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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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