.config.parser.AnnoParser

getHeader() - Method in class org.mulinlab.varnote.config.run.AnnoRunConfig

getHeader() - Method in class org.mulinlab.varnote.config.run.CountRunConfig

getHeader() - Method in class org.mulinlab.varnote.config.run.OverlapRunConfig

getHeader() - Method in class org.mulinlab.varnote.config.run.QueryRegionConfig

getHeader() - Method in class org.mulinlab.varnote.config.run.RunConfig

getHeader() - Method in class org.mulinlab.varnote.operations.readers.query.VCFFileReader

getHeaderList() - Method in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

getHeaderList() - Method in class org.mulinlab.varnote.config.anno.databse.anno.DatabaseAnnoVCFParser

getHeaderPart() - Method in class org.mulinlab.varnote.utils.format.Format

getHeaderPartSize() - Method in class org.mulinlab.varnote.utils.format.Format

getHeaderPartStr() - Method in class org.mulinlab.varnote.utils.format.Format

getHeaderPath() - Method in class org.mulinlab.varnote.config.param.postDB.PostDBParam

getHeaderPath() - Method in class org.mulinlab.varnote.utils.format.Format

getHeaderStart() - Method in class org.mulinlab.varnote.utils.format.Format

getHeaderStr() - Method in class org.mulinlab.varnote.utils.format.Format

getHgvsCdna() - Method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation

getHgvsGenomic() - Method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation

getHgvsProtein() - Method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation

getId() - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual

getIdentifiers() - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree

getIdx() - Method in class org.mulinlab.varnote.utils.database.TbiDatabase

getIndex() - Method in class org.mulinlab.varnote.config.index.IndexWriteConfig

getIndex() - Method in class org.mulinlab.varnote.config.io.temp.ThreadPrintter

getIndex() - Method in class org.mulinlab.varnote.utils.database.Database

getIndex() - Method in enum org.mulinlab.varnote.utils.enumset.PredictionFunc

getIndex() - Method in class org.mulinlab.varnote.utils.gz.BGZReader

getIndexParam() - Method in class org.mulinlab.varnote.config.index.IndexWriteConfig

getIndexType() - Method in class org.mulinlab.varnote.config.param.DBParam

getIndividualById(String) - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree

getIndividuals() - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree

getInfofieldOps() - Method in class org.mulinlab.varnote.config.param.postDB.DBFilterParam

getInfofields() - Method in class org.mulinlab.varnote.config.param.postDB.DBAnnoParam

getInfoFiledToExtract() - Method in class org.mulinlab.varnote.config.anno.databse.anno.ExtractConfig

getInfoForField(String) - Method in class org.mulinlab.varnote.config.anno.databse.anno.ExtractConfig

getInfoHeaderLine(String) - Method in class org.mulinlab.varnote.config.anno.databse.VCFParser

getInfoKeys() - Method in class org.mulinlab.varnote.config.anno.databse.VCFParser

getInfoKeys() - Method in class org.mulinlab.varnote.operations.readers.query.VCFFileReader

getInfoOutputName(String) - Method in class org.mulinlab.varnote.config.anno.databse.anno.ExtractConfig

getInput() - Method in class org.mulinlab.varnote.config.param.IndexParam

getInputFileName() - Method in class org.mulinlab.varnote.config.param.IndexParam

getInputStream() - Method in class org.mulinlab.varnote.utils.stream.ByteInputStream

getIntersect() - Method in class org.mulinlab.varnote.config.param.DBParam

getIs() - Method in class org.mulinlab.varnote.utils.database.index.Index

getIt() - Method in class org.mulinlab.varnote.operations.stack.AbstractReaderStack

getJannovarUtils(String) - Method in class org.mulinlab.varnote.cmdline.collection.VariantEffectArgumentCollection

getLabel() - Method in class org.mulinlab.varnote.config.anno.databse.anno.ExtractConfig

getLabel() - Method in class org.mulinlab.varnote.config.param.postDB.PostDBParam

getLabel() - Method in enum org.mulinlab.varnote.utils.enumset.PredictionFunc

getLabel() - Method in enum org.mulinlab.varnote.utils.enumset.RegFunc

getLine() - Method in class org.mulinlab.varnote.filters.iterator.LineFilterIterator

getLoccodec() - Method in class org.mulinlab.varnote.operations.readers.query.VCFFileReader

getLocCodec() - Method in class org.mulinlab.varnote.utils.database.Database

getLocFilters() - Method in class org.mulinlab.varnote.config.param.query.QueryFileParam

getLocFilters() - Method in class org.mulinlab.varnote.filters.iterator.LocFilterIterator

getLog() - Method in class org.mulinlab.varnote.filters.query.gt.ABGenotypeFilter

getLog() - Method in interface org.mulinlab.varnote.filters.query.gt.GenotypeFilter

getLogs() - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceFilter

getLogs() - Method in interface org.mulinlab.varnote.filters.query.VariantFilter

getLogs() - Method in class org.mulinlab.varnote.filters.query.vc.ABVariantFilter

getLogs() - Method in class org.mulinlab.varnote.filters.RegionFilter

getLongEnd() - Method in class org.mulinlab.varnote.utils.stream.BZIP2InputStream.Spider

getLongStart() - Method in class org.mulinlab.varnote.utils.stream.BZIP2InputStream.Spider

getLvCount() - Method in class org.mulinlab.varnote.operations.mapper.AbstractMapper

getLvCount() - Method in class org.mulinlab.varnote.utils.TimeMetric

getMapValue() - Method in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

getMapValue() - Method in class org.mulinlab.varnote.config.anno.databse.anno.DatabaseAnnoVCFParser

getMax() - Method in class org.mulinlab.varnote.utils.block.SROB

getMaxVariantLength() - Method in class org.mulinlab.varnote.cmdline.collection.RunArgumentCollection

getMaxVariantLength() - Method in class org.mulinlab.varnote.utils.format.Format

getmChr2tid() - Method in class org.mulinlab.varnote.utils.database.index.Index

getMendelianInheritanceFilter(ModeOfInheritance, Pedigree) - Static method in enum org.mulinlab.varnote.utils.enumset.ModeOfInheritance

getMergeReducer(RunConfig) - Static method in class org.mulinlab.varnote.utils.ReducerFactory

getMiFilter() - Method in class org.mulinlab.varnote.config.param.FilterParam

getMin(int) - Method in class org.mulinlab.varnote.operations.readers.db.VannoReader.SROBListRead

getMin() - Method in class org.mulinlab.varnote.utils.block.SROB

getmIndex() - Method in class org.mulinlab.varnote.utils.database.index.TbiIndex

getMinOffForChr(int) - Method in class org.mulinlab.varnote.utils.database.index.Index

getMinOffForChr() - Method in class org.mulinlab.varnote.utils.database.index.Index

getmMeta() - Method in class org.mulinlab.varnote.utils.database.index.Index

getMode() - Method in class org.mulinlab.varnote.config.param.RunParam

getMode() - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceFilter

getMotherId() - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual

getmSeq() - Method in class org.mulinlab.varnote.utils.database.index.Index

getmSeqLen() - Method in class org.mulinlab.varnote.utils.database.index.Index

getName() - Method in class org.mulinlab.varnote.cmdline.programgroups.AnnoProgramGroup

getName() - Method in class org.mulinlab.varnote.cmdline.programgroups.ConfigProgramGroup

getName() - Method in class org.mulinlab.varnote.cmdline.programgroups.IndexProgramGroup

getName() - Method in class org.mulinlab.varnote.cmdline.programgroups.QueryProgramGroup

getName() - Method in class org.mulinlab.varnote.filters.query.gt.ABGenotypeFilter

getName() - Method in interface org.mulinlab.varnote.filters.query.gt.GenotypeFilter

getName() - Method in interface org.mulinlab.varnote.filters.query.VariantFilter

getName() - Method in class org.mulinlab.varnote.filters.query.vc.ABVariantFilter

getName() - Method in class org.mulinlab.varnote.filters.RegionFilter

getName() - Method in enum org.mulinlab.varnote.utils.enumset.GenotypeQC

getName() - Method in enum org.mulinlab.varnote.utils.enumset.IndexType

getName() - Method in enum org.mulinlab.varnote.utils.enumset.IntersectType

getName() - Method in enum org.mulinlab.varnote.utils.enumset.VairantQC

getName() - Method in class org.mulinlab.varnote.utils.jannovar.Gene

getName() - Method in class org.mulinlab.varnote.utils.jannovar.GeneBuilder

getName(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

getNonGZWriter() - Method in class org.mulinlab.varnote.config.io.PrintGZ

getNullReducer() - Static method in class org.mulinlab.varnote.utils.ReducerFactory

getNum() - Method in enum org.mulinlab.varnote.utils.enumset.GenomicRegionType

getNum() - Method in enum org.mulinlab.varnote.utils.enumset.Mode

getNum() - Method in enum org.mulinlab.varnote.utils.enumset.OutMode

getNum() - Method in enum org.mulinlab.varnote.utils.enumset.Priority

getNum() - Method in enum org.mulinlab.varnote.utils.enumset.Snp2PosMode

getOffset() - Method in class org.mulinlab.varnote.utils.block.SROB.Feature

getOffsetMin(int) - Method in class org.mulinlab.varnote.operations.index.IndexWriter.SROBListBean

getOrigStr(LocFeature) - Method in class org.mulinlab.varnote.config.run.OverlapRunConfig

getOrigStr() - Method in class org.mulinlab.varnote.utils.node.LocFeature

getOut() - Method in class org.mulinlab.varnote.utils.gz.MyEndianOutputStream

getOutFormat() - Method in class org.mulinlab.varnote.config.parser.AnnoParser

getOutName() - Method in class org.mulinlab.varnote.config.param.DBParam

getOutName() - Method in class org.mulinlab.varnote.utils.database.Database

getOutNames() - Method in class org.mulinlab.varnote.config.param.postDB.DBAnnoParam

getOutParam(OutParam) - Method in class org.mulinlab.varnote.cmdline.collection.AnnoOutputArgumentCollection

getOutParam(OutParam) - Method in class org.mulinlab.varnote.cmdline.collection.OutputArgumentCollection

getOutParam() - Method in class org.mulinlab.varnote.config.run.RunConfig

getOutputDir() - Method in class org.mulinlab.varnote.config.param.IndexParam

getOutputMode() - Method in class org.mulinlab.varnote.config.param.output.IntersetOutParam

getOutputName(Integer) - Method in class org.mulinlab.varnote.config.anno.databse.anno.ExtractConfig

getOutputName() - Method in class org.mulinlab.varnote.config.param.output.OutParam

getOutputPath() - Method in class org.mulinlab.varnote.config.param.output.OutParam

getOverlapFile() - Method in class org.mulinlab.varnote.config.run.AnnoRunConfig

getPackageList() - Static method in class org.mulinlab.varnote.cmdline.VarNoteCommandLine

getPedigree() - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceFilter

getPos() - Method in class org.mulinlab.varnote.utils.jannovar.AllelePosition

getPosition() - Method in class org.mulinlab.varnote.filters.iterator.LineFilterIterator

getPosition() - Method in class org.mulinlab.varnote.filters.iterator.NoFilterIterator

getPosition() - Method in class org.mulinlab.varnote.operations.readers.itf.BGZReader

getPosition() - Method in class org.mulinlab.varnote.operations.readers.itf.GZIPReader

getPosition() - Method in class org.mulinlab.varnote.operations.readers.itf.LongLineReader

getPosition() - Method in interface org.mulinlab.varnote.operations.readers.itf.QueryReaderItf

getPosition() - Method in class org.mulinlab.varnote.operations.readers.itf.thread.GZIPThreadReader

getPosition() - Method in class org.mulinlab.varnote.operations.readers.itf.thread.SpiderReader

getPosition() - Method in class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

getPosition() - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation

getPosition() - Method in interface org.mulinlab.varnote.utils.jannovar.VariantCoordinates

getPrintter(int) - Method in class org.mulinlab.varnote.config.io.temp.Printter

getProcess() - Method in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

getProgramProperty(Class) - Static method in class org.mulinlab.varnote.cmdline.VarNoteCommandLine

getQuery(Mode, List<Database>, boolean) - Static method in class org.mulinlab.varnote.utils.VannoUtils

getQueryFilePath() - Method in class org.mulinlab.varnote.cmdline.abstractclass.QueryFileProgram

getQueryFilePath() - Method in class org.mulinlab.varnote.cmdline.collection.InputFileArgumentCollection

getQueryFilePath() - Method in class org.mulinlab.varnote.cmdline.tools.Count

getQueryFormat() - Method in class org.mulinlab.varnote.config.param.query.QueryFileParam

getQueryForThread() - Method in class org.mulinlab.varnote.operations.mapper.AbstractMapper

getQueryForThread() - Method in class org.mulinlab.varnote.operations.mapper.AnnoMapper

getQueryForThread() - Method in class org.mulinlab.varnote.operations.mapper.CounterMapper

getQueryForThread() - Method in class org.mulinlab.varnote.operations.mapper.IntersetMapper

getQueryName() - Method in class org.mulinlab.varnote.config.param.query.QueryFileParam

getQueryParam() - Method in class org.mulinlab.varnote.config.run.RunConfig

getQueryParser() - Method in class org.mulinlab.varnote.config.parser.AnnoParser

getQueryPath() - Method in class org.mulinlab.varnote.config.param.query.QueryFileParam

getQueryRegion() - Method in class org.mulinlab.varnote.config.run.QueryRegionConfig

getQuickFormat(QuickFileType) - Static method in class org.mulinlab.varnote.utils.VannoUtils

getReader(QueryReaderItf) - Method in class org.mulinlab.varnote.config.param.query.QueryFileParam

getReader(String) - Static method in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

getReader(String, FileType) - Static method in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

getReader(int) - Method in class org.mulinlab.varnote.utils.stream.GZInputStream

getReader(String, FileType, Format) - Static method in class org.mulinlab.varnote.utils.VannoUtils

getReader(QueryReaderItf, Format) - Static method in class org.mulinlab.varnote.utils.VannoUtils

getRef() - Method in class org.mulinlab.varnote.utils.jannovar.AllelePosition

getRef() - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation

getRef() - Method in interface org.mulinlab.varnote.utils.jannovar.VariantCoordinates

getRefDict() - Method in class org.mulinlab.varnote.utils.jannovar.Gene

getRegion() - Method in class org.mulinlab.varnote.config.param.query.QueryRegionParam

getRegion() - Method in class org.mulinlab.varnote.utils.jannovar.Gene

getRegionFilter() - Method in class org.mulinlab.varnote.config.param.FilterParam

getRegionsContainingVariant(VariantCoordinates) - Method in class org.mulinlab.varnote.utils.jannovar.ChromosomalRegionIndex

getRegionsOverlappingPosition(int, int) - Method in class org.mulinlab.varnote.utils.jannovar.ChromosomalRegionIndex

Use one-based co-ordinates for this method.

getREMMList(LocFeature, int) - Static method in class org.mulinlab.varnote.utils.VannoUtils

getResult() - Method in class org.mulinlab.varnote.config.parser.output.AnnoOut

getResult() - Method in class org.mulinlab.varnote.operations.mapper.AnnoMapper

getResult() - Method in class org.mulinlab.varnote.operations.mapper.CounterMapper

getResult() - Method in class org.mulinlab.varnote.operations.mapper.IntersetMapper

getResult() - Method in class org.mulinlab.varnote.operations.process.CountResultProcess

getResult() - Method in interface org.mulinlab.varnote.operations.process.ProcessResult

getResult() - Method in class org.mulinlab.varnote.operations.process.TabixResultProcess

getResult() - Method in class org.mulinlab.varnote.operations.process.VannoResultProcess

getResult() - Method in interface org.mulinlab.varnote.utils.mapreduce.Mapper

getResult() - Method in interface org.mulinlab.varnote.utils.mapreduce.MapReduce

getResult() - Method in class org.mulinlab.varnote.utils.mapreduce.SimpleMapReduce

getResultCount() - Method in class org.mulinlab.varnote.operations.query.AbstractQuery

getResultCount() - Method in interface org.mulinlab.varnote.operations.query.Query

getResultFeatures() - Method in class org.mulinlab.varnote.operations.query.AbstractQuery

getResultFeatures() - Method in interface org.mulinlab.varnote.operations.query.Query

getResultProcessor() - Method in class org.mulinlab.varnote.operations.stack.AbstractReaderStack

getResults() - Method in class org.mulinlab.varnote.operations.query.AbstractQuery

getResults() - Method in interface org.mulinlab.varnote.operations.query.Query

getResults() - Method in class org.mulinlab.varnote.operations.query.TabixQuery

getResults() - Method in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

getResultSize() - Method in class org.mulinlab.varnote.operations.process.CountResultProcess

getResultSize() - Method in interface org.mulinlab.varnote.operations.process.ProcessResult

getResultSize() - Method in class org.mulinlab.varnote.operations.process.TabixResultProcess

getResultSize() - Method in class org.mulinlab.varnote.operations.process.VannoResultProcess

getResultSize() - Method in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

getRsid() - Method in class org.mulinlab.varnote.config.parser.output.ADOutFeature

getRsid2POSFormat() - Static method in class org.mulinlab.varnote.utils.VannoUtils

getRunParam() - Method in class org.mulinlab.varnote.config.run.RunConfig

getScoreIdx() - Method in enum org.mulinlab.varnote.utils.enumset.RegFunc

getSerPath(String) - Static method in class org.mulinlab.varnote.utils.JannovarUtils

getSex() - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual

getSource() - Method in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

return the source (filename/URL) of that reader

getStart() - Method in interface org.mulinlab.varnote.utils.jannovar.ChromosomalRegion

getStart() - Method in class org.mulinlab.varnote.utils.jannovar.RegulatoryFeature

getStart() - Method in class org.mulinlab.varnote.utils.node.LocFeature

getStatus() - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual

getStr() - Method in class org.mulinlab.varnote.config.anno.ValWithAllele

getString() - Method in class org.mulinlab.varnote.filters.iterator.NoFilterIterator

getStrWithAllele() - Method in class org.mulinlab.varnote.config.anno.ValWithAllele

getStrWithAllele(String) - Method in class org.mulinlab.varnote.config.anno.ValWithAllele

getSuffix() - Method in enum org.mulinlab.varnote.utils.VannoUtils.FileExt

getTag() - Method in class org.mulinlab.varnote.cmdline.collection.TagArgument

getTagAttributes() - Method in class org.mulinlab.varnote.cmdline.collection.TagArgument

getThread() - Method in class org.mulinlab.varnote.config.param.RunParam

getThread() - Method in class org.mulinlab.varnote.config.run.RunConfig

getThreadNum() - Method in class org.mulinlab.varnote.utils.stream.BZIP2InputStream

getThreadReader(int) - Method in class org.mulinlab.varnote.config.param.query.QueryFileParam

getThreads() - Method in class org.mulinlab.varnote.cmdline.collection.RunArgumentCollection

getThreadSize() - Method in class org.mulinlab.varnote.config.param.query.QueryFileParam

getTranscriptAnnotations() - Method in interface org.mulinlab.varnote.utils.jannovar.Variant

getTranscriptAnnotations() - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation

getTranscripts() - Method in class org.mulinlab.varnote.utils.jannovar.Gene

getType() - Method in enum org.mulinlab.varnote.utils.enumset.RegFunc

getType() - Method in class org.mulinlab.varnote.utils.format.Format

getUnaffectedNames() - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceXRFilter

getUncompresedSize(File) - Method in class org.mulinlab.varnote.utils.stream.GZInputStream

getUsage() - Method in class org.mulinlab.varnote.cmdline.abstractclass.CMDProgram

getVal() - Method in class org.mulinlab.varnote.config.anno.NormalField

getVal() - Method in enum org.mulinlab.varnote.utils.enumset.IntersectType

getVannoFile() - Method in class org.mulinlab.varnote.utils.database.VannoDatabase

getVannoFilePointer() - Method in class org.mulinlab.varnote.utils.block.SROB

getVariableName(String, int) - Method in class org.mulinlab.varnote.config.anno.FieldFormat

getVariantEffect() - Method in class org.mulinlab.varnote.utils.jannovar.RegulatoryFeature

getVariantEffect() - Method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation

getVariantEffect() - Method in interface org.mulinlab.varnote.utils.jannovar.Variant

getVariantEffect() - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation

getVariantFilters() - Method in class org.mulinlab.varnote.config.param.FilterParam

getVCFcodec() - Method in class org.mulinlab.varnote.operations.readers.query.VCFFileReader

getVCFFilterParamList() - Method in class org.mulinlab.varnote.config.param.query.QueryFileParam

getVcfHeader() - Method in class org.mulinlab.varnote.config.anno.databse.VCFParser

getVCFHeader() - Method in class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

getVCFHeader() - Method in class org.mulinlab.varnote.config.anno.query.QueryBEDParser

getVCFHeader() - Method in class org.mulinlab.varnote.config.anno.query.QueryVCFParser

getVcfHeaderPathForBED() - Method in class org.mulinlab.varnote.config.run.AnnoRunConfig

getVcfInfoPath() - Method in class org.mulinlab.varnote.config.param.postDB.DBAnnoParam

getVCFLikeFormat() - Static method in class org.mulinlab.varnote.utils.VannoUtils

getVcfParser() - Method in class org.mulinlab.varnote.operations.readers.query.VCFFileReader

getVcfParser() - Method in class org.mulinlab.varnote.utils.database.Database

getVersion() - Method in class org.mulinlab.varnote.cmdline.abstractclass.CMDProgram

getVersion() - Method in class org.mulinlab.varnote.utils.database.index.vannoIndex.VannoIndex

getWriter() - Method in class org.mulinlab.varnote.config.io.temp.ThreadPrintter

GlobalParameter - Class in org.mulinlab.varnote.constants

GlobalParameter() - Constructor for class org.mulinlab.varnote.constants.GlobalParameter

GT_BIN_INTERVAL - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

GT_CHR_END - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

GT_COMPRESS_FILE - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

GT_COMPRESS_FILE_IDX - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

GT_FILE_END - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

GT_IDX - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

GZInputStream - Class in org.mulinlab.varnote.utils.stream

GZInputStream(String, int) - Constructor for class org.mulinlab.varnote.utils.stream.GZInputStream

GZInputStream.GZReader - Class in org.mulinlab.varnote.utils.stream

GZIPReader - Class in org.mulinlab.varnote.operations.readers.itf

GZIPReader(String) - Constructor for class org.mulinlab.varnote.operations.readers.itf.GZIPReader

GZIPThreadReader - Class in org.mulinlab.varnote.operations.readers.itf.thread

GZIPThreadReader(GZInputStream.GZReader) - Constructor for class org.mulinlab.varnote.operations.readers.itf.thread.GZIPThreadReader

GZReader(long, long) - Constructor for class org.mulinlab.varnote.utils.stream.GZInputStream.GZReader

H

HAS_HEADER - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

HAS_HEADER - Static variable in class org.mulinlab.varnote.cmdline.txtreader.anno.AnnoConfigReader

hasExtension(VannoUtils.FileExt, String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

hasFeature() - Method in class org.mulinlab.varnote.utils.block.SROB

hashCode() - Method in class org.mulinlab.varnote.utils.jannovar.AllelePosition

hashCode() - Method in class org.mulinlab.varnote.utils.jannovar.ChromosomalRegionIndex

hashCode() - Method in class org.mulinlab.varnote.utils.jannovar.Gene

hashCode() - Method in class org.mulinlab.varnote.utils.jannovar.RegulatoryFeature

hashCode() - Method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation

hashCode() - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation

hashCode() - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree

hashCode() - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual

hasHeader - Variable in class org.mulinlab.varnote.cmdline.abstractclass.IndexProgram

hasHeader - Variable in class org.mulinlab.varnote.cmdline.collection.InputFileArgumentCollection

hasHeader - Variable in class org.mulinlab.varnote.config.param.postDB.PostDBParam

hasLoc() - Method in class org.mulinlab.varnote.utils.format.Format

hasNext() - Method in class org.mulinlab.varnote.filters.iterator.LineFilterIterator

hasNext() - Method in class org.mulinlab.varnote.filters.iterator.NoFilterIterator

hasPattern(String) - Static method in class org.mulinlab.varnote.utils.IOutils

hasRegionContainingPosition(int, int) - Method in class org.mulinlab.varnote.utils.jannovar.ChromosomalRegionIndex

hasRegionContainingVariant(VariantCoordinates) - Method in class org.mulinlab.varnote.utils.jannovar.ChromosomalRegionIndex

hasTranscriptAnnotations() - Method in interface org.mulinlab.varnote.utils.jannovar.Variant

hasTranscriptAnnotations() - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation

hasVariantEffect - Variable in class org.mulinlab.varnote.config.parser.output.ADOutFeature

HEADER - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

HEADER_PATH - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

HEADER_PATH - Static variable in class org.mulinlab.varnote.cmdline.txtreader.anno.AnnoConfigReader

HeaderFormatReader - Class in org.mulinlab.varnote.utils.headerparser

HeaderFormatReader() - Constructor for class org.mulinlab.varnote.utils.headerparser.HeaderFormatReader

HeaderLineFilter - Class in org.mulinlab.varnote.filters.query.line

HeaderLineFilter() - Constructor for class org.mulinlab.varnote.filters.query.line.HeaderLineFilter

headerParts - Variable in class org.mulinlab.varnote.utils.database.index.vannoIndex.VannoIndex

headerPath - Variable in class org.mulinlab.varnote.config.param.postDB.PostDBParam

help - Variable in class org.mulinlab.varnote.cmdline.abstractclass.CMDProgram

HELP_OPTION - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

HELP_OPTION_ABBR - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

HELP_SIMILARITY_FLOOR - Static variable in class org.mulinlab.varnote.cmdline.constant.CommandLineDefaults

hgvsCdna(String) - Method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation.Builder

hgvsGenomic(String) - Method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation.Builder

hgvsProtein(String) - Method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation.Builder

HYPHEN_CHAR - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

I

ID - Static variable in class org.mulinlab.varnote.cmdline.txtreader.anno.VcfInfoReader

id(String) - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual.Builder

idx - Variable in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

idxArr - Variable in class org.mulinlab.varnote.operations.readers.db.TbiReader

Index - Class in org.mulinlab.varnote.cmdline.index

Index() - Constructor for class org.mulinlab.varnote.cmdline.index.Index

index - Variable in class org.mulinlab.varnote.config.anno.NormalField

index - Variable in class org.mulinlab.varnote.config.io.temp.ThreadPrintter

index - Variable in class org.mulinlab.varnote.operations.mapper.AbstractMapper

index - Variable in class org.mulinlab.varnote.utils.database.Database

Index - Class in org.mulinlab.varnote.utils.database.index

Index(String, boolean) - Constructor for class org.mulinlab.varnote.utils.database.index.Index

Index(BlockCompressedInputStream) - Constructor for class org.mulinlab.varnote.utils.database.index.Index

INDEX_DOC - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INDEX_LIST_CHROM_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INDEX_LITS_CHROM_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INDEX_OUTPUT_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INDEX_OUTPUT_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INDEX_PRINT_FORMAT_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INDEX_PRINT_FORMAT_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INDEX_PRINT_HEADER_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INDEX_PRINT_HEADER_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INDEX_PRINT_META_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INDEX_PRINT_META_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INDEX_REPLACE_HEADER_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INDEX_REPLACE_HEADER_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

IndexArgumentCollection - Class in org.mulinlab.varnote.cmdline.collection

IndexArgumentCollection() - Constructor for class org.mulinlab.varnote.cmdline.collection.IndexArgumentCollection

indexArguments - Variable in class org.mulinlab.varnote.cmdline.index.IndexInfo

indexExtension() - Method in class org.mulinlab.varnote.utils.database.Database

indexExtension() - Method in class org.mulinlab.varnote.utils.database.TbiDatabase

indexExtension() - Method in class org.mulinlab.varnote.utils.database.VannoDatabase

IndexFactory - Class in org.mulinlab.varnote.utils.database.index

IndexFactory() - Constructor for class org.mulinlab.varnote.utils.database.index.IndexFactory

IndexInfo - Class in org.mulinlab.varnote.cmdline.index

IndexInfo() - Constructor for class org.mulinlab.varnote.cmdline.index.IndexInfo

IndexParam - Class in org.mulinlab.varnote.config.param

IndexParam(File) - Constructor for class org.mulinlab.varnote.config.param.IndexParam

IndexParam(File, String) - Constructor for class org.mulinlab.varnote.config.param.IndexParam

IndexParam(File, String, Format) - Constructor for class org.mulinlab.varnote.config.param.IndexParam

IndexProgram - Class in org.mulinlab.varnote.cmdline.abstractclass

IndexProgram() - Constructor for class org.mulinlab.varnote.cmdline.abstractclass.IndexProgram

IndexProgramGroup - Class in org.mulinlab.varnote.cmdline.programgroups

Tools that manipulate read data in SAM, BAM or CRAM format

IndexProgramGroup() - Constructor for class org.mulinlab.varnote.cmdline.programgroups.IndexProgramGroup

IndexType - Enum in org.mulinlab.varnote.utils.enumset

IndexWriteConfig - Class in org.mulinlab.varnote.config.index

IndexWriteConfig(IndexParam) - Constructor for class org.mulinlab.varnote.config.index.IndexWriteConfig

IndexWriter - Class in org.mulinlab.varnote.operations.index

IndexWriter(IndexParam) - Constructor for class org.mulinlab.varnote.operations.index.IndexWriter

IndexWriter.BlockBean - Class in org.mulinlab.varnote.operations.index

IndexWriter.SROBListBean - Class in org.mulinlab.varnote.operations.index

info(String) - Method in class org.mulinlab.varnote.utils.TimeMetric

INFO_COL - Static variable in class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

INFO_COL - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

INFO_EXT - Static variable in class org.mulinlab.varnote.config.anno.databse.anno.ExtractConfig

INFO_FIELD_SEPARATOR - Static variable in class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

INFO_FIELD_SEPARATOR - Static variable in class org.mulinlab.varnote.config.parser.AnnoParser

INFO_FIELD_SEPARATOR - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

INFO_FIELDS - Static variable in class org.mulinlab.varnote.cmdline.txtreader.anno.AnnoConfigReader

InfoField - Class in org.mulinlab.varnote.config.anno

InfoField(String, VCFInfoHeaderLine) - Constructor for class org.mulinlab.varnote.config.anno.InfoField

init() - Method in class org.mulinlab.varnote.cmdline.txtreader.anno.FormatReader

init() - Method in class org.mulinlab.varnote.cmdline.txtreader.anno.VcfInfoReader

init() - Method in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

init() - Method in class org.mulinlab.varnote.config.anno.databse.anno.DatabaseAnnoVCFParser

init(int, String[]) - Method in class org.mulinlab.varnote.config.anno.InfoField

init(int) - Method in class org.mulinlab.varnote.config.anno.NormalField

init() - Method in class org.mulinlab.varnote.config.index.IndexWriteConfig

init() - Method in class org.mulinlab.varnote.config.io.temp.Printter

init() - Method in class org.mulinlab.varnote.config.param.output.AnnoOutParam

init() - Method in class org.mulinlab.varnote.config.param.output.IntersetOutParam

init() - Method in class org.mulinlab.varnote.config.parser.AnnoParser

init() - Method in class org.mulinlab.varnote.config.run.RunConfig

init() - Method in class org.mulinlab.varnote.operations.index.IndexWriter.SROBListBean

init() - Method in class org.mulinlab.varnote.operations.query.AbstractQuery

init() - Method in class org.mulinlab.varnote.operations.query.SweepQuery

init() - Method in class org.mulinlab.varnote.operations.query.TabixQuery

init() - Method in class org.mulinlab.varnote.operations.query.VannoQuery

init() - Method in class org.mulinlab.varnote.operations.readers.db.VannoReader.SROBListRead

init(String) - Method in class org.mulinlab.varnote.utils.gz.BGZReader

init() - Method in class org.mulinlab.varnote.utils.stream.AdvancedBZip2CompressorInputStream

init0() - Method in class org.mulinlab.varnote.utils.stream.AdvancedBZip2CompressorInputStream

initChr() - Method in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

initDB() - Method in class org.mulinlab.varnote.config.run.AnnoRunConfig

initDB() - Method in class org.mulinlab.varnote.config.run.CountRunConfig

initDB() - Method in class org.mulinlab.varnote.config.run.OverlapRunConfig

initDB() - Method in class org.mulinlab.varnote.config.run.QueryRegionConfig

initDB() - Method in class org.mulinlab.varnote.config.run.RunConfig

initFields(LocFeature, int) - Method in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

initFields(LocFeature, int) - Method in class org.mulinlab.varnote.config.anno.databse.anno.DatabaseAnnoVCFParser

initForChr(int) - Method in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

initForChr(int) - Method in class org.mulinlab.varnote.operations.readers.db.TbiMixReader

initForChr(int) - Method in class org.mulinlab.varnote.operations.readers.db.TbiSweepReader

initForChr(int) - Method in class org.mulinlab.varnote.operations.readers.db.VannoMixReader

initForChr(int) - Method in class org.mulinlab.varnote.operations.readers.db.VannoReader

initForChr(int) - Method in class org.mulinlab.varnote.operations.readers.db.VannoSweepReader

initLineFilters() - Method in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

initLineFilters() - Method in class org.mulinlab.varnote.operations.readers.query.BEDFileReader

initLineFilters() - Method in class org.mulinlab.varnote.operations.readers.query.TABFileReader

initLineFilters() - Method in class org.mulinlab.varnote.operations.readers.query.VCFFileReader

initOther() - Method in class org.mulinlab.varnote.config.run.AnnoRunConfig

initOther() - Method in class org.mulinlab.varnote.config.run.CountRunConfig

initOther() - Method in class org.mulinlab.varnote.config.run.OverlapRunConfig

initOther() - Method in class org.mulinlab.varnote.config.run.QueryRegionConfig

initOther() - Method in class org.mulinlab.varnote.config.run.RunConfig

initOutput() - Method in class org.mulinlab.varnote.config.run.AnnoRunConfig

initOutput() - Method in class org.mulinlab.varnote.config.run.CountRunConfig

initOutput() - Method in class org.mulinlab.varnote.config.run.OverlapRunConfig

initOutput() - Method in class org.mulinlab.varnote.config.run.QueryRegionConfig

initOutput() - Method in class org.mulinlab.varnote.config.run.RunConfig

initParam() - Method in class org.mulinlab.varnote.config.anno.databse.anno.ExtractConfig

initPrintter() - Method in class org.mulinlab.varnote.config.run.CountRunConfig

initPrintter() - Method in class org.mulinlab.varnote.config.run.OverlapRunConfig

initPrintter(OutParam, int) - Method in class org.mulinlab.varnote.config.run.RunConfig

initQuery() - Method in class org.mulinlab.varnote.config.run.AnnoRunConfig

initQuery() - Method in class org.mulinlab.varnote.config.run.CountRunConfig

initQuery() - Method in class org.mulinlab.varnote.config.run.OverlapRunConfig

initQuery() - Method in class org.mulinlab.varnote.config.run.QueryRegionConfig

initQuery() - Method in class org.mulinlab.varnote.config.run.RunConfig

initQueryFileForThread() - Method in class org.mulinlab.varnote.config.run.RunConfig

initReader() - Method in class org.mulinlab.varnote.operations.readers.itf.BGZReader

initReader() - Method in class org.mulinlab.varnote.operations.readers.itf.GZIPReader

initReader() - Method in class org.mulinlab.varnote.operations.readers.itf.LongLineReader

initReader() - Method in interface org.mulinlab.varnote.operations.readers.itf.QueryReaderItf

initReader() - Method in class org.mulinlab.varnote.operations.readers.itf.thread.GZIPThreadReader

initReader() - Method in class org.mulinlab.varnote.operations.readers.itf.thread.SpiderReader

initReadersChr() - Method in class org.mulinlab.varnote.operations.query.AbstractQuery

initResult() - Method in class org.mulinlab.varnote.operations.process.CountResultProcess

initResult() - Method in interface org.mulinlab.varnote.operations.process.ProcessResult

initResult() - Method in class org.mulinlab.varnote.operations.process.TabixResultProcess

initResult() - Method in class org.mulinlab.varnote.operations.process.VannoResultProcess

initSROB(int, int, long, long) - Method in class org.mulinlab.varnote.utils.block.SROB

initStack(String, int, int, int) - Method in class org.mulinlab.varnote.operations.readers.db.TbiMixReader

INPUT_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INPUT_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

inputArguments - Variable in class org.mulinlab.varnote.cmdline.abstractclass.QueryFileProgram

inputArguments - Variable in class org.mulinlab.varnote.cmdline.tools.Count

InputFileArgumentCollection - Class in org.mulinlab.varnote.cmdline.collection

InputFileArgumentCollection() - Constructor for class org.mulinlab.varnote.cmdline.collection.InputFileArgumentCollection

INSERTION - Static variable in class org.mulinlab.varnote.utils.VannoUtils

instanceMain(String[]) - Method in class org.mulinlab.varnote.cmdline.abstractclass.CMDProgram

instanceMain(String[], List<String>, String) - Method in class org.mulinlab.varnote.cmdline.VarNoteCommandLine

instanceMain(String[]) - Method in class org.mulinlab.varnote.cmdline.VarNoteCommandLine

INT_START - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

Intersect - Class in org.mulinlab.varnote.cmdline.tools

Intersect() - Constructor for class org.mulinlab.varnote.cmdline.tools.Intersect

INTERSECT_COUNT_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INTERSECT_COUNT_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INTERSECT_ERROR - Static variable in class org.mulinlab.varnote.utils.VannoUtils

INTERSECT_INPUT_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INTERSECT_INPUT_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INTERSECT_LOJ_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INTERSECT_LOJ_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INTERSECT_OUT_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INTERSECT_OUT_MODE_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INTERSECT_OUT_MODE_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INTERSECT_OUT_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INTERSECT_RC_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INTERSECT_RC_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INTERSECT_THREAD_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INTERSECT_THREAD_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INTERSECT_ZIP_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

INTERSECT_ZIP_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

IntersectConfig - Class in org.mulinlab.varnote.cmdline.tools.config

IntersectConfig() - Constructor for class org.mulinlab.varnote.cmdline.tools.config.IntersectConfig

intersectFile - Variable in class org.mulinlab.varnote.cmdline.tools.AnnotationIntersectFile

IntersectRunReader<T> - Class in org.mulinlab.varnote.cmdline.txtreader.run

IntersectRunReader() - Constructor for class org.mulinlab.varnote.cmdline.txtreader.run.IntersectRunReader

IntersectType - Enum in org.mulinlab.varnote.utils.enumset

IntersetMapper - Class in org.mulinlab.varnote.operations.mapper

IntersetMapper(OverlapRunConfig, int) - Constructor for class org.mulinlab.varnote.operations.mapper.IntersetMapper

IntersetOutParam - Class in org.mulinlab.varnote.config.param.output

IntersetOutParam() - Constructor for class org.mulinlab.varnote.config.param.output.IntersetOutParam

IntersetOutParam(String) - Constructor for class org.mulinlab.varnote.config.param.output.IntersetOutParam

IntervalStack - Class in org.mulinlab.varnote.operations.stack

IntervalStack(ProcessResult) - Constructor for class org.mulinlab.varnote.operations.stack.IntervalStack

IntervalStackFC - Class in org.mulinlab.varnote.operations.stack

IntervalStackFC(ProcessResult) - Constructor for class org.mulinlab.varnote.operations.stack.IntervalStackFC

intv - Variable in class org.mulinlab.varnote.operations.decode.LocCodec

InvalidArgumentException - Exception in org.mulinlab.varnote.exceptions

InvalidArgumentException(String) - Constructor for exception org.mulinlab.varnote.exceptions.InvalidArgumentException

InvalidArgumentException() - Constructor for exception org.mulinlab.varnote.exceptions.InvalidArgumentException

InvalidArgumentException(Throwable) - Constructor for exception org.mulinlab.varnote.exceptions.InvalidArgumentException

InvalidGenomeAssemblyException() - Constructor for exception org.mulinlab.varnote.utils.enumset.GenomeAssembly.InvalidGenomeAssemblyException

InvalidGenomeAssemblyException(String) - Constructor for exception org.mulinlab.varnote.utils.enumset.GenomeAssembly.InvalidGenomeAssemblyException

InvalidGenomeAssemblyException(String, Throwable) - Constructor for exception org.mulinlab.varnote.utils.enumset.GenomeAssembly.InvalidGenomeAssemblyException

InvalidGenomeAssemblyException(Throwable) - Constructor for exception org.mulinlab.varnote.utils.enumset.GenomeAssembly.InvalidGenomeAssemblyException

InvalidGenomeAssemblyException(String, Throwable, boolean, boolean) - Constructor for exception org.mulinlab.varnote.utils.enumset.GenomeAssembly.InvalidGenomeAssemblyException

invalidRSID(String) - Method in class org.mulinlab.varnote.operations.decode.RSIDLocCodec

IOutils - Class in org.mulinlab.varnote.utils

IOutils() - Constructor for class org.mulinlab.varnote.utils.IOutils

is - Variable in class org.mulinlab.varnote.operations.readers.db.VannoReader.VannoIteratorImpl

is - Variable in class org.mulinlab.varnote.utils.database.index.Index

isAffected() - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual

isAllowLargeVariants() - Method in class org.mulinlab.varnote.utils.format.Format

isBlockChanged(long) - Method in class org.mulinlab.varnote.operations.index.IndexWriter.SROBListBean

isBlockStart - Variable in class org.mulinlab.varnote.operations.readers.db.VannoReader

isBreak(String) - Method in class org.mulinlab.varnote.cmdline.txtreader.abs.AbstractQueryReader

isBreak(String) - Method in interface org.mulinlab.varnote.cmdline.txtreader.abs.RunReaderInterface

isBreak(String) - Method in class org.mulinlab.varnote.cmdline.txtreader.anno.OverlapHeaderReader

isChromTypeMatch(ChromosomeType) - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceADFilter

isChromTypeMatch(ChromosomeType) - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceARFilter

isChromTypeMatch(ChromosomeType) - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceFilter

isChromTypeMatch(ChromosomeType) - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceXDFilter

isChromTypeMatch(ChromosomeType) - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceXRFilter

isCodingVariant() - Method in interface org.mulinlab.varnote.utils.jannovar.Variant

isCompatibleFamily(GenotypesContext) - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceADFilter

isCompatibleFamily(GenotypesContext) - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceARFilter

isCompatibleFamily(GenotypesContext) - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceFilter

isCompatibleFamily(GenotypesContext) - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceXDFilter

isCompatibleFamily(GenotypesContext) - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceXRFilter

isCompatibleSingleton(GenotypesContext) - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceADFilter

isCompatibleSingleton(GenotypesContext) - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceARFilter

isCompatibleSingleton(GenotypesContext) - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceFilter

isCompatibleSingleton(GenotypesContext) - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceXDFilter

isCompatibleSingleton(GenotypesContext) - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceXRFilter

isCount - Variable in class org.mulinlab.varnote.operations.query.AbstractQuery

isCount - Variable in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

isDecodeFull() - Method in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

isDeletion(String, String) - Static method in class org.mulinlab.varnote.utils.jannovar.AllelePosition

isDisplayLabel - Variable in class org.mulinlab.varnote.cmdline.tools.RandomAccess

isDisplayLabel() - Method in class org.mulinlab.varnote.config.run.QueryRegionConfig

isDominant() - Method in enum org.mulinlab.varnote.utils.enumset.ModeOfInheritance

isEmpty() - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree

isEmptyLine(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

isEnd - Variable in class org.mulinlab.varnote.operations.readers.db.VannoReader

iseof - Variable in class org.mulinlab.varnote.operations.readers.db.TbiReader.TbiIteratorImpl

iseof - Variable in class org.mulinlab.varnote.operations.readers.db.VannoReader.VannoIteratorImpl

iseof - Variable in class org.mulinlab.varnote.operations.stack.AbstractReaderStack

isExclude() - Method in enum org.mulinlab.varnote.utils.enumset.GenomicRegionType

isExist(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

isFiltered - Variable in class org.mulinlab.varnote.filters.iterator.LineFilterIterator

isFilterLine(LocFeature) - Method in interface org.mulinlab.varnote.config.anno.databse.filter.DatababseFilter

isFilterLine(LocFeature) - Method in class org.mulinlab.varnote.config.anno.databse.filter.DatabaseBEDFilter

isFilterLine(LocFeature) - Method in class org.mulinlab.varnote.config.anno.databse.filter.DatabaseVCFFilter

isFilterLine(String, GenotypesContext) - Method in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceFilter

isFilterLine(LocFeature, Genotype) - Method in class org.mulinlab.varnote.filters.query.gt.DepthFilter

isFilterLine(LocFeature, Genotype) - Method in interface org.mulinlab.varnote.filters.query.gt.GenotypeFilter

isFilterLine(LocFeature, Genotype) - Method in class org.mulinlab.varnote.filters.query.gt.GenotypeQualityFilter

isFilterLine(String) - Method in class org.mulinlab.varnote.filters.query.line.HeaderLineFilter

isFilterLine(String) - Method in interface org.mulinlab.varnote.filters.query.line.LineFilter

isFilterLine(String) - Method in class org.mulinlab.varnote.filters.query.line.SkipLineFilter

isFilterLine(T) - Method in interface org.mulinlab.varnote.filters.query.VariantFilter

isFilterLine(LocFeature) - Method in class org.mulinlab.varnote.filters.query.vc.QDFilter

isFilterLine(LocFeature) - Method in class org.mulinlab.varnote.filters.RegionFilter

isFlag() - Method in class org.mulinlab.varnote.config.anno.InfoField

isForceOverlap - Variable in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

isForceOverlap() - Method in class org.mulinlab.varnote.config.run.AnnoRunConfig

isFormatHasAllele() - Method in class org.mulinlab.varnote.config.anno.FieldFormat

isFull() - Method in class org.mulinlab.varnote.config.param.query.QueryFileParam

isFull - Variable in class org.mulinlab.varnote.operations.decode.LocCodec

isGene() - Method in enum org.mulinlab.varnote.utils.enumset.GenomicRegionType

isGZip - Variable in class org.mulinlab.varnote.cmdline.collection.OutputArgumentCollection

isGzip - Variable in class org.mulinlab.varnote.config.param.output.OutParam

isGzip() - Method in class org.mulinlab.varnote.config.param.output.OutParam

isHasHeader() - Method in class org.mulinlab.varnote.config.param.postDB.PostDBParam

isHasHeader() - Method in class org.mulinlab.varnote.utils.format.Format

isHeaderLine(String) - Method in class org.mulinlab.varnote.filters.query.line.BEDHeaderLineFilter

isHeaderLine(String) - Method in class org.mulinlab.varnote.filters.query.line.HeaderLineFilter

isHeaderLine(String) - Method in class org.mulinlab.varnote.filters.query.line.TABHeaderLineFilter

isHeaderLine(String) - Method in class org.mulinlab.varnote.filters.query.line.VCFHeaderLineFilter

isIndel(LocFeature) - Static method in class org.mulinlab.varnote.utils.VannoUtils

isIndel(String, String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

isIndexExsit() - Method in class org.mulinlab.varnote.utils.database.Database

isIndexExsit() - Method in class org.mulinlab.varnote.utils.database.TbiDatabase

isIndexExsit() - Method in class org.mulinlab.varnote.utils.database.VannoDatabase

isInsertion(String, String) - Static method in class org.mulinlab.varnote.utils.jannovar.AllelePosition

isLargeVariants(LocFeature) - Method in class org.mulinlab.varnote.operations.mapper.AbstractMapper

isLargeVariants(LocFeature) - Method in class org.mulinlab.varnote.operations.mapper.CounterMapper

islog - Variable in class org.mulinlab.varnote.cmdline.abstractclass.RunProgram

islog - Variable in class org.mulinlab.varnote.cmdline.tools.RandomAccess

isLOJ - Variable in class org.mulinlab.varnote.cmdline.collection.OutputArgumentCollection

isLoj() - Method in class org.mulinlab.varnote.config.param.output.OutParam

isLoj() - Method in class org.mulinlab.varnote.config.parser.AnnoParser

isMetaLine(String) - Method in class org.mulinlab.varnote.filters.query.line.BEDHeaderLineFilter

isMetaLine(String) - Method in class org.mulinlab.varnote.filters.query.line.HeaderLineFilter

isMetaLine(String) - Method in class org.mulinlab.varnote.filters.query.line.TABHeaderLineFilter

isMetaLine(String) - Method in class org.mulinlab.varnote.filters.query.line.VCFHeaderLineFilter

isNonCodingVariant() - Method in interface org.mulinlab.varnote.utils.jannovar.Variant

isNonCodingVariant(VariantEffect) - Static method in class org.mulinlab.varnote.utils.jannovar.VariantEffectUtility

isNotNull() - Method in class org.mulinlab.varnote.config.param.FilterParam

isOutFormatHasAllele() - Method in class org.mulinlab.varnote.config.anno.FieldFormat

isOverlap(LocFeature, LocFeature) - Method in class org.mulinlab.varnote.filters.RegionFilter

isPos() - Method in class org.mulinlab.varnote.utils.format.Format

isPrintInfo() - Method in class org.mulinlab.varnote.cmdline.collection.IndexArgumentCollection

isReadBlock() - Method in class org.mulinlab.varnote.utils.block.BlockFeature

isRecessive() - Method in enum org.mulinlab.varnote.utils.enumset.ModeOfInheritance

isRefAndAltExsit() - Method in class org.mulinlab.varnote.utils.format.Format

isRegulatoryNonCodingVariant(VariantEffect) - Static method in class org.mulinlab.varnote.utils.jannovar.VariantEffectUtility

isREMM - Variable in class org.mulinlab.varnote.config.parser.output.ADOutFeature

isRemoveCommemt() - Method in class org.mulinlab.varnote.config.param.output.IntersetOutParam

isRemoveComment - Variable in class org.mulinlab.varnote.cmdline.tools.Intersect

isSnv(String, String) - Static method in class org.mulinlab.varnote.utils.jannovar.AllelePosition

isSymbolic(String, String) - Static method in class org.mulinlab.varnote.utils.jannovar.AllelePosition

isSymbolic() - Method in class org.mulinlab.varnote.utils.jannovar.AllelePosition

isZeroBased() - Method in class org.mulinlab.varnote.utils.format.Format

ISZIP - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

it - Variable in class org.mulinlab.varnote.operations.stack.AbstractReaderStack

iterator - Variable in class org.mulinlab.varnote.filters.iterator.LineFilterIterator

iterator - Variable in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

J

JannovarAnnotationService - Class in org.mulinlab.varnote.utils.jannovar

Wrapper to build Jannovar annotations for variants.

JannovarAnnotationService(JannovarData) - Constructor for class org.mulinlab.varnote.utils.jannovar.JannovarAnnotationService

JannovarUtils - Class in org.mulinlab.varnote.utils

JannovarUtils(String) - Constructor for class org.mulinlab.varnote.utils.JannovarUtils

JannovarUtils(GenomeAssembly, TranscriptSource, String) - Constructor for class org.mulinlab.varnote.utils.JannovarUtils

JannovarVariantAnnotator - Class in org.mulinlab.varnote.utils.jannovar

Handles creation of VariantAnnotation using Jannovar.

JannovarVariantAnnotator(GenomeAssembly, JannovarData, ChromosomalRegionIndex<RegulatoryFeature>) - Constructor for class org.mulinlab.varnote.utils.jannovar.JannovarVariantAnnotator

joinFields(StringJoiner) - Method in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

joinFields(StringJoiner) - Method in class org.mulinlab.varnote.config.anno.databse.anno.DatabaseAnnoVCFParser

joinNullVals(StringJoiner) - Method in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

joinNullVals(StringJoiner) - Method in class org.mulinlab.varnote.config.anno.databse.anno.DatabaseAnnoVCFParser

justProband(String) - Static method in class org.mulinlab.varnote.utils.pedigree.Pedigree

K

KBLDRED - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

KBLU - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

KCYN - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

KGRN - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

KNRM - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

KRED - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

KWHT - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

L

label - Variable in class org.mulinlab.varnote.config.param.postDB.PostDBParam

less64(long, long) - Static method in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

lesseq64(long, long) - Static method in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

LEVEL_STARTS - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

LimitInputStream - Class in org.mulinlab.varnote.utils.stream

LimitInputStream(InputStream, long) - Constructor for class org.mulinlab.varnote.utils.stream.LimitInputStream

Wraps another input stream, limiting the number of bytes which can be read.

line - Variable in class org.mulinlab.varnote.filters.iterator.LineFilterIterator

LineFilter - Interface in org.mulinlab.varnote.filters.query.line

LineFilterIterator - Class in org.mulinlab.varnote.filters.iterator

LineFilterIterator(NoFilterIterator, List<LineFilter>) - Constructor for class org.mulinlab.varnote.filters.iterator.LineFilterIterator

lineFilters - Variable in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

listChromsome() - Method in class org.mulinlab.varnote.config.index.IndexWriteConfig

listSeq - Variable in class org.mulinlab.varnote.cmdline.collection.IndexArgumentCollection

loadDB(LocFeature) - Method in class org.mulinlab.varnote.operations.stack.ExactStack

LocalFile - Class in org.mulinlab.varnote.utils.stream

LocalFile() - Constructor for class org.mulinlab.varnote.utils.stream.LocalFile

LocCodec - Class in org.mulinlab.varnote.operations.decode

LocCodec(Format, int, boolean) - Constructor for class org.mulinlab.varnote.operations.decode.LocCodec

locCodec - Variable in class org.mulinlab.varnote.utils.database.Database

LocFeature - Class in org.mulinlab.varnote.utils.node

LocFeature() - Constructor for class org.mulinlab.varnote.utils.node.LocFeature

LocFeature(int, int, String) - Constructor for class org.mulinlab.varnote.utils.node.LocFeature

LocFeature(int, int, String, String, String) - Constructor for class org.mulinlab.varnote.utils.node.LocFeature

LocFilterIterator - Class in org.mulinlab.varnote.filters.iterator

LocFilterIterator(NoFilterIterator, List<LineFilter>, LocCodec) - Constructor for class org.mulinlab.varnote.filters.iterator.LocFilterIterator

locFilters - Variable in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

log - Variable in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

LOG_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

logFormat() - Method in class org.mulinlab.varnote.utils.format.Format

logger - Variable in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

logger - Variable in class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

logger - Variable in class org.mulinlab.varnote.config.io.temp.Printter

logger - Variable in class org.mulinlab.varnote.config.param.Param

logger - Variable in class org.mulinlab.varnote.config.param.query.QueryParam

logger - Variable in class org.mulinlab.varnote.config.run.RunConfig

logger - Static variable in class org.mulinlab.varnote.utils.LoggingUtils

logger - Variable in class org.mulinlab.varnote.utils.TimeMetric

LoggingUtils - Class in org.mulinlab.varnote.utils

LoggingUtils() - Constructor for class org.mulinlab.varnote.utils.LoggingUtils

LOJ - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

loj - Variable in class org.mulinlab.varnote.config.param.output.OutParam

LongLineReader - Class in org.mulinlab.varnote.operations.readers.itf

LongLineReader(String) - Constructor for class org.mulinlab.varnote.operations.readers.itf.LongLineReader

LongLineReader(LongLineBufferedReader) - Constructor for class org.mulinlab.varnote.operations.readers.itf.LongLineReader

LOOP - Static variable in class org.mulinlab.varnote.config.anno.FieldFormat

LOOP_INDENTIFIER - Static variable in class org.mulinlab.varnote.config.anno.FieldFormat

lvCount - Variable in class org.mulinlab.varnote.utils.TimeMetric

M

MAGIC_NUMBER - Static variable in class org.mulinlab.varnote.utils.database.index.IndexFactory

main(String[]) - Static method in class org.mulinlab.varnote.cmdline.index.Index

main(String[]) - Static method in class org.mulinlab.varnote.cmdline.txtreader.anno.FormatReader

main(String[]) - Static method in class org.mulinlab.varnote.cmdline.txtreader.anno.VcfInfoReader

main(String[]) - Static method in class org.mulinlab.varnote.cmdline.VarNoteCommandLine

main(String[]) - Static method in class org.mulinlab.varnote.config.anno.FieldFormat

main(String[]) - Static method in class org.mulinlab.varnote.operations.readers.db.VannoMixReader

main(String[]) - Static method in class org.mulinlab.varnote.operations.readers.db.VannoSweepReader

main(String[]) - Static method in class org.mulinlab.varnote.utils.database.index.TbiIndex

main(String[]) - Static method in class org.mulinlab.varnote.utils.gz.BGZReader

main(String[]) - Static method in class org.mulinlab.varnote.utils.IOutils

main(String[]) - Static method in class org.mulinlab.varnote.utils.stream.ByteInputStream

main(String[]) - Static method in class org.mulinlab.varnote.utils.stream.BZIP2InputStream

main(String[]) - Static method in class org.mulinlab.varnote.utils.stream.LocalFile

makeBGZ(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

makeFilePointer(long, int) - Static method in class org.mulinlab.varnote.utils.gz.BlockCompressedFilePointerUtil

makeFirstVannoFeature() - Method in class org.mulinlab.varnote.utils.block.BlockFeature

makeIndex() - Method in class org.mulinlab.varnote.operations.index.IndexWriter

makeTemp() - Method in class org.mulinlab.varnote.config.io.temp.Printter

makeVannoFeature(BlockCompressedInputStream, byte) - Method in class org.mulinlab.varnote.utils.block.BlockFeature

Mapper<T> - Interface in org.mulinlab.varnote.utils.mapreduce

Mapper Interface

MapReduce<T,M> - Interface in org.mulinlab.varnote.utils.mapreduce

mark(int) - Method in class org.mulinlab.varnote.utils.stream.LimitInputStream

MAX_BINS - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

MAX_BLOCK_ADDRESS - Static variable in class org.mulinlab.varnote.utils.gz.BlockCompressedFilePointerUtil

MAX_BYTE - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

MAX_BYTE_UNSIGNED - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

MAX_HEADER_COMPARE_LENGTH - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

MAX_HEADER_COMPARE_LENGTH - Static variable in class org.mulinlab.varnote.utils.format.Format

MAX_LEN - Static variable in class org.mulinlab.varnote.utils.VannoUtils

MAX_OFFSET - Static variable in class org.mulinlab.varnote.utils.gz.BlockCompressedFilePointerUtil

MAX_SHORT - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

MAX_SHORT_UNSIGNED - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

MAX_VARIANT_LENGTH - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

maxCount - Variable in class org.mulinlab.varnote.utils.TimeMetric

maybeBgzfWrapOutputStream(File, OutputStream) - Static method in class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

mBc - Variable in class org.mulinlab.varnote.utils.database.index.Index

mChr2tid - Variable in class org.mulinlab.varnote.utils.database.index.Index

mEc - Variable in class org.mulinlab.varnote.utils.database.index.Index

MendelianInheritanceADFilter - Class in org.mulinlab.varnote.filters.mendelian

MendelianInheritanceADFilter(Pedigree) - Constructor for class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceADFilter

MendelianInheritanceARFilter - Class in org.mulinlab.varnote.filters.mendelian

MendelianInheritanceARFilter(Pedigree) - Constructor for class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceARFilter

MendelianInheritanceFilter - Class in org.mulinlab.varnote.filters.mendelian

MendelianInheritanceFilter(ModeOfInheritance, Pedigree) - Constructor for class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceFilter

MendelianInheritanceXDFilter - Class in org.mulinlab.varnote.filters.mendelian

MendelianInheritanceXDFilter(Pedigree) - Constructor for class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceXDFilter

MendelianInheritanceXRFilter - Class in org.mulinlab.varnote.filters.mendelian

MendelianInheritanceXRFilter(Pedigree) - Constructor for class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceXRFilter

MERGE_LABEL - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

mergeFile() - Method in class org.mulinlab.varnote.config.io.temp.Printter

mergeResult() - Method in class org.mulinlab.varnote.config.run.AnnoRunConfig

mergeResult() - Method in class org.mulinlab.varnote.config.run.CountRunConfig

mergeResult() - Method in class org.mulinlab.varnote.config.run.RunConfig

mergeResults() - Method in class org.mulinlab.varnote.config.io.temp.Printter

MetaReader - Class in org.mulinlab.varnote.utils.headerparser

MetaReader() - Constructor for class org.mulinlab.varnote.utils.headerparser.MetaReader

mFp - Variable in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

MINIMUM_SUBSTRING_LENGTH - Static variable in class org.mulinlab.varnote.cmdline.constant.CommandLineDefaults

minOffForChr - Variable in class org.mulinlab.varnote.utils.database.index.Index

minValue - Variable in class org.mulinlab.varnote.filters.query.vc.ABVariantFilter

MixIteratorImpl(TabixUtils.TPair64[], String) - Constructor for class org.mulinlab.varnote.operations.readers.db.TbiMixReader.MixIteratorImpl

MixVannoIteratorImpl(BlockCompressedInputStream) - Constructor for class org.mulinlab.varnote.operations.readers.db.VannoMixReader.MixVannoIteratorImpl

mMeta - Variable in class org.mulinlab.varnote.utils.database.index.Index

MODE - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

mode - Variable in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceFilter

Mode - Enum in org.mulinlab.varnote.utils.enumset

ModeOfInheritance - Enum in org.mulinlab.varnote.utils.enumset

motherId(String) - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual.Builder

mPreset - Variable in class org.mulinlab.varnote.utils.database.index.Index

mSc - Variable in class org.mulinlab.varnote.utils.database.index.Index

mSeq - Variable in class org.mulinlab.varnote.utils.database.index.Index

mSkip - Variable in class org.mulinlab.varnote.utils.database.index.Index

mTid2chr - Variable in class org.mulinlab.varnote.utils.database.index.Index

MyBlockCompressedOutputStream - Class in org.mulinlab.varnote.utils.gz

Writer for a file that is a series of gzip blocks (BGZF format).

MyBlockCompressedOutputStream(String) - Constructor for class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

Uses default compression level, which is 5 unless changed by setCompressionLevel Note: this constructor uses the default DeflaterFactory, see MyBlockCompressedOutputStream.getDefaultDeflaterFactory().

MyBlockCompressedOutputStream(File) - Constructor for class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

Uses default compression level, which is 5 unless changed by setCompressionLevel Note: this constructor uses the default DeflaterFactory, see MyBlockCompressedOutputStream.getDefaultDeflaterFactory().

MyBlockCompressedOutputStream(String, int) - Constructor for class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

Prepare to compress at the given compression level Note: this constructor uses the default DeflaterFactory, see MyBlockCompressedOutputStream.getDefaultDeflaterFactory().

MyBlockCompressedOutputStream(File, int) - Constructor for class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

Prepare to compress at the given compression level

MyBlockCompressedOutputStream(File, int, DeflaterFactory) - Constructor for class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

Prepare to compress at the given compression level

MyBlockCompressedOutputStream(OutputStream, File) - Constructor for class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

Uses default compression level, which is 5 unless changed by setCompressionLevel Note: this constructor uses the default DeflaterFactory, see MyBlockCompressedOutputStream.getDefaultDeflaterFactory().

MyBlockCompressedOutputStream(OutputStream, File, int) - Constructor for class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

Note: this constructor uses the default DeflaterFactory, see MyBlockCompressedOutputStream.getDefaultDeflaterFactory().

MyBlockCompressedOutputStream(OutputStream, File, int, DeflaterFactory) - Constructor for class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

Creates the output stream.

MyEndianOutputStream - Class in org.mulinlab.varnote.utils.gz

MyEndianOutputStream(MyBlockCompressedOutputStream) - Constructor for class org.mulinlab.varnote.utils.gz.MyEndianOutputStream

N

N - Static variable in class org.mulinlab.varnote.config.anno.FieldFormat

N_CHAR - Static variable in class org.mulinlab.varnote.config.anno.FieldFormat

N_INDENTIFIER - Static variable in class org.mulinlab.varnote.config.anno.FieldFormat

name - Variable in class org.mulinlab.varnote.filters.query.gt.ABGenotypeFilter

name - Variable in class org.mulinlab.varnote.filters.query.vc.ABVariantFilter

name - Variable in class org.mulinlab.varnote.utils.TimeMetric

newBED() - Static method in class org.mulinlab.varnote.utils.format.Format

newline - Static variable in class org.mulinlab.varnote.config.io.temp.ThreadPrintter

NEWLINE - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

newTAB() - Static method in class org.mulinlab.varnote.utils.format.Format

newVCF() - Static method in class org.mulinlab.varnote.utils.format.Format

next() - Method in class org.mulinlab.varnote.filters.iterator.LineFilterIterator

next() - Method in class org.mulinlab.varnote.filters.iterator.NoFilterIterator

next() - Method in interface org.mulinlab.varnote.operations.readers.db.AbstractDBReader.Iterator

return null when there is no more data to read

next() - Method in class org.mulinlab.varnote.operations.readers.db.TbiMixReader.MixIteratorImpl

next() - Method in class org.mulinlab.varnote.operations.readers.db.TbiReader.TbiIteratorImpl

next() - Method in class org.mulinlab.varnote.operations.readers.db.TbiSweepReader.SweepIteratorImpl

next() - Method in class org.mulinlab.varnote.operations.readers.db.VannoReader.VannoIteratorImpl

nextBlock() - Method in class org.mulinlab.varnote.operations.readers.db.VannoReader

nextNode() - Method in interface org.mulinlab.varnote.operations.readers.db.AbstractDBReader.Iterator

nextNode() - Method in class org.mulinlab.varnote.operations.readers.db.TbiReader.TbiIteratorImpl

nextNode() - Method in class org.mulinlab.varnote.operations.readers.db.VannoReader.VannoIteratorImpl

nextString() - Method in class org.mulinlab.varnote.filters.iterator.LineFilterIterator

nMembers - Variable in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceFilter

NO_CALL_IDX - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

NO_COL - Static variable in class org.mulinlab.varnote.utils.format.Format

NO_VAL - Static variable in class org.mulinlab.varnote.config.anno.NormalField

node - Variable in class org.mulinlab.varnote.operations.readers.db.TbiReader.TbiIteratorImpl

node - Variable in class org.mulinlab.varnote.operations.readers.db.VannoReader.VannoIteratorImpl

NodeWithFilePointer - Class in org.mulinlab.varnote.utils.node

NodeWithFilePointer(long, int) - Constructor for class org.mulinlab.varnote.utils.node.NodeWithFilePointer

NodeWithFilePointer(int, int, long, int) - Constructor for class org.mulinlab.varnote.utils.node.NodeWithFilePointer

NoFilterIterator - Class in org.mulinlab.varnote.filters.iterator

NoFilterIterator(QueryReaderItf) - Constructor for class org.mulinlab.varnote.filters.iterator.NoFilterIterator

NoFilterIterator(String, FileType) - Constructor for class org.mulinlab.varnote.filters.iterator.NoFilterIterator

NoFilterIterator(String) - Constructor for class org.mulinlab.varnote.filters.iterator.NoFilterIterator

nonNull(T, String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

NormalField - Class in org.mulinlab.varnote.config.anno

NormalField(String) - Constructor for class org.mulinlab.varnote.config.anno.NormalField

NOT_INDEL - Static variable in class org.mulinlab.varnote.utils.VannoUtils

NOT_MATCH - Static variable in class org.mulinlab.varnote.config.anno.NormalField

NULLVALUE - Static variable in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

NULLVALUE - Static variable in class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

NULLVALUE - Static variable in class org.mulinlab.varnote.config.parser.AnnoParser

NULLVALUE - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

numFamilies() - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree

O

of(int, String, String) - Static method in class org.mulinlab.varnote.utils.jannovar.AllelePosition

of(Collection<T>) - Static method in class org.mulinlab.varnote.utils.jannovar.ChromosomalRegionIndex

Static constructor for creating a ChromosomalRegionIndex from a collection of ChromosomalRegion objects of a given type.

of(Collection<Pedigree.Individual>) - Static method in class org.mulinlab.varnote.utils.pedigree.Pedigree

of(Pedigree.Individual...) - Static method in class org.mulinlab.varnote.utils.pedigree.Pedigree

onShutdown() - Method in class org.mulinlab.varnote.cmdline.abstractclass.CMDProgram

onShutdown() - Method in class org.mulinlab.varnote.cmdline.abstractclass.ConfigProgram

onShutdown() - Method in class org.mulinlab.varnote.cmdline.abstractclass.RunProgram

onShutdown() - Method in class org.mulinlab.varnote.cmdline.tools.RandomAccess

onStartup() - Method in class org.mulinlab.varnote.cmdline.abstractclass.CMDProgram

onStartup() - Method in class org.mulinlab.varnote.cmdline.abstractclass.ConfigProgram

onStartup() - Method in class org.mulinlab.varnote.cmdline.abstractclass.IndexProgram

onStartup() - Method in class org.mulinlab.varnote.cmdline.abstractclass.RunProgram

onStartup() - Method in class org.mulinlab.varnote.cmdline.tools.RandomAccess

org.mulinlab.varnote.cmdline - package org.mulinlab.varnote.cmdline

org.mulinlab.varnote.cmdline.abstractclass - package org.mulinlab.varnote.cmdline.abstractclass

org.mulinlab.varnote.cmdline.collection - package org.mulinlab.varnote.cmdline.collection

org.mulinlab.varnote.cmdline.constant - package org.mulinlab.varnote.cmdline.constant

org.mulinlab.varnote.cmdline.index - package org.mulinlab.varnote.cmdline.index

org.mulinlab.varnote.cmdline.programgroups - package org.mulinlab.varnote.cmdline.programgroups

org.mulinlab.varnote.cmdline.tools - package org.mulinlab.varnote.cmdline.tools

org.mulinlab.varnote.cmdline.tools.config - package org.mulinlab.varnote.cmdline.tools.config

org.mulinlab.varnote.cmdline.txtreader.abs - package org.mulinlab.varnote.cmdline.txtreader.abs

org.mulinlab.varnote.cmdline.txtreader.anno - package org.mulinlab.varnote.cmdline.txtreader.anno

org.mulinlab.varnote.cmdline.txtreader.run - package org.mulinlab.varnote.cmdline.txtreader.run

org.mulinlab.varnote.config.anno - package org.mulinlab.varnote.config.anno

org.mulinlab.varnote.config.anno.databse - package org.mulinlab.varnote.config.anno.databse

org.mulinlab.varnote.config.anno.databse.anno - package org.mulinlab.varnote.config.anno.databse.anno

org.mulinlab.varnote.config.anno.databse.filter - package org.mulinlab.varnote.config.anno.databse.filter

org.mulinlab.varnote.config.anno.query - package org.mulinlab.varnote.config.anno.query

org.mulinlab.varnote.config.index - package org.mulinlab.varnote.config.index

org.mulinlab.varnote.config.io - package org.mulinlab.varnote.config.io

org.mulinlab.varnote.config.io.temp - package org.mulinlab.varnote.config.io.temp

org.mulinlab.varnote.config.param - package org.mulinlab.varnote.config.param

org.mulinlab.varnote.config.param.output - package org.mulinlab.varnote.config.param.output

org.mulinlab.varnote.config.param.postDB - package org.mulinlab.varnote.config.param.postDB

org.mulinlab.varnote.config.param.query - package org.mulinlab.varnote.config.param.query

org.mulinlab.varnote.config.parser - package org.mulinlab.varnote.config.parser

org.mulinlab.varnote.config.parser.output - package org.mulinlab.varnote.config.parser.output

org.mulinlab.varnote.config.run - package org.mulinlab.varnote.config.run

org.mulinlab.varnote.constants - package org.mulinlab.varnote.constants

org.mulinlab.varnote.exceptions - package org.mulinlab.varnote.exceptions

org.mulinlab.varnote.filters - package org.mulinlab.varnote.filters

org.mulinlab.varnote.filters.iterator - package org.mulinlab.varnote.filters.iterator

org.mulinlab.varnote.filters.mendelian - package org.mulinlab.varnote.filters.mendelian

org.mulinlab.varnote.filters.query - package org.mulinlab.varnote.filters.query

org.mulinlab.varnote.filters.query.gt - package org.mulinlab.varnote.filters.query.gt

org.mulinlab.varnote.filters.query.line - package org.mulinlab.varnote.filters.query.line

org.mulinlab.varnote.filters.query.vc - package org.mulinlab.varnote.filters.query.vc

org.mulinlab.varnote.operations.decode - package org.mulinlab.varnote.operations.decode

org.mulinlab.varnote.operations.index - package org.mulinlab.varnote.operations.index

org.mulinlab.varnote.operations.mapper - package org.mulinlab.varnote.operations.mapper

org.mulinlab.varnote.operations.process - package org.mulinlab.varnote.operations.process

org.mulinlab.varnote.operations.query - package org.mulinlab.varnote.operations.query

org.mulinlab.varnote.operations.readers.db - package org.mulinlab.varnote.operations.readers.db

org.mulinlab.varnote.operations.readers.itf - package org.mulinlab.varnote.operations.readers.itf

org.mulinlab.varnote.operations.readers.itf.thread - package org.mulinlab.varnote.operations.readers.itf.thread

org.mulinlab.varnote.operations.readers.query - package org.mulinlab.varnote.operations.readers.query

org.mulinlab.varnote.operations.stack - package org.mulinlab.varnote.operations.stack

org.mulinlab.varnote.utils - package org.mulinlab.varnote.utils

org.mulinlab.varnote.utils.block - package org.mulinlab.varnote.utils.block

org.mulinlab.varnote.utils.database - package org.mulinlab.varnote.utils.database

org.mulinlab.varnote.utils.database.index - package org.mulinlab.varnote.utils.database.index

org.mulinlab.varnote.utils.database.index.vannoIndex - package org.mulinlab.varnote.utils.database.index.vannoIndex

org.mulinlab.varnote.utils.enumset - package org.mulinlab.varnote.utils.enumset

org.mulinlab.varnote.utils.format - package org.mulinlab.varnote.utils.format

org.mulinlab.varnote.utils.gz - package org.mulinlab.varnote.utils.gz

org.mulinlab.varnote.utils.headerparser - package org.mulinlab.varnote.utils.headerparser

org.mulinlab.varnote.utils.jannovar - package org.mulinlab.varnote.utils.jannovar

org.mulinlab.varnote.utils.mapreduce - package org.mulinlab.varnote.utils.mapreduce

org.mulinlab.varnote.utils.node - package org.mulinlab.varnote.utils.node

org.mulinlab.varnote.utils.pedigree - package org.mulinlab.varnote.utils.pedigree

org.mulinlab.varnote.utils.stream - package org.mulinlab.varnote.utils.stream

origStr - Variable in class org.mulinlab.varnote.utils.node.LocFeature

OUT_FORMAT - Static variable in class org.mulinlab.varnote.cmdline.txtreader.anno.FormatReader

OUT_LEN - Static variable in class org.mulinlab.varnote.utils.VannoUtils

OUT_NAMES - Static variable in class org.mulinlab.varnote.cmdline.txtreader.anno.AnnoConfigReader

outFileSuffix - Variable in class org.mulinlab.varnote.config.param.output.OutParam

outFormat - Variable in class org.mulinlab.varnote.cmdline.collection.AnnoOutputArgumentCollection

OutMode - Enum in org.mulinlab.varnote.utils.enumset

outModeValue - Variable in class org.mulinlab.varnote.cmdline.tools.Intersect

outParam - Variable in class org.mulinlab.varnote.config.io.temp.Printter

OutParam - Class in org.mulinlab.varnote.config.param.output

OutParam() - Constructor for class org.mulinlab.varnote.config.param.output.OutParam

OutParam(String) - Constructor for class org.mulinlab.varnote.config.param.output.OutParam

outParam - Variable in class org.mulinlab.varnote.config.run.RunConfig

outPath - Variable in class org.mulinlab.varnote.cmdline.collection.OutputArgumentCollection

outPath - Variable in class org.mulinlab.varnote.cmdline.tools.Count

OUTPUT_MODE - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

OUTPUT_PATH - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

OutputArgumentCollection - Class in org.mulinlab.varnote.cmdline.collection

OutputArgumentCollection() - Constructor for class org.mulinlab.varnote.cmdline.collection.OutputArgumentCollection

outputArguments - Variable in class org.mulinlab.varnote.cmdline.tools.Annotation

outputArguments - Variable in class org.mulinlab.varnote.cmdline.tools.AnnotationIntersectFile

outputArguments - Variable in class org.mulinlab.varnote.cmdline.tools.Intersect

outputFolder - Variable in class org.mulinlab.varnote.cmdline.index.Index

outputMode - Variable in class org.mulinlab.varnote.config.param.output.OutParam

outputName - Variable in class org.mulinlab.varnote.config.param.output.OutParam

outputPath - Variable in class org.mulinlab.varnote.config.param.output.OutParam

OVERLAP_EQUAL - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.AbstractQueryReader

OVERLAP_EQUAL - Static variable in class org.mulinlab.varnote.config.run.OverlapRunConfig

OVERLAP_EQUAL - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

OVERLAP_NOTE - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.AbstractQueryReader

OVERLAP_NOTE - Static variable in class org.mulinlab.varnote.config.run.OverlapRunConfig

OVERLAP_NOTE - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

OVERLAP_NOTE - Static variable in class org.mulinlab.varnote.utils.RunFactory

OVERLAP_RESULT_SUFFIX - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

OverlapHeaderReader<T> - Class in org.mulinlab.varnote.cmdline.txtreader.anno

OverlapHeaderReader() - Constructor for class org.mulinlab.varnote.cmdline.txtreader.anno.OverlapHeaderReader

OverlapRunConfig - Class in org.mulinlab.varnote.config.run

OverlapRunConfig() - Constructor for class org.mulinlab.varnote.config.run.OverlapRunConfig

OverlapRunConfig(String, String[]) - Constructor for class org.mulinlab.varnote.config.run.OverlapRunConfig

OverlapRunConfig(QueryFileParam, List<DBParam>) - Constructor for class org.mulinlab.varnote.config.run.OverlapRunConfig

OverlapRunConfig(String, String[], IntersetOutParam, int) - Constructor for class org.mulinlab.varnote.config.run.OverlapRunConfig

OverlapRunConfig(QueryFileParam, List<DBParam>, IntersetOutParam, int) - Constructor for class org.mulinlab.varnote.config.run.OverlapRunConfig

P

Param - Class in org.mulinlab.varnote.config.param

Param() - Constructor for class org.mulinlab.varnote.config.param.Param

parseArgs(String[]) - Method in class org.mulinlab.varnote.cmdline.abstractclass.CMDProgram

parseIndexFileFormat(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

parsePedigree(Stream<String>) - Static method in class org.mulinlab.varnote.utils.pedigree.PedFiles

parseReg(String) - Method in class org.mulinlab.varnote.utils.database.index.Index

Parse a region in the format of "chr1", "chr1:100" or "chr1:100-1000"

parserFormat(String, boolean) - Method in class org.mulinlab.varnote.config.anno.FieldFormat

parserHeader(String, String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

parserHeaderComma(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

parseValue(String) - Static method in enum org.mulinlab.varnote.utils.enumset.TranscriptSource

parts - Variable in class org.mulinlab.varnote.operations.decode.LocCodec

parts - Variable in class org.mulinlab.varnote.utils.node.LocFeature

PedFiles - Class in org.mulinlab.varnote.utils.pedigree

pedigree - Variable in class org.mulinlab.varnote.filters.mendelian.MendelianInheritanceFilter

Pedigree - Class in org.mulinlab.varnote.utils.pedigree

Pedigree.Individual - Class in org.mulinlab.varnote.utils.pedigree

Pedigree.Individual.Builder - Class in org.mulinlab.varnote.utils.pedigree

Pedigree.Individual.Sex - Enum in org.mulinlab.varnote.utils.pedigree

Pedigree.Individual.Status - Enum in org.mulinlab.varnote.utils.pedigree

PedigreeConverter - Class in org.mulinlab.varnote.utils.pedigree

peek() - Method in class org.mulinlab.varnote.filters.iterator.NoFilterIterator

Population - Enum in org.mulinlab.varnote.utils.enumset

pos - Variable in class org.mulinlab.varnote.filters.iterator.NoFilterIterator

POS_RSID_LABEL - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

posAlleleToNode(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

position(int) - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation.Builder

posStr() - Method in class org.mulinlab.varnote.utils.node.LocFeature

posTabStr() - Method in class org.mulinlab.varnote.utils.node.LocFeature

PostDBParam - Class in org.mulinlab.varnote.config.param.postDB

PostDBParam() - Constructor for class org.mulinlab.varnote.config.param.postDB.PostDBParam

posToNode(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

preBeg - Variable in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

PredictionFunc - Enum in org.mulinlab.varnote.utils.enumset

print(String) - Method in class org.mulinlab.varnote.config.io.temp.FlatThreadPrintter

print(String, int) - Method in class org.mulinlab.varnote.config.io.temp.Printter

print(String) - Method in class org.mulinlab.varnote.config.io.temp.ThreadPrintter

print(String) - Method in class org.mulinlab.varnote.config.io.temp.ZipThreadPrintter

printFormat - Variable in class org.mulinlab.varnote.cmdline.collection.IndexArgumentCollection

printFormat() - Method in class org.mulinlab.varnote.config.index.IndexWriteConfig

PrintGZ - Class in org.mulinlab.varnote.config.io

PrintGZ(String, boolean) - Constructor for class org.mulinlab.varnote.config.io.PrintGZ

printHeader - Variable in class org.mulinlab.varnote.cmdline.collection.IndexArgumentCollection

printHeader() - Method in class org.mulinlab.varnote.config.index.IndexWriteConfig

printHeader(List<String>) - Method in class org.mulinlab.varnote.config.io.temp.Printter

printLog() - Method in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

printLog() - Method in class org.mulinlab.varnote.config.param.DBParam

printLog() - Method in class org.mulinlab.varnote.config.param.output.OutParam

printLog() - Method in class org.mulinlab.varnote.config.param.query.QueryFileParam

printLog() - Method in class org.mulinlab.varnote.config.param.query.QueryParam

printLog() - Method in class org.mulinlab.varnote.config.param.query.QueryRegionParam

printLog() - Method in class org.mulinlab.varnote.config.parser.AnnoParser

printLogHeader(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

printLVCount() - Method in class org.mulinlab.varnote.utils.TimeMetric

printLVLog(LocFeature) - Method in class org.mulinlab.varnote.operations.mapper.AbstractMapper

printMergeLog() - Static method in class org.mulinlab.varnote.utils.ReducerFactory

printMeta - Variable in class org.mulinlab.varnote.cmdline.collection.IndexArgumentCollection

printMetaData() - Method in class org.mulinlab.varnote.config.index.IndexWriteConfig

printRecord(LocFeature, String, int) - Method in class org.mulinlab.varnote.config.run.OverlapRunConfig

printRecord(LocFeature, Map<String, String[]>, int) - Method in class org.mulinlab.varnote.config.run.OverlapRunConfig

printRecord(Map<String, String[]>) - Method in class org.mulinlab.varnote.config.run.QueryRegionConfig

Printter - Class in org.mulinlab.varnote.config.io.temp

Printter(OutParam) - Constructor for class org.mulinlab.varnote.config.io.temp.Printter

printter - Variable in class org.mulinlab.varnote.config.run.RunConfig

printUnknown(Set<Class<?>>, String) - Static method in class org.mulinlab.varnote.cmdline.VarNoteCommandLine

printUsage(PrintStream, Set<Class<?>>, String) - Static method in class org.mulinlab.varnote.cmdline.VarNoteCommandLine

Priority - Enum in org.mulinlab.varnote.utils.enumset

PRO_CMD - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

PRO_NAME - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

processAllCommandLinePrograms(List<String>, BiConsumer<Class<CMDProgram>, CommandLineProgramProperties>) - Static method in class org.mulinlab.varnote.cmdline.VarNoteCommandLine

processBeg() - Method in class org.mulinlab.varnote.operations.decode.BEDLocCodec

processBeg() - Method in class org.mulinlab.varnote.operations.decode.LocCodec

processBeg() - Method in class org.mulinlab.varnote.operations.decode.RSIDLocCodec

processBeg() - Method in class org.mulinlab.varnote.operations.decode.TABLocCodec

processBeg() - Method in class org.mulinlab.varnote.operations.decode.VCFLocCodec

ProcessBlock - Interface in org.mulinlab.varnote.operations.process

processBlock(byte) - Method in class org.mulinlab.varnote.operations.readers.db.VannoMixReader.MixVannoIteratorImpl

processBlock(byte) - Method in class org.mulinlab.varnote.operations.readers.db.VannoReader.VannoIteratorImpl

processBlock(byte) - Method in class org.mulinlab.varnote.operations.readers.db.VannoSweepReader.SweepIteratorImpl

processDBFeature(LocFeature, int) - Method in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

processDBFeature(LocFeature, int) - Method in class org.mulinlab.varnote.config.anno.databse.anno.DatabaseAnnoVCFParser

processEnd() - Method in class org.mulinlab.varnote.operations.decode.BEDLocCodec

processEnd() - Method in class org.mulinlab.varnote.operations.decode.LocCodec

processEnd() - Method in class org.mulinlab.varnote.operations.decode.RSIDLocCodec

processEnd() - Method in class org.mulinlab.varnote.operations.decode.TABLocCodec

processEnd() - Method in class org.mulinlab.varnote.operations.decode.VCFLocCodec

processLine(String) - Method in class org.mulinlab.varnote.cmdline.txtreader.abs.AbstractQueryReader

processLine(String) - Method in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

processLine(String) - Method in interface org.mulinlab.varnote.cmdline.txtreader.abs.RunReaderInterface

processLine(String) - Method in class org.mulinlab.varnote.cmdline.txtreader.run.FileQueryReader

processLine(String) - Method in class org.mulinlab.varnote.filters.iterator.LineFilterIterator

processLine(String) - Method in class org.mulinlab.varnote.filters.iterator.LocFilterIterator

processLine(String) - Method in class org.mulinlab.varnote.filters.iterator.VCFFilterIterator

processNode(LocFeature, Map<String, LocFeature[]>) - Method in class org.mulinlab.varnote.config.parser.AnnoParser

processNode(LocFeature, Map<String, LocFeature[]>) - Method in interface org.mulinlab.varnote.config.parser.ResultParser

processNode(LocFeature, Integer[], int) - Method in class org.mulinlab.varnote.config.run.CountRunConfig

processOther() - Method in class org.mulinlab.varnote.operations.decode.BEDLocCodec

processOther() - Method in class org.mulinlab.varnote.operations.decode.LocCodec

processOther() - Method in class org.mulinlab.varnote.operations.decode.RSIDLocCodec

processOther() - Method in class org.mulinlab.varnote.operations.decode.TABLocCodec

processOther() - Method in class org.mulinlab.varnote.operations.decode.VCFLocCodec

ProcessResult - Interface in org.mulinlab.varnote.operations.process

processToken() - Method in class org.mulinlab.varnote.operations.decode.LocCodec

pushedBackBytes(long) - Method in class org.mulinlab.varnote.utils.stream.CompressorInputStream

Decrements the counter of already read bytes.

putValue(String, String) - Method in class org.mulinlab.varnote.cmdline.txtreader.abs.AbstractQueryReader

putValue(String, String) - Method in class org.mulinlab.varnote.cmdline.txtreader.anno.AnnoConfigReader

putValue(String, String) - Method in class org.mulinlab.varnote.cmdline.txtreader.anno.FormatReader

putValue(String, String) - Method in class org.mulinlab.varnote.cmdline.txtreader.anno.OverlapHeaderReader

putValue(String, String) - Method in class org.mulinlab.varnote.cmdline.txtreader.anno.VcfInfoReader

Q

QDFilter - Class in org.mulinlab.varnote.filters.query.vc

QDFilter(int) - Constructor for class org.mulinlab.varnote.filters.query.vc.QDFilter

QUERY - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

Query - Interface in org.mulinlab.varnote.operations.query

query(String) - Method in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

query(LocFeature) - Method in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

query(LocFeature) - Method in class org.mulinlab.varnote.operations.readers.db.TbiMixReader

query(LocFeature) - Method in class org.mulinlab.varnote.operations.readers.db.TbiSweepReader

query(LocFeature) - Method in class org.mulinlab.varnote.operations.readers.db.VannoMixReader

query(LocFeature) - Method in class org.mulinlab.varnote.operations.readers.db.VannoSweepReader

QUERY_ALT - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

QUERY_BEGIN - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

QUERY_CHROM - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

QUERY_DOC - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

QUERY_END - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

QUERY_FORMAT - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

QUERY_INPUT_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

QUERY_INPUT_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

QUERY_LABEL_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

QUERY_LABEL_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

QUERY_REF - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

QUERY_START - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

QUERY_START - Static variable in class org.mulinlab.varnote.utils.RunFactory

QueryBEDParser - Class in org.mulinlab.varnote.config.anno.query

QueryBEDParser(Format, String) - Constructor for class org.mulinlab.varnote.config.anno.query.QueryBEDParser

queryEngine - Variable in class org.mulinlab.varnote.operations.mapper.AbstractMapper

queryFile - Variable in class org.mulinlab.varnote.cmdline.collection.InputFileArgumentCollection

queryFileParam - Variable in class org.mulinlab.varnote.cmdline.txtreader.run.FileQueryReader

QueryFileParam - Class in org.mulinlab.varnote.config.param.query

QueryFileParam(String, boolean) - Constructor for class org.mulinlab.varnote.config.param.query.QueryFileParam

QueryFileParam(String, Format, boolean) - Constructor for class org.mulinlab.varnote.config.param.query.QueryFileParam

QueryFileParam(String, Format, boolean, FilterParam) - Constructor for class org.mulinlab.varnote.config.param.query.QueryFileParam

QueryFileProgram - Class in org.mulinlab.varnote.cmdline.abstractclass

QueryFileProgram() - Constructor for class org.mulinlab.varnote.cmdline.abstractclass.QueryFileProgram

queryLoc - Variable in class org.mulinlab.varnote.config.parser.output.ADOutFeature

QueryParam - Class in org.mulinlab.varnote.config.param.query

QueryParam() - Constructor for class org.mulinlab.varnote.config.param.query.QueryParam

queryParam - Variable in class org.mulinlab.varnote.config.run.RunConfig

QueryProgram - Class in org.mulinlab.varnote.cmdline.abstractclass

QueryProgram() - Constructor for class org.mulinlab.varnote.cmdline.abstractclass.QueryProgram

QueryProgramGroup - Class in org.mulinlab.varnote.cmdline.programgroups

Tools that manipulate read data in SAM, BAM or CRAM format

QueryProgramGroup() - Constructor for class org.mulinlab.varnote.cmdline.programgroups.QueryProgramGroup

QueryReader<T> - Class in org.mulinlab.varnote.cmdline.txtreader.abs

QueryReader() - Constructor for class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

QueryReaderItf - Interface in org.mulinlab.varnote.operations.readers.itf

queryRegion - Variable in class org.mulinlab.varnote.cmdline.tools.RandomAccess

QueryRegionConfig - Class in org.mulinlab.varnote.config.run

QueryRegionConfig(String, String[]) - Constructor for class org.mulinlab.varnote.config.run.QueryRegionConfig

QueryRegionConfig(String, String[], boolean) - Constructor for class org.mulinlab.varnote.config.run.QueryRegionConfig

QueryRegionConfig(String, List<DBParam>, boolean) - Constructor for class org.mulinlab.varnote.config.run.QueryRegionConfig

QueryRegionParam - Class in org.mulinlab.varnote.config.param.query

QueryRegionParam(String) - Constructor for class org.mulinlab.varnote.config.param.query.QueryRegionParam

QueryVCFParser - Class in org.mulinlab.varnote.config.anno.query

QueryVCFParser(Format, VCFParser) - Constructor for class org.mulinlab.varnote.config.anno.query.QueryVCFParser

QuickFileType - Enum in org.mulinlab.varnote.utils.enumset

R

Rand - Class in org.mulinlab.varnote.utils.stream

This code is from teh

Rand() - Constructor for class org.mulinlab.varnote.utils.stream.Rand

RandomAccess - Class in org.mulinlab.varnote.cmdline.tools

RandomAccess() - Constructor for class org.mulinlab.varnote.cmdline.tools.RandomAccess

randomAccessQuery(LocFeature) - Method in class org.mulinlab.varnote.operations.query.TabixQuery

read(String) - Method in class org.mulinlab.varnote.cmdline.txtreader.abs.AbstractQueryReader

read(String) - Method in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

read(String) - Method in interface org.mulinlab.varnote.cmdline.txtreader.abs.RunReaderInterface

read(InputStream) - Static method in class org.mulinlab.varnote.constants.GlobalParameter

read() - Method in class org.mulinlab.varnote.utils.database.index.Index

read() - Method in class org.mulinlab.varnote.utils.database.index.TbiIndex

read() - Method in class org.mulinlab.varnote.utils.stream.AdvancedBZip2CompressorInputStream

read(byte[], int, int) - Method in class org.mulinlab.varnote.utils.stream.AdvancedBZip2CompressorInputStream

read() - Method in class org.mulinlab.varnote.utils.stream.LimitInputStream

read(byte[], int, int) - Method in class org.mulinlab.varnote.utils.stream.LimitInputStream

readActualHeader(LineIterator) - Method in class org.mulinlab.varnote.operations.decode.LocCodec

readBlock(BlockCompressedInputStream, int, int, byte[]) - Method in class org.mulinlab.varnote.utils.block.BlockFeature

readBoolean(InputStream) - Static method in class org.mulinlab.varnote.constants.GlobalParameter

readBytes(InputStream, byte[], int, int) - Static method in class org.mulinlab.varnote.utils.VannoUtils

readDatabase(DBParam) - Static method in class org.mulinlab.varnote.utils.database.DatabaseFactory

readDatabaseFromConfig(List<DBParam>) - Static method in class org.mulinlab.varnote.utils.database.DatabaseFactory

readDefaultHeader(String, FileType, Format, boolean) - Static method in class org.mulinlab.varnote.utils.headerparser.HeaderFormatReader

readDefaultHeader(QueryReaderItf, Format, boolean) - Static method in class org.mulinlab.varnote.utils.headerparser.HeaderFormatReader

reader - Variable in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

readers - Variable in class org.mulinlab.varnote.operations.query.AbstractQuery

readFileWithPattern(String) - Static method in class org.mulinlab.varnote.utils.IOutils

readFormat() - Method in class org.mulinlab.varnote.utils.database.index.Index

readFormat() - Method in class org.mulinlab.varnote.utils.database.index.TbiIndex

readFormat() - Method in class org.mulinlab.varnote.utils.database.index.vannoIndex.VannoIndex

readFormat() - Method in class org.mulinlab.varnote.utils.database.index.vannoIndex.VannoIndexV1

readFormatString(String) - Static method in class org.mulinlab.varnote.utils.format.Format

readHeader() - Method in class org.mulinlab.varnote.utils.database.Database

readHeader() - Method in class org.mulinlab.varnote.utils.database.index.vannoIndex.VannoIndexV1

readHeader(Format, String, FileType) - Static method in class org.mulinlab.varnote.utils.headerparser.HeaderFormatReader

readHeader(Format, String, String) - Static method in class org.mulinlab.varnote.utils.headerparser.MetaReader

readHeaderFromArray(String[], Format) - Static method in class org.mulinlab.varnote.utils.headerparser.HeaderFormatReader

readIndex(LocFeature) - Method in class org.mulinlab.varnote.operations.readers.db.VannoReader

readIndex() - Method in class org.mulinlab.varnote.utils.database.Database

readIndex() - Method in class org.mulinlab.varnote.utils.database.index.Index

readIndex(String) - Static method in class org.mulinlab.varnote.utils.database.index.IndexFactory

readIndex() - Method in class org.mulinlab.varnote.utils.database.index.TbiIndex

readIndex() - Method in class org.mulinlab.varnote.utils.database.index.vannoIndex.VannoIndex

readIndex() - Method in class org.mulinlab.varnote.utils.database.index.vannoIndex.VannoIndexV1

readInt(InputStream) - Static method in class org.mulinlab.varnote.constants.GlobalParameter

readLine() - Method in class org.mulinlab.varnote.operations.readers.itf.BGZReader

readLine() - Method in class org.mulinlab.varnote.operations.readers.itf.GZIPReader

readLine() - Method in class org.mulinlab.varnote.operations.readers.itf.LongLineReader

readLine() - Method in interface org.mulinlab.varnote.operations.readers.itf.QueryReaderItf

readLine() - Method in class org.mulinlab.varnote.operations.readers.itf.thread.GZIPThreadReader

readLine() - Method in class org.mulinlab.varnote.operations.readers.itf.thread.SpiderReader

readLine(long) - Method in class org.mulinlab.varnote.utils.gz.BGZReader

readLine(int[]) - Method in class org.mulinlab.varnote.utils.stream.ByteInputStream

readLine() - Method in class org.mulinlab.varnote.utils.stream.ByteInputStream

readLine(int[]) - Method in class org.mulinlab.varnote.utils.stream.BZIP2InputStream.Spider

readLine() - Method in class org.mulinlab.varnote.utils.stream.BZIP2InputStream.Spider

readLine() - Method in class org.mulinlab.varnote.utils.stream.GZInputStream.GZReader

readLong(InputStream, byte[]) - Static method in class org.mulinlab.varnote.constants.GlobalParameter

readMagic() - Method in class org.mulinlab.varnote.utils.database.index.Index

readMagic() - Method in class org.mulinlab.varnote.utils.database.index.TbiIndex

readMagic() - Method in class org.mulinlab.varnote.utils.database.index.vannoIndex.VannoIndex

readPedigree(Path) - Static method in class org.mulinlab.varnote.utils.pedigree.PedFiles

readSeq() - Method in class org.mulinlab.varnote.utils.database.index.Index

readShort(InputStream) - Static method in class org.mulinlab.varnote.constants.GlobalParameter

readShort(BlockCompressedInputStream) - Method in class org.mulinlab.varnote.utils.block.BlockFeature

Reducer<T,V extends Mapper<M>,M> - Interface in org.mulinlab.varnote.utils.mapreduce

Reducer Interface

ReducerFactory - Class in org.mulinlab.varnote.utils

ReducerFactory() - Constructor for class org.mulinlab.varnote.utils.ReducerFactory

ref(String) - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation.Builder

ref - Variable in class org.mulinlab.varnote.utils.node.LocFeature

REF_IDX - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

refPositionColumn - Variable in class org.mulinlab.varnote.utils.format.Format

reg2bins(int, int, int[]) - Static method in class org.mulinlab.varnote.constants.GlobalParameter

RegFunc - Enum in org.mulinlab.varnote.utils.enumset

RegionFilter - Class in org.mulinlab.varnote.filters

RegionFilter(List<LocFeature>, boolean, boolean) - Constructor for class org.mulinlab.varnote.filters.RegionFilter

regionToBin4(int, int) - Static method in class org.mulinlab.varnote.constants.GlobalParameter

regionToNode(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

RegulatoryFeature - Class in org.mulinlab.varnote.utils.jannovar

RegulatoryFeature(int, int, int, RegulatoryFeature.FeatureType) - Constructor for class org.mulinlab.varnote.utils.jannovar.RegulatoryFeature

RegulatoryFeature.FeatureType - Enum in org.mulinlab.varnote.utils.jannovar

REMOVE_COMMENT - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

removeLog4JLoggingPath(String) - Static method in class org.mulinlab.varnote.utils.LoggingUtils

removeRSParam(List<DBParam>) - Static method in class org.mulinlab.varnote.utils.VannoUtils

replaceHeader - Variable in class org.mulinlab.varnote.cmdline.collection.IndexArgumentCollection

replaceHeader(String) - Method in class org.mulinlab.varnote.config.index.IndexWriteConfig

replaceQuote(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

reset() - Method in class org.mulinlab.varnote.utils.stream.LimitInputStream

ResultParser - Interface in org.mulinlab.varnote.config.parser

resultProcessor - Variable in class org.mulinlab.varnote.operations.stack.AbstractReaderStack

results - Variable in class org.mulinlab.varnote.operations.query.AbstractQuery

resultsFeatures - Variable in class org.mulinlab.varnote.operations.query.AbstractQuery

retrieveData(String, List<String[]>, int, String, String, boolean) - Static method in class org.mulinlab.varnote.utils.stream.LocalFile

retrieve data from a text file whith limited rows

retrieveData(String, List<String[]>, String) - Static method in class org.mulinlab.varnote.utils.stream.LocalFile

simply retrieve data from a file

retrieveData(String, Map<String, String>, String, int, int) - Static method in class org.mulinlab.varnote.utils.stream.LocalFile

retrieveData(String, StringBuilder) - Static method in class org.mulinlab.varnote.utils.stream.LocalFile

simply retrieve data from a file

retrieveData(String, Set<String>) - Static method in class org.mulinlab.varnote.utils.stream.LocalFile

simply retrieve data from a file

retrieveData(String, Set<String>, int) - Static method in class org.mulinlab.varnote.utils.stream.LocalFile

simply retrieve data from a file

retrieveData(String, List<String[]>, int[], Set<String>, int[], String) - Static method in class org.mulinlab.varnote.utils.stream.LocalFile

retrieve data from a text file it is based on split,

retrieveData(String, List<String[]>, int[], String) - Static method in class org.mulinlab.varnote.utils.stream.LocalFile

retrieve data from a text file it is based on tokenizor, but the order in the indices will be changed to the order of the files.

retrieveData(String, int) - Static method in class org.mulinlab.varnote.utils.stream.LocalFile

retrieve data from a text file it is based on tokenizor, but the order in the indices will be changed to the order of the files.

retrieveData(String, ArrayList<String[]>, int[], String[], int, String) - Static method in class org.mulinlab.varnote.utils.stream.LocalFile

retrieve data from a text file it is based on split,

rsid - Variable in class org.mulinlab.varnote.config.parser.output.ADOutFeature

RSID_POS_LABEL - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

RSIDLocCodec - Class in org.mulinlab.varnote.operations.decode

RSIDLocCodec(Format) - Constructor for class org.mulinlab.varnote.operations.decode.RSIDLocCodec

rsidPositionColumn - Variable in class org.mulinlab.varnote.utils.format.Format

run(OverlapRunConfig) - Static method in class org.mulinlab.varnote.utils.RunFactory

runAnnoFromOverlapFile(AnnoRunConfig) - Static method in class org.mulinlab.varnote.utils.RunFactory

RunArgumentCollection - Class in org.mulinlab.varnote.cmdline.collection

RunArgumentCollection() - Constructor for class org.mulinlab.varnote.cmdline.collection.RunArgumentCollection

runArguments - Variable in class org.mulinlab.varnote.cmdline.abstractclass.QueryFileProgram

RunConfig - Class in org.mulinlab.varnote.config.run

RunConfig() - Constructor for class org.mulinlab.varnote.config.run.RunConfig

RunConfig(QueryParam, List<DBParam>) - Constructor for class org.mulinlab.varnote.config.run.RunConfig

runCount(CountRunConfig) - Static method in class org.mulinlab.varnote.utils.RunFactory

RunFactory - Class in org.mulinlab.varnote.utils

RunFactory() - Constructor for class org.mulinlab.varnote.utils.RunFactory

runParam - Variable in class org.mulinlab.varnote.cmdline.txtreader.run.FileQueryReader

RunParam - Class in org.mulinlab.varnote.config.param

RunParam() - Constructor for class org.mulinlab.varnote.config.param.RunParam

RunParam(int) - Constructor for class org.mulinlab.varnote.config.param.RunParam

runParam - Variable in class org.mulinlab.varnote.config.run.RunConfig

RunProgram - Class in org.mulinlab.varnote.cmdline.abstractclass

RunProgram() - Constructor for class org.mulinlab.varnote.cmdline.abstractclass.RunProgram

runQuery(QueryRegionConfig) - Static method in class org.mulinlab.varnote.utils.RunFactory

RunReaderInterface<T> - Interface in org.mulinlab.varnote.cmdline.txtreader.abs

Mapper Interface

runTool() - Method in class org.mulinlab.varnote.cmdline.abstractclass.CMDProgram

S

seek(long) - Method in class org.mulinlab.varnote.operations.readers.db.VannoReader.VannoIteratorImpl

setAllele(String) - Method in class org.mulinlab.varnote.config.anno.ValWithAllele

setAllowLargeVariants(boolean) - Method in class org.mulinlab.varnote.utils.format.Format

setAnnoConfig(String) - Method in class org.mulinlab.varnote.config.run.AnnoRunConfig

setAnnoOutFormat(AnnoOutFormat) - Method in class org.mulinlab.varnote.config.param.output.AnnoOutParam

setAnnoOutFormat(String) - Method in class org.mulinlab.varnote.config.param.output.AnnoOutParam

setAutoThread() - Method in class org.mulinlab.varnote.config.param.RunParam

setBlockSize100k(int) - Method in class org.mulinlab.varnote.utils.stream.AdvancedBZip2CompressorInputStream

setCols(String) - Method in class org.mulinlab.varnote.config.param.postDB.DBAnnoParam

setCommentIndicator(String) - Method in class org.mulinlab.varnote.config.param.postDB.PostDBParam

setCommentIndicator(String) - Method in class org.mulinlab.varnote.utils.format.Format

setConfig(AnnoRunConfig) - Method in class org.mulinlab.varnote.cmdline.collection.AnnoConfigArgumentCollection

setDataStr(String) - Method in class org.mulinlab.varnote.utils.format.Format

setDB() - Method in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

setDbParams(String[]) - Method in class org.mulinlab.varnote.config.run.RunConfig

setDbParams(List<DBParam>) - Method in class org.mulinlab.varnote.config.run.RunConfig

setDbPath(String) - Method in class org.mulinlab.varnote.config.param.DBParam

setDecodeFull(boolean) - Method in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

setDecodeLoc(boolean) - Method in class org.mulinlab.varnote.operations.readers.query.VCFFileReader

setDefalutOutFormat(Format) - Method in class org.mulinlab.varnote.config.param.output.AnnoOutParam

setDefalutOutPath(String) - Method in class org.mulinlab.varnote.config.param.output.OutParam

setDefaultCol(String[]) - Static method in class org.mulinlab.varnote.utils.VannoUtils

setDefaultCompressionLevel(int) - Static method in class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

Sets the GZip compression level for subsequent BlockCompressedOutputStream object creation that do not specify the compression level.

setDefaultDeflaterFactory(DeflaterFactory) - Static method in class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

Sets the default DeflaterFactory that will be used for all instances unless specified otherwise in the constructor.

setDefaultLocCodec(boolean) - Method in class org.mulinlab.varnote.utils.database.Database

setDefaultOutDir() - Method in class org.mulinlab.varnote.config.param.IndexParam

setDelimiter(Delimiter) - Method in class org.mulinlab.varnote.utils.format.Format

setDisplayLabel(boolean) - Method in class org.mulinlab.varnote.config.run.QueryRegionConfig

setEnd(int) - Method in class org.mulinlab.varnote.utils.block.BlockFeature.VannoFeature

setFields(String) - Method in class org.mulinlab.varnote.config.param.postDB.DBAnnoParam

setFilePointer(long) - Method in class org.mulinlab.varnote.operations.index.IndexWriter.BlockBean

setFilePointer(long) - Method in class org.mulinlab.varnote.operations.readers.db.VannoReader.SROBListRead

setFilterParam(FilterParam) - Method in class org.mulinlab.varnote.config.param.query.QueryFileParam

setForceOverlap(boolean) - Method in class org.mulinlab.varnote.config.run.AnnoRunConfig

setForceOverlap(String) - Method in class org.mulinlab.varnote.config.run.AnnoRunConfig

setFormat(Format) - Method in class org.mulinlab.varnote.cmdline.collection.TagArgument

setformat(Format) - Method in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

setFormat(Format) - Method in class org.mulinlab.varnote.config.param.IndexParam

setFormat(Format) - Method in class org.mulinlab.varnote.utils.database.Database

setformatHeader(Format) - Method in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

setFull(boolean) - Method in class org.mulinlab.varnote.operations.decode.LocCodec

setGenome(GenomeAssembly) - Method in class org.mulinlab.varnote.utils.JannovarUtils

setGenotypeFilters(List<GenotypeFilter>) - Method in class org.mulinlab.varnote.config.param.FilterParam

setGzip(boolean) - Method in class org.mulinlab.varnote.config.param.output.OutParam

setHasHeader(boolean) - Method in class org.mulinlab.varnote.config.param.postDB.PostDBParam

setHasHeaderInFile(boolean) - Method in class org.mulinlab.varnote.utils.format.Format

setHeader(String) - Method in class org.mulinlab.varnote.utils.format.Format

setHeaderPart(String[]) - Method in class org.mulinlab.varnote.utils.format.Format

setHeaderPath(String) - Method in class org.mulinlab.varnote.config.param.postDB.PostDBParam

setHeaderPath(String) - Method in class org.mulinlab.varnote.utils.format.Format

setIndexType(IndexType) - Method in class org.mulinlab.varnote.config.param.DBParam

setIndexType(String) - Method in class org.mulinlab.varnote.config.param.DBParam

setInfofieldOps(String) - Method in class org.mulinlab.varnote.config.param.postDB.DBFilterParam

setInfofields(String) - Method in class org.mulinlab.varnote.config.param.postDB.DBAnnoParam

setIntersect(String) - Method in class org.mulinlab.varnote.config.param.DBParam

setIntersect(IntersectType) - Method in class org.mulinlab.varnote.config.param.DBParam

setIseof(boolean) - Method in class org.mulinlab.varnote.operations.stack.AbstractReaderStack

setIterator(AbstractDBReader.Iterator) - Method in class org.mulinlab.varnote.operations.stack.AbstractReaderStack

setJannovarData() - Method in class org.mulinlab.varnote.utils.JannovarUtils

setLabel(String) - Method in class org.mulinlab.varnote.config.param.postDB.PostDBParam

setLocFilter() - Method in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

setLocFilters(List<VariantFilter>) - Method in class org.mulinlab.varnote.config.param.query.QueryFileParam

setLocFilters(List<VariantFilter>) - Method in class org.mulinlab.varnote.filters.iterator.LocFilterIterator

setLocFilters(List<VariantFilter>) - Method in class org.mulinlab.varnote.operations.readers.query.AbstractFileReader

setLog4JLoggingPath(String, String) - Static method in class org.mulinlab.varnote.utils.LoggingUtils

setLoggingLevel(Log.LogLevel) - Static method in class org.mulinlab.varnote.utils.LoggingUtils

setLoj(boolean) - Method in class org.mulinlab.varnote.config.param.output.OutParam

setMax(int) - Method in class org.mulinlab.varnote.utils.block.SROB

setMaxCount(int) - Method in class org.mulinlab.varnote.utils.TimeMetric

setMaxVariantLength(int) - Method in class org.mulinlab.varnote.utils.format.Format

setMFP(BlockCompressedInputStream) - Method in class org.mulinlab.varnote.operations.process.VannoResultProcess

setMiFilter(MendelianInheritanceFilter) - Method in class org.mulinlab.varnote.config.param.FilterParam

setMin(int) - Method in class org.mulinlab.varnote.utils.block.SROB

setMode(Mode) - Method in class org.mulinlab.varnote.config.param.RunParam

setName(String) - Method in class org.mulinlab.varnote.utils.jannovar.GeneBuilder

setOutFileSuffix(String) - Method in class org.mulinlab.varnote.config.param.output.OutParam

setOutName(String) - Method in class org.mulinlab.varnote.config.param.DBParam

setOutNames(String) - Method in class org.mulinlab.varnote.config.param.postDB.DBAnnoParam

setOutParam(OutParam) - Method in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

setOutParam(OutParam) - Method in class org.mulinlab.varnote.config.run.RunConfig

setOutputDir(String) - Method in class org.mulinlab.varnote.config.param.IndexParam

setOutputMode(OutMode) - Method in class org.mulinlab.varnote.config.param.output.OutParam

setOutputMode(int) - Method in class org.mulinlab.varnote.config.param.output.OutParam

setOutputName(String) - Method in class org.mulinlab.varnote.config.param.output.OutParam

setOutputPath(String) - Method in class org.mulinlab.varnote.config.param.output.OutParam

setOverlapFile(String) - Method in class org.mulinlab.varnote.config.run.AnnoRunConfig

setParam() - Method in class org.mulinlab.varnote.cmdline.abstractclass.IndexProgram

setParam(Database) - Method in class org.mulinlab.varnote.utils.database.Database

setPrintter(int) - Method in class org.mulinlab.varnote.config.io.temp.Printter

setQueryParam(QueryParam) - Method in class org.mulinlab.varnote.config.run.RunConfig

setReadBlock(boolean) - Method in class org.mulinlab.varnote.utils.block.BlockFeature

setRegion(String) - Method in class org.mulinlab.varnote.config.param.query.QueryRegionParam

setRegionFilter(RegionFilter) - Method in class org.mulinlab.varnote.config.param.FilterParam

setRemoveCommemt(boolean) - Method in class org.mulinlab.varnote.config.param.output.IntersetOutParam

setResult(String) - Method in class org.mulinlab.varnote.config.parser.output.AnnoOut

setResultProcessor(ProcessResult) - Method in class org.mulinlab.varnote.operations.stack.AbstractReaderStack

setRsid(String) - Method in class org.mulinlab.varnote.config.parser.output.ADOutFeature

setRunParam(RunParam) - Method in class org.mulinlab.varnote.config.run.RunConfig

setSROB(long, int, int) - Method in class org.mulinlab.varnote.utils.block.SROB

setTag(String) - Method in class org.mulinlab.varnote.cmdline.collection.TagArgument

setTagAttributes(Map<String, String>) - Method in class org.mulinlab.varnote.cmdline.collection.TagArgument

setThread(int) - Method in class org.mulinlab.varnote.config.param.RunParam

setThread(int) - Method in class org.mulinlab.varnote.config.run.RunConfig

setVannoFeature(int, int, int) - Method in class org.mulinlab.varnote.utils.block.BlockFeature.VannoFeature

setVannoFilePointer(long) - Method in class org.mulinlab.varnote.utils.block.SROB

setVariantEffect(JannovarUtils) - Method in class org.mulinlab.varnote.config.parser.output.ADOutFeature

setVariantFilters(List<VariantFilter>) - Method in class org.mulinlab.varnote.config.param.FilterParam

setVariantFilters(FilterParam) - Method in class org.mulinlab.varnote.operations.readers.query.VCFFileReader

setVcfHeaderPathForBED(String) - Method in class org.mulinlab.varnote.config.run.AnnoRunConfig

setVcfInfoPath(String) - Method in class org.mulinlab.varnote.config.param.postDB.DBAnnoParam

setVCFLocCodec(boolean) - Method in class org.mulinlab.varnote.utils.database.Database

setVcfParser(VCFParser) - Method in class org.mulinlab.varnote.operations.readers.query.VCFFileReader

setZeroBased() - Method in class org.mulinlab.varnote.utils.format.Format

sex(Pedigree.Individual.Sex) - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual.Builder

SimpleMapReduce<T,M> - Class in org.mulinlab.varnote.utils.mapreduce

SimpleMapReduce(int, Reducer<T, Mapper<M>, M>) - Constructor for class org.mulinlab.varnote.utils.mapreduce.SimpleMapReduce

size() - Method in class org.mulinlab.varnote.utils.jannovar.ChromosomalRegionIndex

Returns the number of intervals stored in the index.

size() - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree

skip - Variable in class org.mulinlab.varnote.cmdline.index.Index

skip(long) - Method in class org.mulinlab.varnote.utils.stream.LimitInputStream

SkipLineFilter - Class in org.mulinlab.varnote.filters.query.line

SkipLineFilter(int) - Constructor for class org.mulinlab.varnote.filters.query.line.SkipLineFilter

Snp2PosMode - Enum in org.mulinlab.varnote.utils.enumset

spider - Variable in class org.mulinlab.varnote.utils.stream.BZIP2InputStream

Spider(int, int, long, long, char) - Constructor for class org.mulinlab.varnote.utils.stream.BZIP2InputStream.Spider

SpiderReader - Class in org.mulinlab.varnote.operations.readers.itf.thread

SpiderReader(BZIP2InputStream.Spider) - Constructor for class org.mulinlab.varnote.operations.readers.itf.thread.SpiderReader

splitFile(int) - Method in class org.mulinlab.varnote.config.param.query.QueryFileParam

splitLine(String) - Method in class org.mulinlab.varnote.cmdline.txtreader.abs.AbstractQueryReader

splitLine(String) - Method in class org.mulinlab.varnote.cmdline.txtreader.anno.OverlapHeaderReader

srob - Variable in class org.mulinlab.varnote.operations.readers.db.VannoReader

SROB - Class in org.mulinlab.varnote.utils.block

SROB(int, int, long, long) - Constructor for class org.mulinlab.varnote.utils.block.SROB

SROB(long, int, int) - Constructor for class org.mulinlab.varnote.utils.block.SROB

SROB.Feature - Class in org.mulinlab.varnote.utils.block

SROBListBean() - Constructor for class org.mulinlab.varnote.operations.index.IndexWriter.SROBListBean

SROBListRead() - Constructor for class org.mulinlab.varnote.operations.readers.db.VannoReader.SROBListRead

srobRead - Variable in class org.mulinlab.varnote.operations.readers.db.VannoReader

st - Variable in class org.mulinlab.varnote.operations.stack.ExactStack

st - Variable in class org.mulinlab.varnote.operations.stack.IntervalStack

stack - Variable in class org.mulinlab.varnote.operations.readers.db.AbstractDBReader

start - Variable in class org.mulinlab.varnote.utils.TimeMetric

START_COMPARE_LENGTH - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

START_COMPARE_LENGTH - Static variable in class org.mulinlab.varnote.utils.format.Format

status(Pedigree.Individual.Status) - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual.Builder

STOP - Static variable in class org.mulinlab.varnote.operations.readers.db.VannoReader

stripQueryStringIfPathIsAnHttpUrl(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

strToBool(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

strToRegion(List<String>) - Static method in class org.mulinlab.varnote.utils.GenomicRegionUtils

SweepIteratorImpl(int) - Constructor for class org.mulinlab.varnote.operations.readers.db.TbiSweepReader.SweepIteratorImpl

SweepIteratorImpl(BlockCompressedInputStream) - Constructor for class org.mulinlab.varnote.operations.readers.db.VannoSweepReader.SweepIteratorImpl

SweepQuery - Class in org.mulinlab.varnote.operations.query

SweepQuery(List<Database>) - Constructor for class org.mulinlab.varnote.operations.query.SweepQuery

T

TAB - Static variable in class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

TAB - Static variable in class org.mulinlab.varnote.config.parser.AnnoParser

TAB - Static variable in class org.mulinlab.varnote.config.run.RunConfig

TAB - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

TAB - Static variable in class org.mulinlab.varnote.utils.RunFactory

TABFileReader - Class in org.mulinlab.varnote.operations.readers.query

TABFileReader(QueryReaderItf, Format) - Constructor for class org.mulinlab.varnote.operations.readers.query.TABFileReader

TABFileReader(String, Format) - Constructor for class org.mulinlab.varnote.operations.readers.query.TABFileReader

TABFileReader(String, FileType, Format) - Constructor for class org.mulinlab.varnote.operations.readers.query.TABFileReader

TABHeaderLineFilter - Class in org.mulinlab.varnote.filters.query.line

TABHeaderLineFilter(Format) - Constructor for class org.mulinlab.varnote.filters.query.line.TABHeaderLineFilter

TabixQuery - Class in org.mulinlab.varnote.operations.query

TabixQuery(List<Database>) - Constructor for class org.mulinlab.varnote.operations.query.TabixQuery

TabixResultProcess - Class in org.mulinlab.varnote.operations.process

TabixResultProcess() - Constructor for class org.mulinlab.varnote.operations.process.TabixResultProcess

TABLocCodec - Class in org.mulinlab.varnote.operations.decode

TABLocCodec(Format, boolean) - Constructor for class org.mulinlab.varnote.operations.decode.TABLocCodec

TagArgument - Class in org.mulinlab.varnote.cmdline.collection

TagArgument(String) - Constructor for class org.mulinlab.varnote.cmdline.collection.TagArgument

TagArgument(String, String) - Constructor for class org.mulinlab.varnote.cmdline.collection.TagArgument

TbiDatabase - Class in org.mulinlab.varnote.utils.database

TbiDatabase(DBParam) - Constructor for class org.mulinlab.varnote.utils.database.TbiDatabase

TbiIndex - Class in org.mulinlab.varnote.utils.database.index

TbiIndex(String) - Constructor for class org.mulinlab.varnote.utils.database.index.TbiIndex

TbiIteratorImpl(int) - Constructor for class org.mulinlab.varnote.operations.readers.db.TbiReader.TbiIteratorImpl

TbiMixReader - Class in org.mulinlab.varnote.operations.readers.db

TbiMixReader(String) - Constructor for class org.mulinlab.varnote.operations.readers.db.TbiMixReader

TbiMixReader(String, boolean) - Constructor for class org.mulinlab.varnote.operations.readers.db.TbiMixReader

TbiMixReader(Database) - Constructor for class org.mulinlab.varnote.operations.readers.db.TbiMixReader

TbiMixReader(Database, boolean) - Constructor for class org.mulinlab.varnote.operations.readers.db.TbiMixReader

TbiMixReader.MixIteratorImpl - Class in org.mulinlab.varnote.operations.readers.db

TbiReader - Class in org.mulinlab.varnote.operations.readers.db

TbiReader(Database, boolean) - Constructor for class org.mulinlab.varnote.operations.readers.db.TbiReader

TbiReader(Database) - Constructor for class org.mulinlab.varnote.operations.readers.db.TbiReader

TbiReader(String) - Constructor for class org.mulinlab.varnote.operations.readers.db.TbiReader

TbiReader(String, boolean) - Constructor for class org.mulinlab.varnote.operations.readers.db.TbiReader

TbiReader.TbiIteratorImpl - Class in org.mulinlab.varnote.operations.readers.db

TbiSweepReader - Class in org.mulinlab.varnote.operations.readers.db

TbiSweepReader(String) - Constructor for class org.mulinlab.varnote.operations.readers.db.TbiSweepReader

TbiSweepReader(String, boolean) - Constructor for class org.mulinlab.varnote.operations.readers.db.TbiSweepReader

TbiSweepReader(Database) - Constructor for class org.mulinlab.varnote.operations.readers.db.TbiSweepReader

TbiSweepReader(Database, boolean) - Constructor for class org.mulinlab.varnote.operations.readers.db.TbiSweepReader

TbiSweepReader.SweepIteratorImpl - Class in org.mulinlab.varnote.operations.readers.db

teardown() - Method in class org.mulinlab.varnote.operations.query.AbstractQuery

teardown() - Method in class org.mulinlab.varnote.operations.query.TabixQuery

tearDownPrintter() - Method in class org.mulinlab.varnote.config.io.temp.ThreadPrintter

TEMP - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

tempFolderPath - Variable in class org.mulinlab.varnote.config.io.temp.Printter

tempNode - Variable in class org.mulinlab.varnote.operations.stack.ExactStack

tempNode - Variable in class org.mulinlab.varnote.operations.stack.IntervalStack

THREAD - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

ThreadPrintter - Class in org.mulinlab.varnote.config.io.temp

ThreadPrintter(String, int) - Constructor for class org.mulinlab.varnote.config.io.temp.ThreadPrintter

threadPrintters - Variable in class org.mulinlab.varnote.config.io.temp.Printter

threadReaders - Variable in class org.mulinlab.varnote.config.param.query.QueryFileParam

tid - Variable in class org.mulinlab.varnote.operations.readers.db.TbiReader.TbiIteratorImpl

tid2chr(int) - Method in class org.mulinlab.varnote.utils.database.index.Index

timeFmt - Static variable in class org.mulinlab.varnote.utils.TimeMetric

timeMetric - Variable in class org.mulinlab.varnote.operations.mapper.AbstractMapper

TimeMetric - Class in org.mulinlab.varnote.utils

TimeMetric(String) - Constructor for class org.mulinlab.varnote.utils.TimeMetric

toBEDHeader(StringJoiner) - Method in class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

toBEDHeader(StringJoiner) - Method in class org.mulinlab.varnote.config.anno.query.QueryBEDParser

toBEDHeader(StringJoiner) - Method in class org.mulinlab.varnote.config.anno.query.QueryVCFParser

toBEDRecord(LocFeature, StringJoiner) - Method in class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

toBEDRecord(LocFeature, StringJoiner) - Method in class org.mulinlab.varnote.config.anno.query.QueryBEDParser

toBEDRecord(LocFeature, StringJoiner) - Method in class org.mulinlab.varnote.config.anno.query.QueryVCFParser

toCellMark(String) - Static method in enum org.mulinlab.varnote.utils.enumset.CellMark

toChromosomeType(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

toDelimiter(String) - Static method in enum org.mulinlab.varnote.utils.enumset.Delimiter

toGenomicRegionType(int) - Static method in enum org.mulinlab.varnote.utils.enumset.GenomicRegionType

toIntersectType(int) - Static method in enum org.mulinlab.varnote.utils.enumset.IntersectType

toLines(File) - Static method in class org.mulinlab.varnote.utils.GenomicRegionUtils

toOutMode(int) - Static method in enum org.mulinlab.varnote.utils.enumset.OutMode

toPriority(int) - Static method in enum org.mulinlab.varnote.utils.enumset.Priority

toRs2PosMode(int) - Static method in enum org.mulinlab.varnote.utils.enumset.Snp2PosMode

toString() - Method in class org.mulinlab.varnote.cmdline.collection.TagArgument

toString() - Method in class org.mulinlab.varnote.operations.readers.db.TbiSweepReader

toString() - Method in class org.mulinlab.varnote.operations.readers.db.VannoMixReader

toString() - Method in class org.mulinlab.varnote.operations.readers.db.VannoSweepReader

toString() - Method in enum org.mulinlab.varnote.utils.enumset.GenomeAssembly

toString() - Method in enum org.mulinlab.varnote.utils.enumset.TranscriptSource

toString() - Method in class org.mulinlab.varnote.utils.format.Format

toString() - Method in class org.mulinlab.varnote.utils.jannovar.AllelePosition

toString() - Method in class org.mulinlab.varnote.utils.jannovar.Gene

toString() - Method in class org.mulinlab.varnote.utils.jannovar.RegulatoryFeature

toString() - Method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation

toString() - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation

toString() - Method in class org.mulinlab.varnote.utils.node.LocFeature

toString() - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree.Individual

toString() - Method in class org.mulinlab.varnote.utils.pedigree.Pedigree

toVCFHeader() - Method in class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

toVCFHeader() - Method in class org.mulinlab.varnote.config.anno.query.QueryBEDParser

toVCFHeader() - Method in class org.mulinlab.varnote.config.anno.query.QueryVCFParser

toVCFRecord(LocFeature, StringJoiner) - Method in class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

toVCFRecord(LocFeature, StringJoiner) - Method in class org.mulinlab.varnote.config.anno.query.QueryBEDParser

toVCFRecord(LocFeature, StringJoiner) - Method in class org.mulinlab.varnote.config.anno.query.QueryVCFParser

TranscriptAnnotation - Class in org.mulinlab.varnote.utils.jannovar

TranscriptAnnotation.Builder - Class in org.mulinlab.varnote.utils.jannovar

transcriptSource - Variable in class org.mulinlab.varnote.cmdline.collection.VariantEffectArgumentCollection

TranscriptSource - Enum in org.mulinlab.varnote.utils.enumset

trim(int, String, String) - Static method in class org.mulinlab.varnote.utils.jannovar.AllelePosition

Trims the right, then left side of the given variant allele.

trimAndLC(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

TYPE - Static variable in class org.mulinlab.varnote.cmdline.txtreader.anno.VcfInfoReader

type - Variable in class org.mulinlab.varnote.utils.format.Format

U

UNDERLINE - Static variable in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

UNDERLINE - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

UNSET_GENOMIC_LOCATION - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

updateMax(LocFeature, int) - Method in class org.mulinlab.varnote.utils.block.SROB

USE_JDK_DEFLATER - Variable in class org.mulinlab.varnote.cmdline.abstractclass.IndexProgram

USE_JDK_INFLATER - Variable in class org.mulinlab.varnote.cmdline.abstractclass.RunProgram

USE_JDK_INFLATER - Variable in class org.mulinlab.varnote.cmdline.tools.RandomAccess

USE_JDK_INFLATER - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

USE_JDK_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

USE_JDK_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

USE_JDKI_LONG - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

USE_JDKI_SHORT - Static variable in class org.mulinlab.varnote.cmdline.constant.Arguments

V

VairantQC - Enum in org.mulinlab.varnote.utils.enumset

validRsid(String) - Static method in class org.mulinlab.varnote.utils.VannoUtils

validTypes() - Static method in enum org.mulinlab.varnote.utils.enumset.GenomicRegionType

valueHash - Variable in class org.mulinlab.varnote.cmdline.txtreader.abs.AbstractQueryReader

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.AFSource

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.AnnoOutFormat

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.CellMark

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.CellType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.ChromosomeType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.Delimiter

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.FileType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.FormatType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.GenomeAssembly

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.GenomicRegionType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.GenotypeQC

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.IndexType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.IntersectType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.Mode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.ModeOfInheritance

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.OutMode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.Population

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.PredictionFunc

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.Priority

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.QuickFileType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.RegFunc

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.Snp2PosMode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.TranscriptSource

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.VairantQC

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.enumset.VariantType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.jannovar.RegulatoryFeature.FeatureType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.pedigree.Pedigree.Individual.Sex

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.pedigree.Pedigree.Individual.Status

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.mulinlab.varnote.utils.VannoUtils.FileExt

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.AFSource

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.AnnoOutFormat

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.CellMark

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.CellType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.ChromosomeType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.Delimiter

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.FileType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.FormatType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.GenomeAssembly

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.GenomicRegionType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.GenotypeQC

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.IndexType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.IntersectType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.Mode

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.ModeOfInheritance

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.OutMode

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.Population

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.PredictionFunc

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.Priority

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.QuickFileType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.RegFunc

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.Snp2PosMode

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.TranscriptSource

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.VairantQC

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.enumset.VariantType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.jannovar.RegulatoryFeature.FeatureType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.pedigree.Pedigree.Individual.Sex

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.pedigree.Pedigree.Individual.Status

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.mulinlab.varnote.utils.VannoUtils.FileExt

Returns an array containing the constants of this enum type, in the order they are declared.

ValWithAllele - Class in org.mulinlab.varnote.config.anno

ValWithAllele(String, String) - Constructor for class org.mulinlab.varnote.config.anno.ValWithAllele

VANNO_FILE_END - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

VannoDatabase - Class in org.mulinlab.varnote.utils.database

VannoDatabase(DBParam) - Constructor for class org.mulinlab.varnote.utils.database.VannoDatabase

vannoFeature - Variable in class org.mulinlab.varnote.operations.readers.db.VannoReader.VannoIteratorImpl

VannoFeature() - Constructor for class org.mulinlab.varnote.utils.block.BlockFeature.VannoFeature

vannoFile - Variable in class org.mulinlab.varnote.cmdline.index.IndexInfo

vannoFile - Variable in class org.mulinlab.varnote.operations.readers.db.VannoReader

VannoIndex - Class in org.mulinlab.varnote.utils.database.index.vannoIndex

VannoIndex(BlockCompressedInputStream, int) - Constructor for class org.mulinlab.varnote.utils.database.index.vannoIndex.VannoIndex

vannoIndexFile - Variable in class org.mulinlab.varnote.operations.readers.db.VannoReader

VannoIndexV1 - Class in org.mulinlab.varnote.utils.database.index.vannoIndex

VannoIndexV1(BlockCompressedInputStream, int) - Constructor for class org.mulinlab.varnote.utils.database.index.vannoIndex.VannoIndexV1

VannoIteratorImpl(BlockCompressedInputStream) - Constructor for class org.mulinlab.varnote.operations.readers.db.VannoReader.VannoIteratorImpl

VannoMixReader - Class in org.mulinlab.varnote.operations.readers.db

VannoMixReader(String) - Constructor for class org.mulinlab.varnote.operations.readers.db.VannoMixReader

VannoMixReader(String, boolean) - Constructor for class org.mulinlab.varnote.operations.readers.db.VannoMixReader

VannoMixReader(Database) - Constructor for class org.mulinlab.varnote.operations.readers.db.VannoMixReader

VannoMixReader(Database, boolean) - Constructor for class org.mulinlab.varnote.operations.readers.db.VannoMixReader

VannoMixReader.MixVannoIteratorImpl - Class in org.mulinlab.varnote.operations.readers.db

VannoQuery - Class in org.mulinlab.varnote.operations.query

VannoQuery(List<Database>) - Constructor for class org.mulinlab.varnote.operations.query.VannoQuery

VannoQuery(List<Database>, boolean) - Constructor for class org.mulinlab.varnote.operations.query.VannoQuery

VannoReader - Class in org.mulinlab.varnote.operations.readers.db

VannoReader(String) - Constructor for class org.mulinlab.varnote.operations.readers.db.VannoReader

VannoReader(String, boolean) - Constructor for class org.mulinlab.varnote.operations.readers.db.VannoReader

VannoReader(Database) - Constructor for class org.mulinlab.varnote.operations.readers.db.VannoReader

VannoReader(Database, boolean) - Constructor for class org.mulinlab.varnote.operations.readers.db.VannoReader

VannoReader.SROBListRead - Class in org.mulinlab.varnote.operations.readers.db

VannoReader.VannoIteratorImpl - Class in org.mulinlab.varnote.operations.readers.db

VannoResultProcess - Class in org.mulinlab.varnote.operations.process

VannoResultProcess() - Constructor for class org.mulinlab.varnote.operations.process.VannoResultProcess

VannoSweepReader - Class in org.mulinlab.varnote.operations.readers.db

VannoSweepReader(String) - Constructor for class org.mulinlab.varnote.operations.readers.db.VannoSweepReader

VannoSweepReader(String, boolean) - Constructor for class org.mulinlab.varnote.operations.readers.db.VannoSweepReader

VannoSweepReader(Database) - Constructor for class org.mulinlab.varnote.operations.readers.db.VannoSweepReader

VannoSweepReader(Database, boolean) - Constructor for class org.mulinlab.varnote.operations.readers.db.VannoSweepReader

VannoSweepReader.SweepIteratorImpl - Class in org.mulinlab.varnote.operations.readers.db

VannoUtils - Class in org.mulinlab.varnote.utils

VannoUtils() - Constructor for class org.mulinlab.varnote.utils.VannoUtils

VannoUtils.FileExt - Enum in org.mulinlab.varnote.utils

VARIABLE_BEGIN - Static variable in class org.mulinlab.varnote.config.anno.FieldFormat

Variant - Interface in org.mulinlab.varnote.utils.jannovar

VariantAnnotation - Class in org.mulinlab.varnote.utils.jannovar

Simple immutable data class to represent annotations for a variant.

VariantAnnotation.Builder - Class in org.mulinlab.varnote.utils.jannovar

VariantAnnotator - Interface in org.mulinlab.varnote.utils.jannovar

variantContext - Variable in class org.mulinlab.varnote.utils.node.LocFeature

VariantCoordinates - Interface in org.mulinlab.varnote.utils.jannovar

variantEffect - Variable in class org.mulinlab.varnote.config.parser.output.ADOutFeature

variantEffect(VariantEffect) - Method in class org.mulinlab.varnote.utils.jannovar.TranscriptAnnotation.Builder

variantEffect(VariantEffect) - Method in class org.mulinlab.varnote.utils.jannovar.VariantAnnotation.Builder

VariantEffectArgumentCollection - Class in org.mulinlab.varnote.cmdline.collection

VariantEffectArgumentCollection() - Constructor for class org.mulinlab.varnote.cmdline.collection.VariantEffectArgumentCollection

VariantEffectUtility - Class in org.mulinlab.varnote.utils.jannovar

VariantFilter<T> - Interface in org.mulinlab.varnote.filters.query

VariantType - Enum in org.mulinlab.varnote.utils.enumset

VarNoteCommandLine - Class in org.mulinlab.varnote.cmdline

VarNoteCommandLine() - Constructor for class org.mulinlab.varnote.cmdline.VarNoteCommandLine

varValues() - Static method in enum org.mulinlab.varnote.utils.enumset.FormatType

VCF_FIELD - Static variable in class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

VCF_FIELD - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

VCF_HEADER_INDICATOR - Static variable in class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

VCF_HEADER_INDICATOR - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

VCF_HEADER_PATH_FOR_BED - Static variable in class org.mulinlab.varnote.cmdline.txtreader.run.AnnoRunReader

VCF_INFO_EQUAL - Static variable in class org.mulinlab.varnote.config.anno.databse.anno.AbstractDatababseAnnoParser

VCF_INFO_EQUAL - Static variable in class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

VCF_INFO_EQUAL - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

VCFFileReader - Class in org.mulinlab.varnote.operations.readers.query

VCFFileReader(QueryReaderItf, Format) - Constructor for class org.mulinlab.varnote.operations.readers.query.VCFFileReader

VCFFileReader(String) - Constructor for class org.mulinlab.varnote.operations.readers.query.VCFFileReader

VCFFileReader(String, Format) - Constructor for class org.mulinlab.varnote.operations.readers.query.VCFFileReader

VCFFileReader(String, FileType, Format) - Constructor for class org.mulinlab.varnote.operations.readers.query.VCFFileReader

VCFFilterIterator - Class in org.mulinlab.varnote.filters.iterator

VCFFilterIterator(NoFilterIterator, List<LineFilter>, FilterParam, VCFLocCodec) - Constructor for class org.mulinlab.varnote.filters.iterator.VCFFilterIterator

VCFHeaderLineFilter - Class in org.mulinlab.varnote.filters.query.line

VCFHeaderLineFilter() - Constructor for class org.mulinlab.varnote.filters.query.line.VCFHeaderLineFilter

VCFINFO - Static variable in class org.mulinlab.varnote.cmdline.txtreader.anno.AnnoConfigReader

VcfInfoReader<T> - Class in org.mulinlab.varnote.cmdline.txtreader.anno

VcfInfoReader() - Constructor for class org.mulinlab.varnote.cmdline.txtreader.anno.VcfInfoReader

VCFLocCodec - Class in org.mulinlab.varnote.operations.decode

VCFLocCodec(Format, boolean, VCFHeader) - Constructor for class org.mulinlab.varnote.operations.decode.VCFLocCodec

VCFLocCodec(Format, boolean, VCFParser) - Constructor for class org.mulinlab.varnote.operations.decode.VCFLocCodec

VCFParser - Class in org.mulinlab.varnote.config.anno.databse

VCFParser(String) - Constructor for class org.mulinlab.varnote.config.anno.databse.VCFParser

VCFParser(String, FileType) - Constructor for class org.mulinlab.varnote.config.anno.databse.VCFParser

vcfParser - Variable in class org.mulinlab.varnote.utils.database.Database

VERBOSE - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

version - Static variable in class org.mulinlab.varnote.constants.GlobalParameter

version - Variable in class org.mulinlab.varnote.utils.database.index.vannoIndex.VannoIndex

vt - Variable in class org.mulinlab.varnote.utils.node.LocFeature

W

write(MyEndianOutputStream, int, int) - Method in class org.mulinlab.varnote.operations.index.IndexWriter

write(byte[]) - Method in class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

Writes b.length bytes from the specified byte array to this output stream.

write(byte[], int, int) - Method in class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

Writes len bytes from the specified byte array starting at offset off to this output stream.

write(int) - Method in class org.mulinlab.varnote.utils.gz.MyBlockCompressedOutputStream

Writes the specified byte to this output stream.

write(int) - Method in class org.mulinlab.varnote.utils.gz.MyEndianOutputStream

writeBoolean(boolean) - Method in class org.mulinlab.varnote.utils.gz.MyEndianOutputStream

writeByte(int) - Method in class org.mulinlab.varnote.utils.gz.MyEndianOutputStream

writeBytes(String) - Method in class org.mulinlab.varnote.utils.gz.MyEndianOutputStream

writeChar(int) - Method in class org.mulinlab.varnote.utils.gz.MyEndianOutputStream

writeData(String, List<String[]>, String, boolean) - Static method in class org.mulinlab.varnote.utils.stream.LocalFile

write data to a text file

writeData(BufferedWriter, List<String[]>, String) - Static method in class org.mulinlab.varnote.utils.stream.LocalFile

writeDouble(double) - Method in class org.mulinlab.varnote.utils.gz.MyEndianOutputStream

writeFloat(float) - Method in class org.mulinlab.varnote.utils.gz.MyEndianOutputStream

writeFormats(MyEndianOutputStream, Format, String[], List<String>, Map<Integer, Long>) - Static method in class org.mulinlab.varnote.utils.VannoUtils

writeIndex(IndexWriteConfig) - Static method in class org.mulinlab.varnote.utils.RunFactory

writeIndexForBGZ(AbstractFileReader) - Method in class org.mulinlab.varnote.operations.index.IndexWriter

writeInt(int) - Method in class org.mulinlab.varnote.utils.gz.MyEndianOutputStream

writeLine(String) - Method in class org.mulinlab.varnote.config.io.PrintGZ

writeLong(long) - Method in class org.mulinlab.varnote.utils.gz.MyEndianOutputStream

writeObject2Text(String, List<Object[]>, String) - Static method in class org.mulinlab.varnote.utils.stream.LocalFile

write data to a text file

writeShort(MyEndianOutputStream, int) - Method in class org.mulinlab.varnote.operations.index.IndexWriter

writeShort(int) - Method in class org.mulinlab.varnote.utils.gz.MyEndianOutputStream

Z

ZERO_BASED - Static variable in class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

ZipPrintter - Class in org.mulinlab.varnote.config.io.temp

ZipPrintter(OutParam) - Constructor for class org.mulinlab.varnote.config.io.temp.ZipPrintter

ZipThreadPrintter - Class in org.mulinlab.varnote.config.io.temp

ZipThreadPrintter(String, int) - Constructor for class org.mulinlab.varnote.config.io.temp.ZipThreadPrintter

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