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comparison PsiCLASS-1.0.2/samtools-0.1.19/bcftools/kfunc.c @ 0:903fc43d6227 draft default tip
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author | lsong10 |
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date | Fri, 26 Mar 2021 16:52:45 +0000 |
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1 #include <math.h> | |
2 | |
3 | |
4 /* Log gamma function | |
5 * \log{\Gamma(z)} | |
6 * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245 | |
7 */ | |
8 double kf_lgamma(double z) | |
9 { | |
10 double x = 0; | |
11 x += 0.1659470187408462e-06 / (z+7); | |
12 x += 0.9934937113930748e-05 / (z+6); | |
13 x -= 0.1385710331296526 / (z+5); | |
14 x += 12.50734324009056 / (z+4); | |
15 x -= 176.6150291498386 / (z+3); | |
16 x += 771.3234287757674 / (z+2); | |
17 x -= 1259.139216722289 / (z+1); | |
18 x += 676.5203681218835 / z; | |
19 x += 0.9999999999995183; | |
20 return log(x) - 5.58106146679532777 - z + (z-0.5) * log(z+6.5); | |
21 } | |
22 | |
23 /* complementary error function | |
24 * \frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2} dt | |
25 * AS66, 2nd algorithm, http://lib.stat.cmu.edu/apstat/66 | |
26 */ | |
27 double kf_erfc(double x) | |
28 { | |
29 const double p0 = 220.2068679123761; | |
30 const double p1 = 221.2135961699311; | |
31 const double p2 = 112.0792914978709; | |
32 const double p3 = 33.912866078383; | |
33 const double p4 = 6.37396220353165; | |
34 const double p5 = .7003830644436881; | |
35 const double p6 = .03526249659989109; | |
36 const double q0 = 440.4137358247522; | |
37 const double q1 = 793.8265125199484; | |
38 const double q2 = 637.3336333788311; | |
39 const double q3 = 296.5642487796737; | |
40 const double q4 = 86.78073220294608; | |
41 const double q5 = 16.06417757920695; | |
42 const double q6 = 1.755667163182642; | |
43 const double q7 = .08838834764831844; | |
44 double expntl, z, p; | |
45 z = fabs(x) * M_SQRT2; | |
46 if (z > 37.) return x > 0.? 0. : 2.; | |
47 expntl = exp(z * z * - .5); | |
48 if (z < 10. / M_SQRT2) // for small z | |
49 p = expntl * ((((((p6 * z + p5) * z + p4) * z + p3) * z + p2) * z + p1) * z + p0) | |
50 / (((((((q7 * z + q6) * z + q5) * z + q4) * z + q3) * z + q2) * z + q1) * z + q0); | |
51 else p = expntl / 2.506628274631001 / (z + 1. / (z + 2. / (z + 3. / (z + 4. / (z + .65))))); | |
52 return x > 0.? 2. * p : 2. * (1. - p); | |
53 } | |
54 | |
55 /* The following computes regularized incomplete gamma functions. | |
56 * Formulas are taken from Wiki, with additional input from Numerical | |
57 * Recipes in C (for modified Lentz's algorithm) and AS245 | |
58 * (http://lib.stat.cmu.edu/apstat/245). | |
59 * | |
60 * A good online calculator is available at: | |
61 * | |
62 * http://www.danielsoper.com/statcalc/calc23.aspx | |
63 * | |
64 * It calculates upper incomplete gamma function, which equals | |
65 * kf_gammaq(s,z)*tgamma(s). | |
66 */ | |
67 | |
68 #define KF_GAMMA_EPS 1e-14 | |
69 #define KF_TINY 1e-290 | |
70 | |
71 // regularized lower incomplete gamma function, by series expansion | |
72 static double _kf_gammap(double s, double z) | |
73 { | |
74 double sum, x; | |
75 int k; | |
76 for (k = 1, sum = x = 1.; k < 100; ++k) { | |
77 sum += (x *= z / (s + k)); | |
78 if (x / sum < KF_GAMMA_EPS) break; | |
79 } | |
80 return exp(s * log(z) - z - kf_lgamma(s + 1.) + log(sum)); | |
81 } | |
82 // regularized upper incomplete gamma function, by continued fraction | |
83 static double _kf_gammaq(double s, double z) | |
84 { | |
85 int j; | |
86 double C, D, f; | |
87 f = 1. + z - s; C = f; D = 0.; | |
88 // Modified Lentz's algorithm for computing continued fraction | |
89 // See Numerical Recipes in C, 2nd edition, section 5.2 | |
90 for (j = 1; j < 100; ++j) { | |
91 double a = j * (s - j), b = (j<<1) + 1 + z - s, d; | |
92 D = b + a * D; | |
93 if (D < KF_TINY) D = KF_TINY; | |
94 C = b + a / C; | |
95 if (C < KF_TINY) C = KF_TINY; | |
96 D = 1. / D; | |
97 d = C * D; | |
98 f *= d; | |
99 if (fabs(d - 1.) < KF_GAMMA_EPS) break; | |
100 } | |
101 return exp(s * log(z) - z - kf_lgamma(s) - log(f)); | |
102 } | |
103 | |
104 double kf_gammap(double s, double z) | |
105 { | |
106 return z <= 1. || z < s? _kf_gammap(s, z) : 1. - _kf_gammaq(s, z); | |
107 } | |
108 | |
109 double kf_gammaq(double s, double z) | |
110 { | |
111 return z <= 1. || z < s? 1. - _kf_gammap(s, z) : _kf_gammaq(s, z); | |
112 } | |
113 | |
114 /* Regularized incomplete beta function. The method is taken from | |
115 * Numerical Recipe in C, 2nd edition, section 6.4. The following web | |
116 * page calculates the incomplete beta function, which equals | |
117 * kf_betai(a,b,x) * gamma(a) * gamma(b) / gamma(a+b): | |
118 * | |
119 * http://www.danielsoper.com/statcalc/calc36.aspx | |
120 */ | |
121 static double kf_betai_aux(double a, double b, double x) | |
122 { | |
123 double C, D, f; | |
124 int j; | |
125 if (x == 0.) return 0.; | |
126 if (x == 1.) return 1.; | |
127 f = 1.; C = f; D = 0.; | |
128 // Modified Lentz's algorithm for computing continued fraction | |
129 for (j = 1; j < 200; ++j) { | |
130 double aa, d; | |
131 int m = j>>1; | |
132 aa = (j&1)? -(a + m) * (a + b + m) * x / ((a + 2*m) * (a + 2*m + 1)) | |
133 : m * (b - m) * x / ((a + 2*m - 1) * (a + 2*m)); | |
134 D = 1. + aa * D; | |
135 if (D < KF_TINY) D = KF_TINY; | |
136 C = 1. + aa / C; | |
137 if (C < KF_TINY) C = KF_TINY; | |
138 D = 1. / D; | |
139 d = C * D; | |
140 f *= d; | |
141 if (fabs(d - 1.) < KF_GAMMA_EPS) break; | |
142 } | |
143 return exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b) + a * log(x) + b * log(1.-x)) / a / f; | |
144 } | |
145 double kf_betai(double a, double b, double x) | |
146 { | |
147 return x < (a + 1.) / (a + b + 2.)? kf_betai_aux(a, b, x) : 1. - kf_betai_aux(b, a, 1. - x); | |
148 } | |
149 | |
150 #ifdef KF_MAIN | |
151 #include <stdio.h> | |
152 int main(int argc, char *argv[]) | |
153 { | |
154 double x = 5.5, y = 3; | |
155 double a, b; | |
156 printf("erfc(%lg): %lg, %lg\n", x, erfc(x), kf_erfc(x)); | |
157 printf("upper-gamma(%lg,%lg): %lg\n", x, y, kf_gammaq(y, x)*tgamma(y)); | |
158 a = 2; b = 2; x = 0.5; | |
159 printf("incomplete-beta(%lg,%lg,%lg): %lg\n", a, b, x, kf_betai(a, b, x) / exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b))); | |
160 return 0; | |
161 } | |
162 #endif |