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C

change(char, double) - Static method in class edu.unc.csbio.RNASim.ReadModifier
the method to change original nucleotide based on given error probability
chrOffset - Static variable in class edu.unc.csbio.util.VCFReader
 
chrom - Variable in class edu.unc.csbio.data.Feature
The chromosome of the feature.
chrom - Static variable in class edu.unc.csbio.RNASim.MainCmdline
this will be the prefix of the all read ID
chromMatching - Static variable in class edu.unc.csbio.RNASim.MainCmdline
specify the matching of chromosome string, Exact or Fuzzy.
chromPool - Static variable in class edu.unc.csbio.RNASim.MainCmdline
a TreeSet that stores the chromosome names
close() - Method in class edu.unc.csbio.util.FqWriter
this method will close BufferedWriter out
close() - Method in class edu.unc.csbio.util.VCFReader
Close the buffer
compareTo(Feature) - Method in class edu.unc.csbio.data.Feature
A necessary method for the Comparable interface.
Config - Class in edu.unc.csbio.RNASim
The class Config is for reading and processing configuration file.
Config(String[]) - Constructor for class edu.unc.csbio.RNASim.Config
a constructor for object Config.
Config.OrderPreservedProperties - Class in edu.unc.csbio.RNASim
 
Config.OrderPreservedProperties() - Constructor for class edu.unc.csbio.RNASim.Config.OrderPreservedProperties
 
configuration - Static variable in class edu.unc.csbio.RNASim.Config
A LinkHashMap that maps configuration description to configuration data.
coverageFactor - Static variable in class edu.unc.csbio.RNASim.MainCmdline
coverage factor = total read length / total sequence size
CreateQualityGenertor() - Static method in class edu.unc.csbio.RNASim.QualityGeneratorFactory
this method creates different quality score generator object based on configuration.

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