- read - Variable in class uni.bielefeld.cmg.sparkhit.pipeline.OnePipe
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- read - Variable in class uni.bielefeld.cmg.sparkhit.struct.ReadInfo
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- readClassNotFoundException(ClassNotFoundException) - Method in class uni.bielefeld.cmg.sparkhit.util.InfoDumper
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This method records a ClassNotFoundException message.
- readClassNotFoundException(ClassNotFoundException) - Method in class uni.bielefeld.cmg.sparkhit.util.InfoLogger
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This method records a ClassNotFoundException message.
- readClassNotFoundException(ClassNotFoundException) - Method in interface uni.bielefeld.cmg.sparkhit.util.InfoManager
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This is an abstract method for recording ClassNotFoundException messages.
- ReadFasta - Class in uni.bielefeld.cmg.sparkhit.io
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Returns an object for buffering input fasta files.
- ReadFasta() - Constructor for class uni.bielefeld.cmg.sparkhit.io.ReadFasta
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A constructor that construct an object of
ReadFasta class.
- ReadFastq - Class in uni.bielefeld.cmg.sparkhit.io
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Returns an object for buffering input fastq files.
- ReadFastq() - Constructor for class uni.bielefeld.cmg.sparkhit.io.ReadFastq
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A constructor that construct an object of
ReadFastq class.
- readFileNotFoundException(FileNotFoundException) - Method in class uni.bielefeld.cmg.sparkhit.util.InfoDumper
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This method records a FileNotFoundException message.
- readFileNotFoundException(FileNotFoundException) - Method in class uni.bielefeld.cmg.sparkhit.util.InfoLogger
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This method records a FileNotFoundException message.
- readFileNotFoundException(FileNotFoundException) - Method in interface uni.bielefeld.cmg.sparkhit.util.InfoManager
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This is an abstract method for recording FileNotFoundException messages.
- readId - Variable in class uni.bielefeld.cmg.sparkhit.io.readInfo
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- readIdentity - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- readInfo - Class in uni.bielefeld.cmg.sparkhit.io
-
This is a data structure class.
- readInfo() - Constructor for class uni.bielefeld.cmg.sparkhit.io.readInfo
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- ReadInfo - Class in uni.bielefeld.cmg.sparkhit.struct
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A data structure class that stores all parameters for a sequence read.
- ReadInfo(String) - Constructor for class uni.bielefeld.cmg.sparkhit.struct.ReadInfo
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A constructor that construct an object of
ReadInfo class.
- ReadInfo(readInfo) - Constructor for class uni.bielefeld.cmg.sparkhit.struct.ReadInfo
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A constructor that construct an object of
ReadInfo class.
- readInObject() - Method in class uni.bielefeld.cmg.sparkhit.serializer.JavaSerializer
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Return the input object from input deserialization stream.
- readIOException(IOException) - Method in class uni.bielefeld.cmg.sparkhit.util.InfoDumper
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This method records an IOException message.
- readIOException(IOException) - Method in class uni.bielefeld.cmg.sparkhit.util.InfoLogger
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This method records an IOException message.
- readIOException(IOException) - Method in interface uni.bielefeld.cmg.sparkhit.util.InfoManager
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This is an abstract method for recording IOException messages.
- readMessage(String) - Method in class uni.bielefeld.cmg.sparkhit.util.InfoDumper
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This method records a specified message.
- readMessage(String) - Method in class uni.bielefeld.cmg.sparkhit.util.InfoLogger
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This method records a specified message.
- readMessage(String) - Method in interface uni.bielefeld.cmg.sparkhit.util.InfoManager
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This is an abstract method for recording specified messages.
- readName - Variable in class uni.bielefeld.cmg.sparkhit.struct.ReadInfo
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- readObject(FileInputStream, Class) - Method in class uni.bielefeld.cmg.sparkhit.serializer.kryoSerializer
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Return the input object from input deserialization stream.
- readParagraphedMessages(String) - Method in class uni.bielefeld.cmg.sparkhit.util.InfoDumper
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This method records a paragraph of message.
- readPlus - Variable in class uni.bielefeld.cmg.sparkhit.io.readInfo
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- readQual - Variable in class uni.bielefeld.cmg.sparkhit.io.readInfo
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- reads - Variable in class uni.bielefeld.cmg.sparkhit.io.FastqUnitBuffer
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- readSeq - Variable in class uni.bielefeld.cmg.sparkhit.io.readInfo
-
- readSize - Variable in class uni.bielefeld.cmg.sparkhit.struct.ReadInfo
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- recruit(readInfo) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.BatchAlignPipe
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This method recruits one sequencing read to the reference genomes.
- RefInfo - Class in uni.bielefeld.cmg.sparkhit.struct
-
A data structure class that stores all parameters for a reference genome.
- RefInfo() - Constructor for class uni.bielefeld.cmg.sparkhit.struct.RefInfo
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A constructor that construct an object of
RefInfo class.
- RefIOManager - Interface in uni.bielefeld.cmg.sparkhit.reference
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This is an interface for the input and output of reference genomes.
- RefManager - Interface in uni.bielefeld.cmg.sparkhit.reference
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This is an interface for reference index management.
- refName - Variable in class uni.bielefeld.cmg.sparkhit.struct.RefInfo
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- RefSerializer - Interface in uni.bielefeld.cmg.sparkhit.reference
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This is an interface for reference genome serialization.
- refSize - Variable in class uni.bielefeld.cmg.sparkhit.struct.RefInfo
-
- RefStructBuilder - Class in uni.bielefeld.cmg.sparkhit.reference
-
Returns an object for building reference index.
- RefStructBuilder() - Constructor for class uni.bielefeld.cmg.sparkhit.reference.RefStructBuilder
-
- RefStructManager - Interface in uni.bielefeld.cmg.sparkhit.reference
-
This is an interface for building reference data structures.
- RefStructSerializer - Class in uni.bielefeld.cmg.sparkhit.reference
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Returns an object for serializing reference indices.
- RefStructSerializer() - Constructor for class uni.bielefeld.cmg.sparkhit.reference.RefStructSerializer
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- RefTitle - Class in uni.bielefeld.cmg.sparkhit.struct
-
A data structure class that stores all names of reference contigs (scaffolds or chromosomes).
- RefTitle() - Constructor for class uni.bielefeld.cmg.sparkhit.struct.RefTitle
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A constructor that construct an object of
RefTitle class.
- registerClasses(Kryo) - Method in class uni.bielefeld.cmg.sparkhit.serializer.SparkKryoRegistrator
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This method registers all classes that are going to be serialized by kryo
- repeatSb(String, int) - Method in class uni.bielefeld.cmg.sparkhit.reference.RefStructBuilder
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This method uses StringBuilder to concatenate repeat sequences.
- reportRepeatHits - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- revKmers - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
-
- run() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.OnePipe
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This method runs the fragment recruitment pipeline within this thread.
- runChangeFormat() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.FastPipe
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This method changes the format of the sequencing data.