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S

sampleColumn - Static variable in class edu.unc.csbio.util.VCFReader
 
sampleName - Static variable in class edu.unc.csbio.util.VCFReader
 
sampleOffset - Static variable in class edu.unc.csbio.util.VCFReader
 
sequence - Variable in class edu.unc.csbio.data.Read
The read represented as a char string
SequenceBuffer - Class in edu.unc.csbio.data
The class for sequence information, including sequence string and the offset
SequenceBuffer(String, int) - Constructor for class edu.unc.csbio.data.SequenceBuffer
A constructor for object SequenceBuffer
shuffle(Object[]) - Static method in class edu.unc.csbio.RNASim.MainCmdline
given an array, this method sequentially changes a position with another randomly selected position, for n times, where n is the size of array.
start - Variable in class edu.unc.csbio.data.Feature
The start position of the feature.
startTime - Static variable in class edu.unc.csbio.RNASim.MainCmdline
time when program start running
stripLine(String) - Static method in class edu.unc.csbio.util.GTFParser
A method to remove the leading and trailing whitespaces.
sv - Variable in class edu.unc.csbio.data.ExtendedSequenceBuffer
An ArrayList of Feature representing structure variants in the sequence
svPool - Static variable in class edu.unc.csbio.RNASim.MainCmdline
an array that stores the structure variants

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