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conf.json
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conf.json
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{
"constants": {
"smallInitialSize": 15000,
"smallTestsPerYear": 3000,
"mediumInitialSize": 150000,
"mediumTestsPerYear": 30000,
"largeInitialSize": 1000000,
"largeTestsPerYear": 450000,
"p0": {
"low": 0,
"med": 0,
"hi": 0
},
"p1_PM3": {
"low": 0,
"med": 0,
"hi": 0
},
"p2_PM6": {
"low": 0.0014,
"med": 0.007,
"hi": 0.025
},
"p3_BS2": {
"low": 0,
"med": 0,
"hi": 0
},
"p4_BP2": {
"low": "0.001 * self.frequency",
"med": "0.005 * self.frequency",
"hi": "0.02 * self.frequency"
},
"p5_BP5": {
"low": 0.00002,
"med": 0.0001,
"hi": 0.0021505376
},
"p6_PP1": {
"low": 0.05,
"med": 0.23,
"hi": 0.67
},
"p7_PS2": {
"low": 0.0006,
"med": 0.003,
"hi": 0.02
},
"p8_BS4": {
"low": 0.0001,
"med": 0.001,
"hi": 0.17
},
"b0": {
"low": 0,
"med": 0,
"hi": 0
},
"b1_PM3": {
"low": 0,
"med": 0,
"hi": 0
},
"b2_PM6": {
"low": 0.0007,
"med": 0.0035,
"hi": 0.01
},
"b3_BS2": {
"low": 0,
"med": 0,
"hi": 0
},
"b4_BP2": {
"low": "self.frequency",
"med": "self.frequency",
"hi": "self.frequency"
},
"b5_BP5": {
"low": 0.038,
"med": 0.099,
"hi": 0.36
},
"b6_PP1": {
"low": 0.005,
"med": 0.01,
"hi": 0.0625
},
"b7_PS2": {
"low": 0.0001,
"med": 0.0015,
"hi": 0.005
},
"b8_BS4": {
"low": 0.025,
"med": 0.1,
"hi": 0.4063
},
"PS": 18.7,
"PM": 4.3,
"PP": 2.08,
"BS": 0.053475935828877004,
"BP": 0.4807692307692307,
"PSF": 2.0,
"benignThreshold": -3,
"likelyBenignThreshold": -1.256958152560932,
"neutralThreshold": 0,
"likelyPathogenicThreshold": 1.256958152560932,
"pathogenicThreshold": 2.0
},
"simulation": {
"name": "mySim",
"nSmall": 1,
"nMedium": 1,
"nLarge": 1,
"numVariants": 1,
"frequency": 1e-5,
"years": 5,
"seed": 18,
"numThreads": 2
}
}