--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/bcftools/mut.c	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,127 @@
+#include <stdlib.h>
+#include <stdint.h>
+#include "bcf.h"
+
+#define MAX_GENO 359
+
+int8_t seq_bitcnt[] = { 4, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4 };
+char *seq_nt16rev = "XACMGRSVTWYHKDBN";
+
+uint32_t *bcf_trio_prep(int is_x, int is_son)
+{
+	int i, j, k, n, map[10];
+	uint32_t *ret;
+	ret = calloc(MAX_GENO, 4);
+	for (i = 0, k = 0; i < 4; ++i)
+		for (j = i; j < 4; ++j)
+			map[k++] = 1<<i|1<<j;
+	for (i = 0, n = 1; i < 10; ++i) { // father
+		if (is_x && seq_bitcnt[map[i]] != 1) continue;
+		if (is_x && is_son) {
+			for (j = 0; j < 10; ++j) // mother
+				for (k = 0; k < 10; ++k) // child
+					if (seq_bitcnt[map[k]] == 1 && (map[j]&map[k]))
+						ret[n++] = j<<16 | i<<8 | k;
+		} else {
+			for (j = 0; j < 10; ++j) // mother
+				for (k = 0; k < 10; ++k) // child
+					if ((map[i]&map[k]) && (map[j]&map[k]) && ((map[i]|map[j])&map[k]) == map[k])
+						ret[n++] = j<<16 | i<<8 | k;
+		}
+	}
+	ret[0] = n - 1;
+	return ret;
+}
+
+
+int bcf_trio_call(const uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt)
+{
+	int i, j, k;
+	const bcf_ginfo_t *PL;
+	uint8_t *gl10;
+	int map[10];
+	if (b->n_smpl != 3) return -1; // not a trio
+	for (i = 0; i < b->n_gi; ++i)
+		if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+	if (i == b->n_gi) return -1; // no PL
+	gl10 = alloca(10 * b->n_smpl);
+	if (bcf_gl10(b, gl10) < 0) {
+		if (bcf_gl10_indel(b, gl10) < 0) return -1;
+	}
+	PL = b->gi + i;
+	for (i = 0, k = 0; i < 4; ++i)
+		for (j = i; j < 4; ++j)
+			map[k++] = seq_nt16rev[1<<i|1<<j];
+	for (j = 0; j < 3; ++j) // check if ref hom is the most probable in all members
+		if (((uint8_t*)PL->data)[j * PL->len] != 0) break;
+	if (j < 3) { // we need to go through the complex procedure
+		uint8_t *g[3];
+		int minc = 1<<30, minc_j = -1, minf = 0, gtf = 0, gtc = 0;
+		g[0] = gl10;
+		g[1] = gl10 + 10;
+		g[2] = gl10 + 20;
+		for (j = 1; j <= (int)prep[0]; ++j) { // compute LK with constraint
+			int sum = g[0][prep[j]&0xff] + g[1][prep[j]>>8&0xff] + g[2][prep[j]>>16&0xff];
+			if (sum < minc) minc = sum, minc_j = j;
+		}
+		gtc |= map[prep[minc_j]&0xff]; gtc |= map[prep[minc_j]>>8&0xff]<<8; gtc |= map[prep[minc_j]>>16]<<16;
+		for (j = 0; j < 3; ++j) { // compute LK without constraint
+			int min = 1<<30, min_k = -1;
+			for (k = 0; k < 10; ++k)
+				if (g[j][k] < min) min = g[j][k], min_k = k;
+			gtf |= map[min_k]<<(j*8);
+			minf += min;
+		}
+		*llr = minc - minf; *gt = (int64_t)gtc<<32 | gtf;
+	} else *llr = 0, *gt = -1;
+	return 0;
+}
+
+int bcf_pair_call(const bcf1_t *b)
+{
+	int i, j, k;
+	const bcf_ginfo_t *PL;
+	if (b->n_smpl != 2) return -1; // not a pair
+	for (i = 0; i < b->n_gi; ++i)
+		if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+	if (i == b->n_gi) return -1; // no PL
+	PL = b->gi + i;
+	for (j = 0; j < 2; ++j) // check if ref hom is the most probable in all members
+		if (((uint8_t*)PL->data)[j * PL->len] != 0) break;
+	if (j < 2) { // we need to go through the complex procedure
+		uint8_t *g[2];
+		int minc = 1<<30, minf = 0;
+		g[0] = PL->data;
+		g[1] = (uint8_t*)PL->data + PL->len;
+		for (j = 0; j < PL->len; ++j) // compute LK with constraint
+			minc = minc < g[0][j] + g[1][j]? minc : g[0][j] + g[1][j];
+		for (j = 0; j < 2; ++j) { // compute LK without constraint
+			int min = 1<<30;
+			for (k = 0; k < PL->len; ++k)
+				min = min < g[j][k]? min : g[j][k];
+			minf += min;
+		}
+		return minc - minf;
+	} else return 0;
+}
+
+int bcf_min_diff(const bcf1_t *b)
+{
+	int i, min = 1<<30;
+	const bcf_ginfo_t *PL;
+	for (i = 0; i < b->n_gi; ++i)
+		if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
+	if (i == b->n_gi) return -1; // no PL
+	PL = b->gi + i;
+	for (i = 0; i < b->n_smpl; ++i) {
+		int m1, m2, j;
+		const uint8_t *p = (uint8_t*)PL->data;
+		m1 = m2 = 1<<30;
+		for (j = 0; j < PL->len; ++j) {
+			if ((int)p[j] < m1) m2 = m1, m1 = p[j];
+			else if ((int)p[j] < m2) m2 = p[j];
+		}
+		min = min < m2 - m1? min : m2 - m1;
+	}
+	return min;
+}