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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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