callMethylation         callMethylation
extractPatterns         extractPatterns
generateBedEcdf         generateBedEcdf
generateBedReport       generateBedReport
generateCytosineReport
                        generateCytosineReport
generateMhlReport       generateMhlReport
generateVcfReport       generateVcfReport
plotPatterns            plotPatterns
preprocessBam           preprocessBam
preprocessGenome        preprocessGenome
simulateBam             simulateBam
