- bandLeft - Variable in class uni.bielefeld.cmg.sparkhit.struct.Qgram
-
- bandRight - Variable in class uni.bielefeld.cmg.sparkhit.struct.Qgram
-
- bandWidth - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
- BatchAlignPipe - Class in uni.bielefeld.cmg.sparkhit.pipeline
-
Returns an object for recruiting one read to the reference genomes.
- BatchAlignPipe(DefaultParam) - Constructor for class uni.bielefeld.cmg.sparkhit.pipeline.BatchAlignPipe
-
- BatchAlignPipe() - Constructor for class uni.bielefeld.cmg.sparkhit.pipeline.BatchAlignPipe
-
- BBList - Variable in class uni.bielefeld.cmg.sparkhit.pipeline.BatchAlignPipe
-
- BBList - Variable in class uni.bielefeld.cmg.sparkhit.reference.RefStructBuilder
-
- begin - Variable in class uni.bielefeld.cmg.sparkhit.struct.Block
-
- begin - Variable in class uni.bielefeld.cmg.sparkhit.struct.CandidateBlock
-
- begin - Variable in class uni.bielefeld.cmg.sparkhit.struct.Qgram
-
- bestKmers - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
-
- bestKmers - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
- bestNas - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
-
- bestNas - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
- bestPigeon - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
-
- bestPigeon - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
- bestScore - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
-
- BinaryBlock - Class in uni.bielefeld.cmg.sparkhit.struct
-
A data structure class that stores a k-mer block in binary.
- BinaryBlock() - Constructor for class uni.bielefeld.cmg.sparkhit.struct.BinaryBlock
-
A constructor that construct an object of
BinaryBlock class.
- block - Variable in class uni.bielefeld.cmg.sparkhit.reference.RefStructBuilder
-
- Block - Class in uni.bielefeld.cmg.sparkhit.struct
-
A data structure class that stores the locus of each binary block.
- Block() - Constructor for class uni.bielefeld.cmg.sparkhit.struct.Block
-
A constructor that construct an object of
Block class.
- bRead - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
-
- bRevRead - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
-
- BufferedFastqUnit - Variable in class uni.bielefeld.cmg.sparkhit.io.ReadFastq
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- bufferInputFile(String) - Method in interface uni.bielefeld.cmg.sparkhit.io.FileManager
-
This is an abstract method for buffering input stream of input files.
- bufferInputFile(String) - Method in interface uni.bielefeld.cmg.sparkhit.io.InputFileManager
-
This is an abstract method for buffering input stream of input files.
- bufferInputFile(String) - Method in class uni.bielefeld.cmg.sparkhit.io.ObjectFileInput
-
This method sets the full path of an input file.
- bufferInputFile(String) - Method in class uni.bielefeld.cmg.sparkhit.io.ObjectFileOutput
-
This method sets the full path of an input file.
- bufferInputFile(String) - Method in interface uni.bielefeld.cmg.sparkhit.io.OutputFileManager
-
This is an abstract method for buffering input stream of input files.
- bufferInputFile(String) - Method in class uni.bielefeld.cmg.sparkhit.io.ReadFasta
-
This method sets up an input fasta file stream based on an input file path.
- bufferInputFile(String) - Method in class uni.bielefeld.cmg.sparkhit.io.ReadFastq
-
This method sets up an input fastq file stream based on an input file path.
- bufferInputFile(String) - Method in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferInput
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This method sets up an input file buffer based on an input file path.
- bufferInputFile(String) - Method in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferOutput
-
This method sets up an input file buffer based on an input file path.
- bufferOutputFile(String) - Method in interface uni.bielefeld.cmg.sparkhit.io.FileManager
-
This is an abstract method for buffering input stream of output files.
- bufferOutputFile(String) - Method in interface uni.bielefeld.cmg.sparkhit.io.InputFileManager
-
This is an abstract method for buffering output stream of output files.
- bufferOutputFile(String) - Method in class uni.bielefeld.cmg.sparkhit.io.ObjectFileInput
-
This method is deprecated.
- bufferOutputFile(String) - Method in class uni.bielefeld.cmg.sparkhit.io.ObjectFileOutput
-
This method set the full path of an output file.
- bufferOutputFile(String) - Method in interface uni.bielefeld.cmg.sparkhit.io.OutputFileManager
-
This is an abstract method for buffering output stream of output files.
- bufferOutputFile(String) - Method in class uni.bielefeld.cmg.sparkhit.io.ReadFasta
-
This method sets the full path of an output file.
- bufferOutputFile(String) - Method in class uni.bielefeld.cmg.sparkhit.io.ReadFastq
-
This method sets the full path of an output file.
- bufferOutputFile(String) - Method in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferInput
-
This method sets up an output file buffer based on an output file path.
- bufferOutputFile(String) - Method in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferOutput
-
This method sets up an output file buffer based on an output file path.
- buildIndex() - Method in class uni.bielefeld.cmg.sparkhit.reference.RefStructBuilder
-
This method build the reference index based on the input
reference genomes.
- buildJavaReference() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method deserializes the reference index using default Java serializer.
- buildReference() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method deserializes the reference index using kryo serializer.
- buildReferenceForSpark() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method builds the reference index.