- fasta - Variable in class uni.bielefeld.cmg.sparkhit.io.ReadFasta
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- FastPipe - Class in uni.bielefeld.cmg.sparkhit.pipeline
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Returns an object for running fast mode of fragment recruitment.
- FastPipe() - Constructor for class uni.bielefeld.cmg.sparkhit.pipeline.FastPipe
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- fastq - Variable in class uni.bielefeld.cmg.sparkhit.io.ReadFastq
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- FastqUnitBuffer - Class in uni.bielefeld.cmg.sparkhit.io
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Returns an object for buffering Fastq files.
- FastqUnitBuffer(BufferedReader) - Constructor for class uni.bielefeld.cmg.sparkhit.io.FastqUnitBuffer
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A constructor that sets input BufferedReader for buffering input Fastq files.
- FastqUnitBuffer(BufferedReader, int) - Constructor for class uni.bielefeld.cmg.sparkhit.io.FastqUnitBuffer
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This constructor is deprecated
- FileManager - Interface in uni.bielefeld.cmg.sparkhit.io
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This is an interface for managing input and output files via different
input and output buffers.
- filename - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- filterFastq - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- filterToFasta - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- flagChains - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- fourMer - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
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- fourMerBegin - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
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- fourMerLoci - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
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- fourMerScore - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
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- fourNtBits - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
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- fromFirst - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
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- fromFirstMatrix - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
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- fromSecond - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
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- fromSecondMatrix - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
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