All Classes
ABGenotypeFilter
AbstractDatababseAnnoParser
AbstractDatabaseFilter
AbstractDBReader
AbstractDBReader.Iterator
AbstractFileReader
AbstractMapper
AbstractQuery
AbstractQueryParser
AbstractQueryReader
AbstractReaderStack
ABVariantFilter
ADOutFeature
AdvancedBZip2CompressorInputStream
AFSource
AllelePosition
AnnoConfigArgumentCollection
AnnoConfigReader
AnnoMapper
AnnoOut
AnnoOutFormat
AnnoOutParam
AnnoOutputArgumentCollection
AnnoParser
AnnoProgramGroup
AnnoRunConfig
AnnoRunReader
Annotation
AnnotationConfig
AnnotationIntersectFile
Arguments
BEDFileReader
BEDHeaderLineFilter
BEDLocCodec
BGZReader
BGZReader
BlockCompressedFilePointerUtil
BlockFeature
ByteInputStream
BZip2Constants
BZIP2InputStream
CellMark
CellType
ChromosomalRegion
ChromosomalRegionIndex
ChromosomeType
CMDProgram
CommandLineDefaults
CompressorInputStream
ConfigProgram
ConfigProgramGroup
Count
CounterMapper
CountResultProcess
CountRunConfig
CRC
DatababseFilter
Database
DatabaseAnnoBEDParser
DatabaseAnnoVCFParser
DatabaseBEDFilter
DatabaseFactory
DatabaseVCFFilter
DBAnnoParam
DBArgumentCollection
DBFilterParam
DBParam
Delimiter
DepthFilter
ExactStack
ExpressionUtils
ExtractConfig
FieldFormat
FileQueryReader
FileType
FilterConfig
FilterParam
FlatPrintter
FlatThreadPrintter
Format
FormatReader
FormatType
Gene
GeneBuilder
GenomeAssembly
GenomeAssembly.InvalidGenomeAssemblyException
GenomicRegionType
GenomicRegionUtils
GenotypeFilter
GenotypeQC
GenotypeQualityFilter
GlobalParameter
GZInputStream
GZIPReader
GZIPThreadReader
HeaderFormatReader
HeaderLineFilter
Index
Index
IndexArgumentCollection
IndexFactory
IndexInfo
IndexParam
IndexProgram
IndexProgramGroup
IndexType
IndexWriteConfig
IndexWriter
InfoField
InputFileArgumentCollection
Intersect
IntersectConfig
IntersectRunReader
IntersectType
IntersetMapper
IntersetOutParam
IntervalStack
IntervalStackFC
InvalidArgumentException
IOutils
JannovarAnnotationService
JannovarUtils
JannovarVariantAnnotator
LimitInputStream
LineFilter
LineFilterIterator
LocalFile
LocCodec
LocFeature
LocFilterIterator
LoggingUtils
LongLineReader
Mapper
MapReduce
MendelianInheritanceADFilter
MendelianInheritanceARFilter
MendelianInheritanceFilter
MendelianInheritanceXDFilter
MendelianInheritanceXRFilter
MetaReader
Mode
ModeOfInheritance
MyBlockCompressedOutputStream
MyEndianOutputStream
NodeWithFilePointer
NoFilterIterator
NormalField
OutMode
OutParam
OutputArgumentCollection
OverlapHeaderReader
OverlapRunConfig
Param
PedFiles
Pedigree
Pedigree.Individual
Pedigree.Individual.Builder
Pedigree.Individual.Sex
Pedigree.Individual.Status
PedigreeConverter
Population
PostDBParam
PredictionFunc
PrintGZ
Printter
Priority
ProcessBlock
ProcessResult
QDFilter
Query
QueryBEDParser
QueryFileParam
QueryFileProgram
QueryParam
QueryProgram
QueryProgramGroup
QueryReader
QueryReaderItf
QueryRegionConfig
QueryRegionParam
QueryVCFParser
QuickFileType
Rand
RandomAccess
Reducer
ReducerFactory
RegFunc
RegionFilter
RegulatoryFeature
RegulatoryFeature.FeatureType
ResultParser
RSIDLocCodec
RunArgumentCollection
RunConfig
RunFactory
RunParam
RunProgram
RunReaderInterface
SimpleMapReduce
SkipLineFilter
Snp2PosMode
SpiderReader
SROB
SweepQuery
TABFileReader
TABHeaderLineFilter
TabixQuery
TabixResultProcess
TABLocCodec
TagArgument
TbiDatabase
TbiIndex
TbiMixReader
TbiReader
TbiSweepReader
ThreadPrintter
TimeMetric
TranscriptAnnotation
TranscriptAnnotation.Builder
TranscriptSource
VairantQC
ValWithAllele
VannoDatabase
VannoIndex
VannoIndexV1
VannoMixReader
VannoQuery
VannoReader
VannoResultProcess
VannoSweepReader
VannoUtils
VannoUtils.FileExt
Variant
VariantAnnotation
VariantAnnotation.Builder
VariantAnnotator
VariantCoordinates
VariantEffectArgumentCollection
VariantEffectUtility
VariantFilter
VariantType
VarNoteCommandLine
VCFFileReader
VCFFilterIterator
VCFHeaderLineFilter
VcfInfoReader
VCFLocCodec
VCFParser
ZipPrintter
ZipThreadPrintter