
exactUpdate = False
topKbyLinReg = 16
logdelta = SP.log(16)

if topKbyLinReg != None:
    outFile = 'examples/ScanISP.exact%d.nSnps%d.logdelta%.2f.out.txt'%(exactUpdate,topKbyLinReg,logdelta)
else:
    outFile = 'examples/ScanISP.exact%d.all.logdelta%.2f.out.txt'%(exactUpdate,logdelta)

obj = ScanISP(
    phenoFile = 'examples/toydataTrain.phe',
    #phenoTestFile = 'examples/toydataTest.phe',

    bedFile = 'examples/toydata',

    #fastlmmPath = 'C:/Users/t-baraki/Users/t-baraki/adaptivelmm/software/FaSTLMM.205.Win/Cpp_MKL',
    fastlmmPath = r"C:\Users\lippert\Projects\FaST-LMM_old\FastLmm\CPP\x64\MKL-Release",
    windowByPosition = 1E1,
    logdelta = logdelta,
    topKbyLinReg = topKbyLinReg,
    exactUpdate = exactUpdate,
    #extractSim = 'examples/LmmGWAS.snps.txt',
    outFile = outFile,
    doPlots = False,
    doDebugging = True
)


exactUpdate = False
topKbyLinReg = 16
logdelta = SP.log(16)

if topKbyLinReg != None:
    outFile = 'examples/ScanISP.exact%d.nSnps%d.logdelta%.2f.out.txt'%(exactUpdate,topKbyLinReg,logdelta)
else:
    outFile = 'examples/ScanISP.exact%d.all.logdelta%.2f.out.txt'%(exactUpdate,logdelta)

obj = ScanISP(
    phenoFile = 'examples/toydataTrain.phe',
    #phenoTestFile = 'examples/toydataTest.phe',

    bedFile = 'examples/toydata',

    #fastlmmPath = 'C:/Users/t-baraki/Users/t-baraki/adaptivelmm/software/FaSTLMM.205.Win/Cpp_MKL',
    fastlmmPath = r"C:\Users\lippert\Projects\FaST-LMM_old\FastLmm\CPP\x64\MKL-Release",
    windowByPosition = 1E1,
    logdelta = logdelta,
    topKbyLinReg = topKbyLinReg,
    exactUpdate = exactUpdate,
    #extractSim = 'examples/LmmGWAS.snps.txt',
    outFile = outFile,
    doPlots = False,
    doDebugging = True
)

#phenoTestFile = 'examples/toydataTest.phe', #fastlmmPath = 'C:/Users/t-baraki/Users/t-baraki/adaptivelmm/software/FaSTLMM.205.Win/Cpp_MKL', #extractSim = 'examples/LmmGWAS.snps.txt',