htslib.kfunc source code

1 /* The MIT License
2 
3    Copyright (C) 2010, 2013-2014 Genome Research Ltd.
4    Copyright (C) 2011 Attractive Chaos <attractor@live.co.uk>
5 
6    Permission is hereby granted, free of charge, to any person obtaining
7    a copy of this software and associated documentation files (the
8    "Software"), to deal in the Software without restriction, including
9    without limitation the rights to use, copy, modify, merge, publish,
10    distribute, sublicense, and/or sell copies of the Software, and to
11    permit persons to whom the Software is furnished to do so, subject to
12    the following conditions:
13 
14    The above copyright notice and this permission notice shall be
15    included in all copies or substantial portions of the Software.
16 
17    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
18    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
19    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
20    NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
21    BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
22    ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
23    CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
24    SOFTWARE.
25 */
26 module htslib.kfunc;
27 
28 @system:
29 nothrow:
30 @nogc:
31 
32 extern (C):
33 
34 /* Log gamma function
35  * \log{\Gamma(z)}
36  * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245
37  */
38 double kf_lgamma(double z);
39 
40 /* complementary error function
41  * \frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2} dt
42  * AS66, 2nd algorithm, http://lib.stat.cmu.edu/apstat/66
43  */
44 double kf_erfc(double x);
45 
46 /* The following computes regularized incomplete gamma functions.
47  * Formulas are taken from Wiki, with additional input from Numerical
48  * Recipes in C (for modified Lentz's algorithm) and AS245
49  * (http://lib.stat.cmu.edu/apstat/245).
50  *
51  * A good online calculator is available at:
52  *
53  *   http://www.danielsoper.com/statcalc/calc23.aspx
54  *
55  * It calculates upper incomplete gamma function, which equals
56  * kf_gammaq(s,z)*tgamma(s).
57  */
58 
59 double kf_gammap(double s, double z);
60 double kf_gammaq(double s, double z);
61 
62 /* Regularized incomplete beta function. The method is taken from
63  * Numerical Recipe in C, 2nd edition, section 6.4. The following web
64  * page calculates the incomplete beta function, which equals
65  * kf_betai(a,b,x) * gamma(a) * gamma(b) / gamma(a+b):
66  *
67  *   http://www.danielsoper.com/statcalc/calc36.aspx
68  */
69 double kf_betai(double a, double b, double x);
70 
71 /*
72  *    n11  n12  | n1_
73  *    n21  n22  | n2_
74  *   -----------+----
75  *    n_1  n_2  | n
76  */
77 double kt_fisher_exact(
78     int n11,
79     int n12,
80     int n21,
81     int n22,
82     double* _left,
83     double* _right,
84     double* two);
85