A B C D E F G H I K L M N O P R S T U V

R

rateOfOccurenceOfCNV - Static variable in class State

read - Variable in class MappedReads

readAndStoreExonFile(String, int) - Static method in class Exon

Reads exon file; stores necessary info in array of exons

readData(BufferedReader) - Static method in class Pileup

Reads and parses the pileup file

readData(ArrayList<Exon>, BufferedReader) - Static method in class Pileup

Reads the pileup and simultaneously updates the exon lists with appropriate values

readExon(String, int) - Static method in class Exon

Parses the file (br) Reads file until the next chromosome Loads into an array of Exon objects

readExon(String, int) - Static method in class Expression

READLENGTH - Static variable in class Exon

readMappedReads(String, int) - Static method in class MappedReads

reads - Variable in class Exon

referenceDirectory - Static variable in class CreateExonFile

referenceSequence - Variable in class Exon

rpkm - Variable in class Expression

rpkmRatio - Variable in class State