X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fprob1.c;h=37dc8ed32f5af45edc9af6fb8a2d2e306a275e97;hb=955605d6cf50290e32ff923da397021361ceb596;hp=4611af1f995fff8832300af10f733bffa41dd29d;hpb=b6f550edaa9384857879894bf01399fad76dac37;p=samtools.git

diff --git a/bcftools/prob1.c b/bcftools/prob1.c
index 4611af1..37dc8ed 100644
--- a/bcftools/prob1.c
+++ b/bcftools/prob1.c
@@ -12,6 +12,8 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 #define MC_MAX_EM_ITER 16
 #define MC_EM_EPS 1e-4
 
+//#define _BCF_QUAD
+
 unsigned char seq_nt4_table[256] = {
 	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
 	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
@@ -32,11 +34,14 @@ unsigned char seq_nt4_table[256] = {
 };
 
 struct __bcf_p1aux_t {
-	int n, M;
+	int n, M, n1;
 	double *q2p, *pdg; // pdg -> P(D|g)
 	double *phi;
 	double *z, *zswap; // aux for afs
+	double *z1, *z2; // only calculated when n1 is set
+	double t, t1, t2;
 	double *afs, *afs1; // afs: accumulative AFS; afs1: site posterior distribution
+	double *k1k2;
 	const uint8_t *PL; // point to PL
 	int PL_len;
 };
@@ -92,20 +97,25 @@ int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn)
 	for (k = 0; k <= ma->M; ++k) ma->phi[k] /= sum;
 	for (k = 0; k <= ma->M; ++k) fprintf(stderr, " %d:%.3lg", k, ma->phi[ma->M - k]);
 	fputc('\n', stderr);
+	for (sum = 0., k = 1; k <= ma->M; ++k) sum += k * ma->phi[ma->M - k];
+	fprintf(stderr, "[heterozygosity] %lf\n", (double)sum / ma->M);
 	return 0;
 }
 
-bcf_p1aux_t *bcf_p1_init(int n) // FIXME: assuming diploid
+bcf_p1aux_t *bcf_p1_init(int n)
 {
 	bcf_p1aux_t *ma;
 	int i;
 	ma = calloc(1, sizeof(bcf_p1aux_t));
+	ma->n1 = -1;
 	ma->n = n; ma->M = 2 * n;
 	ma->q2p = calloc(256, sizeof(double));
 	ma->pdg = calloc(3 * ma->n, sizeof(double));
 	ma->phi = calloc(ma->M + 1, sizeof(double));
 	ma->z = calloc(2 * ma->n + 1, sizeof(double));
 	ma->zswap = calloc(2 * ma->n + 1, sizeof(double));
+	ma->z1 = calloc(ma->M + 1, sizeof(double)); // actually we do not need this large
+	ma->z2 = calloc(ma->M + 1, sizeof(double));
 	ma->afs = calloc(2 * ma->n + 1, sizeof(double));
 	ma->afs1 = calloc(2 * ma->n + 1, sizeof(double));
 	for (i = 0; i < 256; ++i)
@@ -114,13 +124,37 @@ bcf_p1aux_t *bcf_p1_init(int n) // FIXME: assuming diploid
 	return ma;
 }
 
+#ifdef _BCF_QUAD
+static double lbinom(int n, int k)
+{
+	return lgamma(n+1) - lgamma(k+1) - lgamma(n-k+1);
+}
+#endif
+
+int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
+{
+	if (n1 == 0 || n1 >= b->n) return -1;
+	b->n1 = n1;
+#ifdef _BCF_QUAD
+	{
+		int k1, k2, n2 = b->n - b->n1;
+		b->k1k2 = calloc((2*n1+1) * (2*n2+1), sizeof(double));
+		for (k1 = 0; k1 <= 2*n1; ++k1)
+			for (k2 = 0; k2 <= 2*n2; ++k2)
+				b->k1k2[k1*(2*n2+1)+k2] = exp(lbinom(2*n1,k1) + lbinom(2*n2,k2) - lbinom(b->M,k1+k2));
+	}
+#endif
+	return 0;
+}
+
 void bcf_p1_destroy(bcf_p1aux_t *ma)
 {
 	if (ma) {
 		free(ma->q2p); free(ma->pdg);
 		free(ma->phi);
-		free(ma->z); free(ma->zswap);
+		free(ma->z); free(ma->zswap); free(ma->z1); free(ma->z2);
 		free(ma->afs); free(ma->afs1);
+		free(ma->k1k2);
 		free(ma);
 	}
 }
@@ -180,17 +214,17 @@ int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k)
 	}
 	max = 1. - max;
 	if (max < 1e-308) max = 1e-308;
-	q = (int)(-3.434 * log(max) + .499);
+	q = (int)(-4.343 * log(max) + .499);
 	if (q > 99) q = 99;
 	return q<<2|max_i;
 }
 
 #define TINY 1e-20
 
-static void mc_cal_y(bcf_p1aux_t *ma)
+static void mc_cal_y_core(bcf_p1aux_t *ma, int beg)
 {
 	double *z[2], *tmp, *pdg;
-	int k, j, last_min, last_max;
+	int _j, last_min, last_max;
 	z[0] = ma->z;
 	z[1] = ma->zswap;
 	pdg = ma->pdg;
@@ -198,10 +232,11 @@ static void mc_cal_y(bcf_p1aux_t *ma)
 	memset(z[1], 0, sizeof(double) * (ma->M + 1));
 	z[0][0] = 1.;
 	last_min = last_max = 0;
-	for (j = 0; j < ma->n; ++j) {
-		int _min = last_min, _max = last_max;
+	ma->t = 0.;
+	for (_j = beg; _j < ma->n; ++_j) {
+		int k, j = _j - beg, _min = last_min, _max = last_max;
 		double p[3], sum;
-		pdg = ma->pdg + j * 3;
+		pdg = ma->pdg + _j * 3;
 		p[0] = pdg[0]; p[1] = 2. * pdg[1]; p[2] = pdg[2];
 		for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.;
 		for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.;
@@ -215,16 +250,110 @@ static void mc_cal_y(bcf_p1aux_t *ma)
 				+ k*(2*j+2-k) * p[1] * z[0][k-1]
 				+ k*(k-1)* p[2] * z[0][k-2];
 		for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
+		ma->t += log(sum / ((2. * j + 2) * (2. * j + 1)));
 		for (k = _min; k <= _max; ++k) z[1][k] /= sum;
 		if (_min >= 1) z[1][_min-1] = 0.;
 		if (_min >= 2) z[1][_min-2] = 0.;
 		if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.;
+		if (_j == ma->n1 - 1) { // set pop1
+			ma->t1 = ma->t;
+			memcpy(ma->z1, z[1], sizeof(double) * (ma->n1 * 2 + 1));
+		}
 		tmp = z[0]; z[0] = z[1]; z[1] = tmp;
 		last_min = _min; last_max = _max;
 	}
 	if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (ma->M + 1));
 }
 
+static void mc_cal_y(bcf_p1aux_t *ma)
+{
+	if (ma->n1 > 0 && ma->n1 < ma->n) {
+		int k;
+		long double x;
+		memset(ma->z1, 0, sizeof(double) * (2 * ma->n1 + 1));
+		memset(ma->z2, 0, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
+		ma->t1 = ma->t2 = 0.;
+		mc_cal_y_core(ma, ma->n1);
+		ma->t2 = ma->t;
+		memcpy(ma->z2, ma->z, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
+		mc_cal_y_core(ma, 0);
+		// rescale z
+		x = expl(ma->t - (ma->t1 + ma->t2));
+		for (k = 0; k <= ma->M; ++k) ma->z[k] *= x;
+	} else mc_cal_y_core(ma, 0);
+#ifdef _BCF_QUAD
+/*
+	if (ma->n1 > 0 && ma->n1 < ma->n) { // DEBUG: consistency check; z[i] should equal y[i]
+		int i, k1, k2, n1 = ma->n1, n2 = ma->n - n1;
+		double *y;
+		printf("*** ");
+		y = calloc(ma->M + 1, sizeof(double));
+		for (k1 = 0; k1 <= 2*n1; ++k1)
+			for (k2 = 0; k2 <= 2*n2; ++k2)
+				y[k1+k2] += ma->k1k2[k1*(2*n2+1)+k2] * ma->z1[k1] * ma->z2[k2];
+		for (i = 0; i <= ma->M; ++i) printf("(%lf,%lf) ", ma->z[i], y[i]);
+		printf("\n");
+		free(y);
+	}
+*/
+#endif
+}
+
+static void contrast(bcf_p1aux_t *ma, double pc[4]) // mc_cal_y() must be called before hand
+{
+	int k, n1 = ma->n1, n2 = ma->n - ma->n1;
+	long double sum = -1., x, sum_alt;
+	double y;
+	pc[0] = pc[1] = pc[2] = pc[3] = -1.;
+	if (n1 <= 0 || n2 <= 0) return;
+#ifdef _BCF_QUAD
+	{ // FIXME: can be improved by skipping zero cells
+		int k1, k2;
+		long double z[3];
+		z[0] = z[1] = z[2] = 0.;
+		for (k1 = 0; k1 <= 2*n1; ++k1)
+			for (k2 = 0; k2 <= 2*n2; ++k2) {
+				double zz = ma->phi[k1+k2] * ma->z1[k1] * ma->z2[k2] * ma->k1k2[k1*(2*n2+1)+k2];
+				if ((double)k1/n1 < (double)k2/n2) z[0] += zz;
+				else if ((double)k1/n1 > (double)k2/n2) z[1] += zz;
+				else z[2] += zz;
+			}
+		sum = z[0] + z[1] + z[2];
+		pc[2] = z[0] / sum; pc[3] = z[1] / sum;
+	}
+#else
+	pc[2] = pc[3] = 0.;
+#endif
+	for (k = 0, sum_alt = 0.; k <= ma->M; ++k)
+		sum_alt += (long double)ma->phi[k] * ma->z[k];
+//	printf("* %lg, %lg *\n", (double)sum, (double)sum_alt); // DEBUG: sum should equal sum_alt
+	sum = sum_alt;
+	// the variant is specific to group2
+//	printf("%lg %lg %lg %lg\n", ma->z[2*(n1+n2)]/exp(ma->t - (ma->t1 + ma->t2)), ma->z1[2*n1], ma->z2[2*n2], (double)sum);
+	y = lgamma(2*n2 + 1) - lgamma(ma->M + 1);
+	for (k = 0, x = 0.; k < 2 * n2; ++k)
+		x += ma->phi[2*n1+k] * ma->z2[k] * expl(lgamma(2*n1 + k + 1) - lgamma(k + 1) + y);
+	pc[1] = ma->z1[2*n1] * x / sum;
+	for (k = 1, x = 0.; k <= 2 * n2; ++k)
+		x += ma->phi[k] * ma->z2[k] * expl(lgamma(ma->M - k + 1) - lgamma(2*n2 - k + 1) + y);
+	pc[1] += ma->z1[0] * x / sum;
+	// the variant is specific to group1
+	y = lgamma(2*n1 + 1) - lgamma(ma->M + 1);
+	for (k = 0, x = 0.; k < 2 * n1; ++k)
+		x += ma->phi[2*n2+k] * ma->z1[k] * expl(lgamma(2*n2 + k + 1) - lgamma(k + 1) + y);
+	pc[0] = ma->z2[2*n2] * x / sum;
+	for (k = 1, x = 0.; k <= 2 * n1; ++k)
+		x += ma->phi[k] * ma->z1[k] * expl(lgamma(ma->M - k + 1) - lgamma(2*n1 - k + 1) + y);
+	pc[0] += ma->z2[0] * x / sum;
+	// rescale
+	for (k = 2; k < 4; ++k) {
+		y = 1. - pc[k];
+		if (y <= 0.) y = 1e-100;
+		pc[k] = (int)(-4.343 * log(y) + .499);
+		if (pc[k] > 99.) pc[k] = 99.;
+	}
+}
+
 static double mc_cal_afs(bcf_p1aux_t *ma)
 {
 	int k;
@@ -244,7 +373,7 @@ static double mc_cal_afs(bcf_p1aux_t *ma)
 	return sum / ma->M;
 }
 
-static long double p1_cal_g3(bcf_p1aux_t *p1a, double g[3])
+long double bcf_p1_cal_g3(bcf_p1aux_t *p1a, double g[3])
 {
 	long double pd = 0., g2[3];
 	int i, k;
@@ -304,7 +433,9 @@ int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
 			flast = rst->f_em;
 		}
 	}
-	p1_cal_g3(ma, rst->g);
+	rst->g[0] = rst->g[1] = rst->g[2] = -1.;
+	contrast(ma, rst->pc);
+//	bcf_p1_cal_g3(ma, rst->g);
 	return 0;
 }