- cache - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- calculateExactHWEPValue(int, int, int) - Static method in class uni.bielefeld.cmg.sparkhit.algorithm.Statistic
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deprecated
- calculateHWEP(int, int, int) - Static method in class uni.bielefeld.cmg.sparkhit.algorithm.Statistic
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This method can be used to calculate the expected frequencies of each genotype
based on Hardy–Weinberg principle
- CandidateBlock - Class in uni.bielefeld.cmg.sparkhit.struct
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A data structure class that stores the locus of each candidate block.
- CandidateBlock() - Constructor for class uni.bielefeld.cmg.sparkhit.struct.CandidateBlock
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- chains - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- checkFile(String) - Method in class uni.bielefeld.cmg.sparkhit.io.ObjectFileInput
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This method checks the path of input file.
- checkFile(String) - Method in class uni.bielefeld.cmg.sparkhit.io.ReadFasta
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This method checks the path of an input fasta file.
- checkFile(String) - Method in class uni.bielefeld.cmg.sparkhit.io.ReadFastq
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This method checks the path of input fastq file.
- checkFile(String) - Method in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferInput
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This method checks the path of an input file.
- chr - Variable in class uni.bielefeld.cmg.sparkhit.struct.CandidateBlock
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- chr - Variable in class uni.bielefeld.cmg.sparkhit.struct.HitInfo
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- chr - Variable in class uni.bielefeld.cmg.sparkhit.struct.Qgram
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- clusterNum - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- codeNt - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- codeNtComplement - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- column2End - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- column2Start - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- columnEnd - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- columns - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- columns2 - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- columnStart - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- compare(Qgram, Qgram) - Method in class uni.bielefeld.cmg.sparkhit.struct.QgramComparator
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a compare method that compares the q-gram scores of two q-grams.
- componentNum - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- count - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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- createInputFastaStream(String) - Method in class uni.bielefeld.cmg.sparkhit.io.ReadFasta
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This method sets up an input file stream for an input fasta file.
- createInputFastqStream(String) - Method in class uni.bielefeld.cmg.sparkhit.io.ReadFastq
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Only when you want to creat bufferedReader with this class.
- cRefBlockList - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
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