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#include "shared.h"
/* LOOKUP TABLES
* --------------------------------------------------------------*/
const int lut_char_to_acgt_int[85] = {
-1, -1, -1, -1, -1, -1, -1, -1, -1, // 0, ... ,8
-1, -1, -1, -1, -1, -1, -1, -1, -1, // 9, ... ,17
-1, -1, -1, -1, -1, -1, -1, -1, -1, // 18, ... ,26
-1, -1, -1, -1, -1, -1, -1, -1, -1, // 27, ... ,35
-1, -1, -1, -1, -1, -1, -1, -1, -1, // 36, ... ,44
-1, -1, -1, -1, -1, -1, -1, -1, -1, // 45, ... ,53
-1, -1, -1, -1, -1, -1, -1, -1, -1, // 54, ... ,62
-1, -1, 0, -1, 1, -1, -1, -1, 2, // 63, ... (65=='A'==0) ... (67=='C'==1) ... (71=='G'==2)
-1, -1, -1, -1, -1, -1, -1, -1, -1, // 72, ... ,80
-1, -1, -1, 3 // 81, ... (84=='T'==3) ... ,89
};
const int lut_qs_to_qs2[63] = {
0, 1, 4, 9, 16, 25, 36, 49, 64, 81, 100,
121, 144, 169, 196, 225, 256, 289, 324, 361, 400, 441,
484, 529, 576, 625, 676, 729, 784, 841, 900, 961, 1024,
1089, 1156, 1225, 1296, 1369, 1444, 1521, 1600, 1681, 1764, 1849,
1936, 2025, 2116, 2209, 2304, 2401, 2500, 2601, 2704, 2809, 2916,
3025, 3136, 3249, 3364, 3481, 3600, 3721, 3844 };
const int lut_nAlleles_to_nGenotypes[6] = { 0, 1, 3, 6, 10, 15 };
const double qScore_to_errorProb[63] = { 1,
0.7943282,
0.6309573,
0.5011872,
0.3981072,
0.3162278,
0.2511886,
0.1995262,
0.1584893,
0.1258925,
0.1,
0.07943282,
0.06309573,
0.05011872,
0.03981072,
0.03162278,
0.02511886,
0.01995262,
0.01584893,
0.01258925,
0.01,
0.007943282,
0.006309573,
0.005011872,
0.003981072,
0.003162278,
0.002511886,
0.001995262,
0.001584893,
0.001258925,
0.001,
0.0007943282,
0.0006309573,
0.0005011872,
0.0003981072,
0.0003162278,
0.0002511886,
0.0001995262,
0.0001584893,
0.0001258925,
0.0001,
0.00007943282,
0.00006309573,
0.00005011872,
0.00003981072,
0.00003162278,
0.00002511886,
0.00001995262,
0.00001584893,
0.00001258925,
0.00001,
0.000007943282,
0.000006309573,
0.000005011872,
0.000003981072,
0.000003162278,
0.000002511886,
0.000001995262,
0.000001584893,
0.000001258925,
0.000001,
0.0000007943282,
0.0000006309573
};
const double qScore_to_gl[3][257] = {
{0,0.2056718,0.3690427,0.4988128,0.6018928,0.6837722,0.7488114,0.8004738,0.8415107,0.8741075,0.9,0.9205672,0.9369043,0.9498813,0.9601893,0.9683772,0.9748811,0.9800474,0.9841511,0.9874107,0.99,0.9920567,0.9936904,0.9949881,0.9960189,0.9968377,0.9974881,0.9980047,0.9984151,0.9987411,0.999,0.9992057,0.999369,0.9994988,0.9996019,0.9996838,0.9997488,0.9998005,0.9998415,0.9998741,0.9999,0.9999206,0.9999369,0.9999499,0.9999602,0.9999684,0.9999749,0.99998,0.9999842,0.9999874,0.99999,0.9999921,0.9999937,0.999995,0.999996,0.9999968,0.9999975,0.999998,0.9999984,0.9999987,0.999999,0.9999992,0.9999994,0.9999995,0.9999996,0.9999997,0.9999997,0.9999998,0.9999998,0.9999999,0.9999999,0.9999999,0.9999999,0.9999999,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1},
{0.1666667,0.2352239,0.2896809,0.3329376,0.3672976,0.3945907,0.4162705,0.4334913,0.4471702,0.4580358,0.4666667,0.4735224,0.4789681,0.4832938,0.4867298,0.4894591,0.491627,0.4933491,0.494717,0.4958036,0.4966667,0.4973522,0.4978968,0.4983294,0.498673,0.4989459,0.4991627,0.4993349,0.4994717,0.4995804,0.4996667,0.4997352,0.4997897,0.4998329,0.4998673,0.4998946,0.4999163,0.4999335,0.4999472,0.499958,0.4999667,0.4999735,0.499979,0.4999833,0.4999867,0.4999895,0.4999916,0.4999933,0.4999947,0.4999958,0.4999967,0.4999974,0.4999979,0.4999983,0.4999987,0.4999989,0.4999992,0.4999993,0.4999995,0.4999996,0.4999997,0.4999997,0.4999998,0.4999998,0.4999999,0.4999999,0.4999999,0.4999999,0.4999999,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5},
{0.3333333,0.2647761,0.2103191,0.1670624,0.1327024,0.1054093,0.08372955,0.06650874,0.05282977,0.04196418,0.03333333,0.02647761,0.02103191,0.01670624,0.01327024,0.01054093,0.008372955,0.006650874,0.005282977,0.004196418,0.003333333,0.002647761,0.002103191,0.001670624,0.001327024,0.001054093,0.0008372955,0.0006650874,0.0005282977,0.0004196418,0.0003333333,0.0002647761,0.0002103191,0.0001670624,0.0001327024,0.0001054093,0.00008372955,0.00006650874,0.00005282977,0.00004196418,0.00003333333,0.00002647761,0.00002103191,0.00001670624,0.00001327024,0.00001054093,0.000008372955,0.000006650874,0.000005282977,0.000004196418,0.000003333333,0.000002647761,0.000002103191,0.000001670624,0.000001327024,0.000001054093,0.0000008372955,0.0000006650874,0.0000005282977,0.0000004196418,0.0000003333333,0.0000002647761,0.0000002103191,0.0000001670624,0.0000001327024,0.0000001054093,0.00000008372955,0.00000006650874,0.00000005282977,0.00000004196418,0.00000003333333,0.00000002647761,0.00000002103191,0.00000001670624,0.00000001327024,0.00000001054093,0.000000008372955,0.000000006650874,0.000000005282977,0.000000004196418,0.000000003333333,0.000000002647761,0.000000002103191,0.000000001670624,0.000000001327024,0.000000001054093,0.0000000008372955,0.0000000006650874,0.0000000005282977,0.0000000004196418,0.0000000003333333,0.0000000002647761,0.0000000002103191,0.0000000001670624,0.0000000001327024,0.0000000001054092,0.00000000008372954,0.00000000006650876,0.00000000005282978,0.00000000004196417,0.00000000003333334,0.0000000000264776,0.00000000002103192,0.00000000001670623,0.00000000001327024,0.00000000001054094,0.000000000008372969,0.000000000006650865,0.000000000005282959,0.000000000004196421,0.000000000003333334,0.000000000002647771,0.000000000002103206,0.000000000001670627,0.000000000001327013,0.000000000001054083,0.0000000000008372932,0.0000000000006650976,0.0000000000005282811,0.0000000000004196273,0.000000000000333326,0.0000000000002647882,0.0000000000002103132,0.0000000000001670516,0.0000000000001327087,0.0000000000001053972,0.00000000000008374782,0.00000000000006650236,0.00000000000005284662,0.00000000000004196643,0.0000000000000333437,0.00000000000002646032,0.00000000000002102022,0.00000000000001669035,0.00000000000001328567,0.00000000000001054712,0.00000000000000836368,0.000000000000006661338,0.000000000000005292063,0.00000000000000418184,0.000000000000003330669,0.000000000000002664535,0.000000000000002109424,0.000000000000001665335,0.000000000000001332268,0.000000000000001036208,0.000000000000000851171,0.0000000000000006661338,0.0000000000000005181041,0.0000000000000004070818,0.0000000000000003330669,0.000000000000000259052,0.0000000000000002220446,0.0000000000000001850372,0.0000000000000001480297,0.0000000000000001110223,0.00000000000000007401487,0.00000000000000007401487,0.00000000000000003700743,0.00000000000000003700743,0.00000000000000003700743,0.00000000000000003700743,0.00000000000000003700743,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}
};
const double qScore_to_ln_gl[3][257] = {
{NEG_INF,-1.581474,-0.996843,-0.6955245,-0.5076759,-0.3801304,-0.2892682,-0.2225515,-0.1725566,-0.134552,-0.1053605,-0.0827653,-0.06517417,-0.05141827,-0.04062484,-0.03213357,-0.02543973,-0.02015436,-0.01597587,-0.01266917,-0.01005034,-0.007974998,-0.006329563,-0.005024474,-0.003989017,-0.003167288,-0.002515047,-0.001997256,-0.00158615,-0.001259719,-0.0010005,-0.0007946439,-0.0006311565,-0.0005013129,-0.0003981864,-0.0003162778,-0.0002512202,-0.0001995461,-0.0001585019,-0.0001259005,-0.000100005,-0.00007943598,-0.00006309773,-0.00005011998,-0.00003981151,-0.00003162328,-0.00002511918,-0.00001995282,-0.00001584906,-0.00001258933,-0.00001000005,-0.000007943314,-0.000006309593,-0.000005011885,-0.00000398108,-0.000003162283,-0.00000251189,-0.000001995264,-0.000001584894,-0.000001258926,-0.000001000001,-0.0000007943286,-0.0000006309575,-0.0000005011874,-0.0000003981072,-0.0000003162278,-0.0000002511887,-0.0000001995263,-0.0000001584893,-0.0000001258925,-0.0000001,-0.00000007943283,-0.00000006309574,-0.00000005011872,-0.00000003981072,-0.00000003162278,-0.00000002511886,-0.00000001995262,-0.00000001584893,-0.00000001258925,-0.00000001,-0.000000007943282,-0.000000006309573,-0.000000005011872,-0.000000003981072,-0.000000003162278,-0.000000002511886,-0.000000001995262,-0.000000001584893,-0.000000001258925,-0.000000001,-0.0000000007943283,-0.0000000006309574,-0.0000000005011872,-0.0000000003981072,-0.0000000003162277,-0.0000000002511886,-0.0000000001995263,-0.0000000001584893,-0.0000000001258925,-0.0000000001,-0.00000000007943279,-0.00000000006309575,-0.00000000005011869,-0.00000000003981071,-0.00000000003162282,-0.00000000002511891,-0.0000000000199526,-0.00000000001584888,-0.00000000001258926,-0.00000000001,-0.000000000007943313,-0.000000000006309619,-0.00000000000501188,-0.000000000003981038,-0.000000000003162248,-0.00000000000251188,-0.000000000001995293,-0.000000000001584843,-0.000000000001258882,-0.0000000000009999779,-0.0000000000007943646,-0.0000000000006309397,-0.0000000000005011547,-0.000000000000398126,-0.0000000000003161915,-0.0000000000002512435,-0.0000000000001995071,-0.0000000000001585398,-0.0000000000001258993,-0.0000000000001000311,-0.00000000000007938095,-0.00000000000006306067,-0.00000000000005007106,-0.00000000000003985701,-0.00000000000003164136,-0.00000000000002509104,-0.00000000000001998401,-0.00000000000001587619,-0.00000000000001254552,-0.000000000000009992007,-0.000000000000007993606,-0.000000000000006328271,-0.000000000000004996004,-0.000000000000003996803,-0.000000000000003108624,-0.000000000000002553513,-0.000000000000001998401,-0.000000000000001554312,-0.000000000000001221245,-0.0000000000000009992007,-0.0000000000000007771561,-0.0000000000000006661338,-0.0000000000000005551115,-0.0000000000000004440892,-0.0000000000000003330669,-0.0000000000000002220446,-0.0000000000000002220446,-0.0000000000000001110223,-0.0000000000000001110223,-0.0000000000000001110223,-0.0000000000000001110223,-0.0000000000000001110223,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0},
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};
const double qScore_to_log10_gl[3][257] = {
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