Package <Unnamed>

Class Summary

CNV	Class to compute where the CNVs are.
CONDR	Main calling function of program Gets data; parses it; computes most likely states
ConvertToExonFormat	File Format of output (tab delimited) chromosome exonStart exonEnd geneName FPKM/coverage SNP levels/BAF .pileup -> .exon
CreateExonFile
Exon	Stores and manipulates relevant exon information
Expression
GammaResult
HiddenMarkovModel	Calculates and stores states according to the exon data
MappedReads
Pileup	Class to handle pileup files
PileupToExon
Probability	Class to abstract away some of the probability computations (so it can be done in log space or normal space)
SimulateExonMeasurements
State	Holds the state name and the associated ratios expected
TabulateResults
TestLogSum