--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/samtools-0.1.16/bcftools/fet.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,112 @@
+#include <math.h>
+#include <stdlib.h>
+
+/* This program is implemented with ideas from this web page:
+ *
+ *   http://www.langsrud.com/fisher.htm
+ */
+
+// log\binom{n}{k}
+static double lbinom(int n, int k)
+{
+	if (k == 0 || n == k) return 0;
+	return lgamma(n+1) - lgamma(k+1) - lgamma(n-k+1);
+}
+
+// n11  n12  | n1_
+// n21  n22  | n2_
+//-----------+----
+// n_1  n_2  | n
+
+// hypergeometric distribution
+static double hypergeo(int n11, int n1_, int n_1, int n)
+{
+	return exp(lbinom(n1_, n11) + lbinom(n-n1_, n_1-n11) - lbinom(n, n_1));
+}
+
+typedef struct {
+	int n11, n1_, n_1, n;
+	double p;
+} hgacc_t;
+
+// incremental version of hypergenometric distribution
+static double hypergeo_acc(int n11, int n1_, int n_1, int n, hgacc_t *aux)
+{
+	if (n1_ || n_1 || n) {
+		aux->n11 = n11; aux->n1_ = n1_; aux->n_1 = n_1; aux->n = n;
+	} else { // then only n11 changed; the rest fixed
+		if (n11%11 && n11 + aux->n - aux->n1_ - aux->n_1) {
+			if (n11 == aux->n11 + 1) { // incremental
+				aux->p *= (double)(aux->n1_ - aux->n11) / n11
+					* (aux->n_1 - aux->n11) / (n11 + aux->n - aux->n1_ - aux->n_1);
+				aux->n11 = n11;
+				return aux->p;
+			}
+			if (n11 == aux->n11 - 1) { // incremental
+				aux->p *= (double)aux->n11 / (aux->n1_ - n11)
+					* (aux->n11 + aux->n - aux->n1_ - aux->n_1) / (aux->n_1 - n11);
+				aux->n11 = n11;
+				return aux->p;
+			}
+		}
+		aux->n11 = n11;
+	}
+	aux->p = hypergeo(aux->n11, aux->n1_, aux->n_1, aux->n);
+	return aux->p;
+}
+
+double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two)
+{
+	int i, j, max, min;
+	double p, q, left, right;
+	hgacc_t aux;
+	int n1_, n_1, n;
+
+	n1_ = n11 + n12; n_1 = n11 + n21; n = n11 + n12 + n21 + n22; // calculate n1_, n_1 and n
+	max = (n_1 < n1_) ? n_1 : n1_; // max n11, for right tail
+	min = n1_ + n_1 - n;
+	if (min < 0) min = 0; // min n11, for left tail
+	*two = *_left = *_right = 1.;
+	if (min == max) return 1.; // no need to do test
+	q = hypergeo_acc(n11, n1_, n_1, n, &aux); // the probability of the current table
+	// left tail
+	p = hypergeo_acc(min, 0, 0, 0, &aux);
+	for (left = 0., i = min + 1; p < 0.99999999 * q; ++i) // loop until underflow
+		left += p, p = hypergeo_acc(i, 0, 0, 0, &aux);
+	--i;
+	if (p < 1.00000001 * q) left += p;
+	else --i;
+	// right tail
+	p = hypergeo_acc(max, 0, 0, 0, &aux);
+	for (right = 0., j = max - 1; p < 0.99999999 * q; --j) // loop until underflow
+		right += p, p = hypergeo_acc(j, 0, 0, 0, &aux);
+	++j;
+	if (p < 1.00000001 * q) right += p;
+	else ++j;
+	// two-tail
+	*two = left + right;
+	if (*two > 1.) *two = 1.;
+	// adjust left and right
+	if (abs(i - n11) < abs(j - n11)) right = 1. - left + q;
+	else left = 1.0 - right + q;
+	*_left = left; *_right = right;
+	return q;
+}
+
+#ifdef FET_MAIN
+#include <stdio.h>
+
+int main(int argc, char *argv[])
+{
+	char id[1024];
+	int n11, n12, n21, n22;
+	double left, right, twotail, prob;
+
+	while (scanf("%s%d%d%d%d", id, &n11, &n12, &n21, &n22) == 5) {
+		prob = kt_fisher_exact(n11, n12, n21, n22, &left, &right, &twotail);
+		printf("%s\t%d\t%d\t%d\t%d\t%.6g\t%.6g\t%.6g\t%.6g\n", id, n11, n12, n21, n22,
+				prob, left, right, twotail);
+	}
+	return 0;
+}
+#endif