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

R

raw - Variable in class edu.unc.csbio.data.SequenceBuffer
The sequence of the object SequenceBuffer
Read - Class in edu.unc.csbio.data
The class for read information, including sequence string and the offset
Read(int, String) - Constructor for class edu.unc.csbio.data.Read
A constructor for Read object
ReadAnnotation() - Static method in class edu.unc.csbio.RNASim.MainCmdline
this method reads annotation file.
ReadConfig(String[]) - Static method in class edu.unc.csbio.RNASim.MainCmdline
this method read configuration file
ReadGenerator - Class in edu.unc.csbio.RNASim
The class generates pair-end reads from a sequence.
ReadGenerator(int, int, int) - Constructor for class edu.unc.csbio.RNASim.ReadGenerator
A constructor for ReadGenerator object
readLength - Static variable in class edu.unc.csbio.RNASim.MainCmdline
read length
readLength - Variable in class edu.unc.csbio.RNASim.ReadGenerator
read length
ReadModifier - Class in edu.unc.csbio.RNASim
The class modifies pair-end reads from a sequence.
ReadModifier() - Constructor for class edu.unc.csbio.RNASim.ReadModifier
 
readNext() - Method in class edu.unc.csbio.util.VCFReader
Read the VCF file and return the next insertion/deletion object.
ReadStructureVariant() - Static method in class edu.unc.csbio.RNASim.MainCmdline
this method read structure variants.
ReadTranscriptAbundance() - Static method in class edu.unc.csbio.RNASim.MainCmdline
this method read the transcript abundance from Abundance_File in Config file
RealQualityGenerator - Class in edu.unc.csbio.RNASim
The class RealQualityGenerator extending QualityGenerator is for generating quality score from real fq files.
RealQualityGenerator(String, String) - Constructor for class edu.unc.csbio.RNASim.RealQualityGenerator
this is the constructor for object RealQualityGenerator
REF - Static variable in class edu.unc.csbio.util.VCFReader
 
refOffset - Static variable in class edu.unc.csbio.util.VCFReader
 
refPos(int) - Method in class edu.unc.csbio.data.Transcript
The method to convert a position in transcript sequence coordinate to the reference coordinate
ResetBufferReader() - Method in class edu.unc.csbio.RNASim.RealQualityGenerator
this method reset BufferReader br1 and br2

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