X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fprob1.c;h=a380484310ccd7dc0ee72f922ba9f97aef6be80a;hp=176a0fc96d4e0b12f14172bc7c0d68297e01a50a;hb=b301e959d73eee0955c57004f344f17af00703f4;hpb=e3b3a0177339fb8c099346986e965e3bd5b85999

diff --git a/bcftools/prob1.c b/bcftools/prob1.c
index 176a0fc..a380484 100644
--- a/bcftools/prob1.c
+++ b/bcftools/prob1.c
@@ -3,13 +3,14 @@
 #include <string.h>
 #include <stdio.h>
 #include <errno.h>
+#include <assert.h>
 #include "prob1.h"
 
 #include "kseq.h"
 KSTREAM_INIT(gzFile, gzread, 16384)
 
 #define MC_MAX_EM_ITER 16
-#define MC_EM_EPS 1e-4
+#define MC_EM_EPS 1e-5
 #define MC_DEF_INDEL 0.15
 
 unsigned char seq_nt4_table[256] = {
@@ -33,10 +34,13 @@ unsigned char seq_nt4_table[256] = {
 
 struct __bcf_p1aux_t {
 	int n, M, n1, is_indel;
+	uint8_t *ploidy; // haploid or diploid ONLY
 	double *q2p, *pdg; // pdg -> P(D|g)
 	double *phi, *phi_indel;
 	double *z, *zswap; // aux for afs
 	double *z1, *z2, *phi1, *phi2; // only calculated when n1 is set
+	double **hg; // hypergeometric distribution
+	double *lf; // log factorial
 	double t, t1, t2;
 	double *afs, *afs1; // afs: accumulative AFS; afs1: site posterior distribution
 	const uint8_t *PL; // point to PL
@@ -123,27 +127,38 @@ int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn)
 	return 0;
 }
 
-bcf_p1aux_t *bcf_p1_init(int n)
+bcf_p1aux_t *bcf_p1_init(int n, uint8_t *ploidy)
 {
 	bcf_p1aux_t *ma;
 	int i;
 	ma = calloc(1, sizeof(bcf_p1aux_t));
 	ma->n1 = -1;
 	ma->n = n; ma->M = 2 * n;
+	if (ploidy) {
+		ma->ploidy = malloc(n);
+		memcpy(ma->ploidy, ploidy, n);
+		for (i = 0, ma->M = 0; i < n; ++i) ma->M += ploidy[i];
+		if (ma->M == 2 * n) {
+			free(ma->ploidy);
+			ma->ploidy = 0;
+		}
+	}
 	ma->q2p = calloc(256, sizeof(double));
 	ma->pdg = calloc(3 * ma->n, sizeof(double));
 	ma->phi = calloc(ma->M + 1, sizeof(double));
 	ma->phi_indel = calloc(ma->M + 1, sizeof(double));
 	ma->phi1 = calloc(ma->M + 1, sizeof(double));
 	ma->phi2 = 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->z = calloc(ma->M + 1, sizeof(double));
+	ma->zswap = calloc(ma->M + 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));
+	ma->afs = calloc(ma->M + 1, sizeof(double));
+	ma->afs1 = calloc(ma->M + 1, sizeof(double));
+	ma->lf = calloc(ma->M + 1, sizeof(double));
 	for (i = 0; i < 256; ++i)
 		ma->q2p[i] = pow(10., -i / 10.);
+	for (i = 0; i <= ma->M; ++i) ma->lf[i] = lgamma(i + 1);
 	bcf_p1_init_prior(ma, MC_PTYPE_FULL, 1e-3); // the simplest prior
 	return ma;
 }
@@ -151,6 +166,10 @@ bcf_p1aux_t *bcf_p1_init(int n)
 int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
 {
 	if (n1 == 0 || n1 >= b->n) return -1;
+	if (b->M != b->n * 2) {
+		fprintf(stderr, "[%s] unable to set `n1' when there are haploid samples.\n", __func__);
+		return -1;
+	}
 	b->n1 = n1;
 	return 0;
 }
@@ -158,7 +177,13 @@ int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
 void bcf_p1_destroy(bcf_p1aux_t *ma)
 {
 	if (ma) {
-		free(ma->q2p); free(ma->pdg);
+		int k;
+		free(ma->lf);
+		if (ma->hg && ma->n1 > 0) {
+			for (k = 0; k <= 2*ma->n1; ++k) free(ma->hg[k]);
+			free(ma->hg);
+		}
+		free(ma->ploidy); free(ma->q2p); free(ma->pdg);
 		free(ma->phi); free(ma->phi_indel); free(ma->phi1); free(ma->phi2);
 		free(ma->z); free(ma->zswap); free(ma->z1); free(ma->z2);
 		free(ma->afs); free(ma->afs1);
@@ -168,18 +193,16 @@ void bcf_p1_destroy(bcf_p1aux_t *ma)
 
 static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma)
 {
-	int i, j, k;
+	int i, j;
 	long *p, tmp;
 	p = alloca(b->n_alleles * sizeof(long));
 	memset(p, 0, sizeof(long) * b->n_alleles);
 	for (j = 0; j < ma->n; ++j) {
 		const uint8_t *pi = ma->PL + j * ma->PL_len;
 		double *pdg = ma->pdg + j * 3;
-		pdg[0] = ma->q2p[pi[b->n_alleles]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]];
-		for (i = k = 0; i < b->n_alleles; ++i) {
-			p[i] += (int)pi[k];
-			k += b->n_alleles - i;
-		}
+		pdg[0] = ma->q2p[pi[2]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]];
+		for (i = 0; i < b->n_alleles; ++i)
+			p[i] += (int)pi[(i+1)*(i+2)/2-1];
 	}
 	for (i = 0; i < b->n_alleles; ++i) p[i] = p[i]<<4 | i;
 	for (i = 1; i < b->n_alleles; ++i) // insertion sort
@@ -189,28 +212,18 @@ static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma)
 		if ((p[i]&0xf) == 0) break;
 	return i;
 }
-// f0 is the reference allele frequency
-static double mc_freq_iter(double f0, const bcf_p1aux_t *ma)
-{
-	double f, f3[3];
-	int i;
-	f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
-	for (i = 0, f = 0.; i < ma->n; ++i) {
-		double *pdg;
-		pdg = ma->pdg + i * 3;
-		f += (pdg[1] * f3[1] + 2. * pdg[2] * f3[2])
-			/ (pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2]);
-	}
-	f /= ma->n * 2.;
-	return f;
-}
 
 int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k)
 {
 	double sum, g[3];
 	double max, f3[3], *pdg = ma->pdg + k * 3;
-	int q, i, max_i;
-	f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
+	int q, i, max_i, ploidy;
+	ploidy = ma->ploidy? ma->ploidy[k] : 2;
+	if (ploidy == 2) {
+		f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
+	} else {
+		f3[0] = 1. - f0; f3[1] = 0; f3[2] = f0;
+	}
 	for (i = 0, sum = 0.; i < 3; ++i)
 		sum += (g[i] = pdg[i] * f3[i]);
 	for (i = 0, max = -1., max_i = 0; i < 3; ++i) {
@@ -230,6 +243,7 @@ static void mc_cal_y_core(bcf_p1aux_t *ma, int beg)
 {
 	double *z[2], *tmp, *pdg;
 	int _j, last_min, last_max;
+	assert(beg == 0 || ma->M == ma->n*2);
 	z[0] = ma->z;
 	z[1] = ma->zswap;
 	pdg = ma->pdg;
@@ -238,41 +252,81 @@ static void mc_cal_y_core(bcf_p1aux_t *ma, int beg)
 	z[0][0] = 1.;
 	last_min = last_max = 0;
 	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;
-		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.;
-		_max += 2;
-		if (_min == 0) 
-			k = 0, z[1][k] = (2*j+2-k)*(2*j-k+1) * p[0] * z[0][k];
-		if (_min <= 1)
-			k = 1, z[1][k] = (2*j+2-k)*(2*j-k+1) * p[0] * z[0][k] + k*(2*j+2-k) * p[1] * z[0][k-1];
-		for (k = _min < 2? 2 : _min; k <= _max; ++k)
-			z[1][k] = (2*j+2-k)*(2*j-k+1) * p[0] * z[0][k]
-				+ 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));
+	if (ma->M == ma->n * 2) {
+		int M = 0;
+		for (_j = beg; _j < ma->n; ++_j) {
+			int k, j = _j - beg, _min = last_min, _max = last_max, M0;
+			double p[3], sum;
+			M0 = M; M += 2;
+			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.;
+			_max += 2;
+			if (_min == 0) k = 0, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k];
+			if (_min <= 1) k = 1, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1];
+			for (k = _min < 2? 2 : _min; k <= _max; ++k)
+				z[1][k] = (M0-k+1)*(M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * 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 / (M * (M - 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->n1==-1 when unset
+				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;
+		}
+		//for (_j = 0; _j < last_min; ++_j) z[0][_j] = 0.; // TODO: are these necessary?
+		//for (_j = last_max + 1; _j < ma->M; ++_j) z[0][_j] = 0.;
+	} else { // this block is very similar to the block above; these two might be merged in future
+		int j, M = 0;
+		for (j = 0; j < ma->n; ++j) {
+			int k, M0, _min = last_min, _max = last_max;
+			double p[3], sum;
+			pdg = ma->pdg + j * 3;
+			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.;
+			M0 = M;
+			M += ma->ploidy[j];
+			if (ma->ploidy[j] == 1) {
+				p[0] = pdg[0]; p[1] = pdg[2];
+				_max++;
+				if (_min == 0) k = 0, z[1][k] = (M0+1-k) * p[0] * z[0][k];
+				for (k = _min < 1? 1 : _min; k <= _max; ++k)
+					z[1][k] = (M0+1-k) * p[0] * z[0][k] + k * p[1] * z[0][k-1];
+				for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
+				ma->t += log(sum / M);
+				for (k = _min; k <= _max; ++k) z[1][k] /= sum;
+				if (_min >= 1) z[1][_min-1] = 0.;
+				if (j < ma->n - 1) z[1][_max+1] = 0.;
+			} else if (ma->ploidy[j] == 2) {
+				p[0] = pdg[0]; p[1] = 2 * pdg[1]; p[2] = pdg[2];
+				_max += 2;
+				if (_min == 0) k = 0, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k];
+				if (_min <= 1) k = 1, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1];
+				for (k = _min < 2? 2 : _min; k <= _max; ++k)
+					z[1][k] = (M0-k+1)*(M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * 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 / (M * (M - 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.;
+			}
+			tmp = z[0]; z[0] = z[1]; z[1] = tmp;
+			last_min = _min; last_max = _max;
 		}
-		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) {
+	if (ma->n1 > 0 && ma->n1 < ma->n && ma->M == ma->n * 2) { // NB: ma->n1 is ineffective when there are haploid samples
 		int k;
 		long double x;
 		memset(ma->z1, 0, sizeof(double) * (2 * ma->n1 + 1));
@@ -288,41 +342,131 @@ static void mc_cal_y(bcf_p1aux_t *ma)
 	} else mc_cal_y_core(ma, 0);
 }
 
-static void contrast(bcf_p1aux_t *ma, double pc[4]) // mc_cal_y() must be called before hand
+#define CONTRAST_TINY 1e-30
+
+extern double kf_gammaq(double s, double z); // incomplete gamma function for chi^2 test
+
+static inline double chi2_test(int a, int b, int c, int d)
+{
+	double x, z;
+	x = (double)(a+b) * (c+d) * (b+d) * (a+c);
+	if (x == 0.) return 1;
+	z = a * d - b * c;
+	return kf_gammaq(.5, .5 * z * z * (a+b+c+d) / x);
+}
+
+// chi2=(a+b+c+d)(ad-bc)^2/[(a+b)(c+d)(a+c)(b+d)]
+static inline double contrast2_aux(const bcf_p1aux_t *p1, double sum, int k1, int k2, double x[3])
+{
+	double p = p1->phi[k1+k2] * p1->z1[k1] * p1->z2[k2] / sum * p1->hg[k1][k2];
+	int n1 = p1->n1, n2 = p1->n - p1->n1;
+	if (p < CONTRAST_TINY) return -1;
+	if (.5*k1/n1 < .5*k2/n2) x[1] += p;
+	else if (.5*k1/n1 > .5*k2/n2) x[2] += p;
+	else x[0] += p;
+	return p * chi2_test(k1, k2, (n1<<1) - k1, (n2<<1) - k2);
+}
+
+static double contrast2(bcf_p1aux_t *p1, double ret[3])
 {
-	int k, n1 = ma->n1, n2 = ma->n - ma->n1;
-	long double sum1, sum2;
-	pc[0] = pc[1] = pc[2] = pc[3] = -1.;
-	if (n1 <= 0 || n2 <= 0) return;
-	for (k = 0, sum1 = 0.; k <= 2*n1; ++k) sum1 += ma->phi1[k] * ma->z1[k];
-	for (k = 0, sum2 = 0.; k <= 2*n2; ++k) sum2 += ma->phi2[k] * ma->z2[k];
-	pc[2] = ma->phi1[2*n1] * ma->z1[2*n1] / sum1;
-	pc[3] = ma->phi2[2*n2] * ma->z2[2*n2] / sum2;
-	for (k = 2; k < 4; ++k) {
-		pc[k] = pc[k] > .5? -(-4.343 * log(1. - pc[k] + TINY) + .499) : -4.343 * log(pc[k] + TINY) + .499;
-		pc[k] = (int)pc[k];
-		if (pc[k] > 99) pc[k] = 99;
-		if (pc[k] < -99) pc[k] = -99;
+	int k, k1, k2, k10, k20, n1, n2;
+	double sum;
+	// get n1 and n2
+	n1 = p1->n1; n2 = p1->n - p1->n1;
+	if (n1 <= 0 || n2 <= 0) return 0.;
+	if (p1->hg == 0) { // initialize the hypergeometric distribution
+		/* NB: the hg matrix may take a lot of memory when there are many samples. There is a way
+		   to avoid precomputing this matrix, but it is slower and quite intricate. The following
+		   computation in this block can be accelerated with a similar strategy, but perhaps this
+		   is not a serious concern for now. */
+		double tmp = lgamma(2*(n1+n2)+1) - (lgamma(2*n1+1) + lgamma(2*n2+1));
+		p1->hg = calloc(2*n1+1, sizeof(void*));
+		for (k1 = 0; k1 <= 2*n1; ++k1) {
+			p1->hg[k1] = calloc(2*n2+1, sizeof(double));
+			for (k2 = 0; k2 <= 2*n2; ++k2)
+				p1->hg[k1][k2] = exp(lgamma(k1+k2+1) + lgamma(p1->M-k1-k2+1) - (lgamma(k1+1) + lgamma(k2+1) + lgamma(2*n1-k1+1) + lgamma(2*n2-k2+1) + tmp));
+		}
+	}
+	{ // compute
+		long double suml = 0;
+		for (k = 0; k <= p1->M; ++k) suml += p1->phi[k] * p1->z[k];
+		sum = suml;
+	}
+	{ // get the max k1 and k2
+		double max;
+		int max_k;
+		for (k = 0, max = 0, max_k = -1; k <= 2*n1; ++k) {
+			double x = p1->phi1[k] * p1->z1[k];
+			if (x > max) max = x, max_k = k;
+		}
+		k10 = max_k;
+		for (k = 0, max = 0, max_k = -1; k <= 2*n2; ++k) {
+			double x = p1->phi2[k] * p1->z2[k];
+			if (x > max) max = x, max_k = k;
+		}
+		k20 = max_k;
+	}
+	{ // We can do the following with one nested loop, but that is an O(N^2) thing. The following code block is much faster for large N.
+		double x[3], y;
+		long double z = 0., L[2];
+		x[0] = x[1] = x[2] = 0; L[0] = L[1] = 0;
+		for (k1 = k10; k1 >= 0; --k1) {
+			for (k2 = k20; k2 >= 0; --k2) {
+				if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+				else z += y;
+			}
+			for (k2 = k20 + 1; k2 <= 2*n2; ++k2) {
+				if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+				else z += y;
+			}
+		}
+		ret[0] = x[0]; ret[1] = x[1]; ret[2] = x[2];
+		x[0] = x[1] = x[2] = 0;
+		for (k1 = k10 + 1; k1 <= 2*n1; ++k1) {
+			for (k2 = k20; k2 >= 0; --k2) {
+				if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+				else z += y;
+			}
+			for (k2 = k20 + 1; k2 <= 2*n2; ++k2) {
+				if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+				else z += y;
+			}
+		}
+		ret[0] += x[0]; ret[1] += x[1]; ret[2] += x[2];
+		if (ret[0] + ret[1] + ret[2] < 0.95) { // in case of bad things happened
+			ret[0] = ret[1] = ret[2] = 0; L[0] = L[1] = 0;
+			for (k1 = 0, z = 0.; k1 <= 2*n1; ++k1)
+				for (k2 = 0; k2 <= 2*n2; ++k2)
+					if ((y = contrast2_aux(p1, sum, k1, k2, ret)) >= 0) z += y;
+			if (ret[0] + ret[1] + ret[2] < 0.95) // It seems that this may be caused by floating point errors. I do not really understand why...
+				z = 1.0, ret[0] = ret[1] = ret[2] = 1./3;
+		}
+		return (double)z;
 	}
-	pc[0] = ma->phi2[2*n2] * ma->z2[2*n2] / sum2 * (1. - ma->phi1[2*n1] * ma->z1[2*n1] / sum1);
-	pc[1] = ma->phi1[2*n1] * ma->z1[2*n1] / sum1 * (1. - ma->phi2[2*n2] * ma->z2[2*n2] / sum2);
-	pc[0] = pc[0] == 1.? 99 : (int)(-4.343 * log(1. - pc[0]) + .499);
-	pc[1] = pc[1] == 1.? 99 : (int)(-4.343 * log(1. - pc[1]) + .499);
 }
 
-static double mc_cal_afs(bcf_p1aux_t *ma)
+static double mc_cal_afs(bcf_p1aux_t *ma, double *p_ref_folded, double *p_var_folded)
 {
 	int k;
-	long double sum = 0.;
+	long double sum = 0., sum2;
 	double *phi = ma->is_indel? ma->phi_indel : ma->phi;
 	memset(ma->afs1, 0, sizeof(double) * (ma->M + 1));
 	mc_cal_y(ma);
+	// compute AFS
 	for (k = 0, sum = 0.; k <= ma->M; ++k)
 		sum += (long double)phi[k] * ma->z[k];
 	for (k = 0; k <= ma->M; ++k) {
 		ma->afs1[k] = phi[k] * ma->z[k] / sum;
 		if (isnan(ma->afs1[k]) || isinf(ma->afs1[k])) return -1.;
 	}
+	// compute folded variant probability
+	for (k = 0, sum = 0.; k <= ma->M; ++k)
+		sum += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k];
+	for (k = 1, sum2 = 0.; k < ma->M; ++k)
+		sum2 += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k];
+	*p_var_folded = sum2 / sum;
+	*p_ref_folded = (phi[k] + phi[ma->M - k]) / 2. * (ma->z[ma->M] + ma->z[0]) / sum;
+	// the expected frequency
 	for (k = 0, sum = 0.; k <= ma->M; ++k) {
 		ma->afs[k] += ma->afs1[k];
 		sum += k * ma->afs1[k];
@@ -330,37 +474,12 @@ static double mc_cal_afs(bcf_p1aux_t *ma)
 	return sum / ma->M;
 }
 
-long double bcf_p1_cal_g3(bcf_p1aux_t *p1a, double g[3])
-{
-	long double pd = 0., g2[3];
-	int i, k;
-	memset(g2, 0, sizeof(long double) * 3);
-	for (k = 0; k < p1a->M; ++k) {
-		double f = (double)k / p1a->M, f3[3], g1[3];
-		long double z = 1.;
-		g1[0] = g1[1] = g1[2] = 0.;
-		f3[0] = (1. - f) * (1. - f); f3[1] = 2. * f * (1. - f); f3[2] = f * f;
-		for (i = 0; i < p1a->n; ++i) {
-			double *pdg = p1a->pdg + i * 3;
-			double x = pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2];
-			z *= x;
-			g1[0] += pdg[0] * f3[0] / x;
-			g1[1] += pdg[1] * f3[1] / x;
-			g1[2] += pdg[2] * f3[2] / x;
-		}
-		pd += p1a->phi[k] * z;
-		for (i = 0; i < 3; ++i)
-			g2[i] += p1a->phi[k] * z * g1[i];
-	}
-	for (i = 0; i < 3; ++i) g[i] = g2[i] / pd;
-	return pd;
-}
-
-int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
+int bcf_p1_cal(const bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
 {
 	int i, k;
 	long double sum = 0.;
 	ma->is_indel = bcf_is_indel(b);
+	rst->perm_rank = -1;
 	// set PL and PL_len
 	for (i = 0; i < b->n_gi; ++i) {
 		if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
@@ -369,11 +488,22 @@ int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
 			break;
 		}
 	}
+	if (i == b->n_gi) return -1; // no PL
 	if (b->n_alleles < 2) return -1; // FIXME: find a better solution
 	// 
 	rst->rank0 = cal_pdg(b, ma);
-	rst->f_exp = mc_cal_afs(ma);
+	rst->f_exp = mc_cal_afs(ma, &rst->p_ref_folded, &rst->p_var_folded);
 	rst->p_ref = ma->afs1[ma->M];
+	for (k = 0, sum = 0.; k < ma->M; ++k)
+		sum += ma->afs1[k];
+	rst->p_var = (double)sum;
+	{ // compute the allele count
+		double max = -1;
+		rst->ac = -1;
+		for (k = 0; k <= ma->M; ++k)
+			if (max < ma->z[k]) max = ma->z[k], rst->ac = k;
+		rst->ac = ma->M - rst->ac;
+	}
 	// calculate f_flat and f_em
 	for (k = 0, sum = 0.; k <= ma->M; ++k)
 		sum += (long double)ma->z[k];
@@ -383,29 +513,33 @@ int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
 		rst->f_flat += k * p;
 	}
 	rst->f_flat /= ma->M;
-	{ // calculate f_em
-		double flast = rst->f_flat;
-		for (i = 0; i < MC_MAX_EM_ITER; ++i) {
-			rst->f_em = mc_freq_iter(flast, ma);
-			if (fabs(rst->f_em - flast) < MC_EM_EPS) break;
-			flast = rst->f_em;
-		}
-	}
 	{ // estimate equal-tail credible interval (95% level)
 		int l, h;
 		double p;
-		for (i = 0, p = 0.; i < ma->M; ++i)
+		for (i = 0, p = 0.; i <= ma->M; ++i)
 			if (p + ma->afs1[i] > 0.025) break;
 			else p += ma->afs1[i];
 		l = i;
-		for (i = ma->M-1, p = 0.; i >= 0; --i)
+		for (i = ma->M, p = 0.; i >= 0; --i)
 			if (p + ma->afs1[i] > 0.025) break;
 			else p += ma->afs1[i];
 		h = i;
 		rst->cil = (double)(ma->M - h) / ma->M; rst->cih = (double)(ma->M - l) / ma->M;
 	}
-	rst->g[0] = rst->g[1] = rst->g[2] = -1.;
-	contrast(ma, rst->pc);
+	if (ma->n1 > 0) { // compute LRT
+		double max0, max1, max2;
+		for (k = 0, max0 = -1; k <= ma->M; ++k)
+			if (max0 < ma->z[k]) max0 = ma->z[k];
+		for (k = 0, max1 = -1; k <= ma->n1 * 2; ++k)
+			if (max1 < ma->z1[k]) max1 = ma->z1[k];
+		for (k = 0, max2 = -1; k <= ma->M - ma->n1 * 2; ++k)
+			if (max2 < ma->z2[k]) max2 = ma->z2[k];
+		rst->lrt = log(max1 * max2 / max0);
+		rst->lrt = rst->lrt < 0? 1 : kf_gammaq(.5, rst->lrt);
+	} else rst->lrt = -1.0;
+	rst->cmp[0] = rst->cmp[1] = rst->cmp[2] = rst->p_chi2 = -1.0;
+	if (do_contrast && rst->p_var > 0.5) // skip contrast2() if the locus is a strong non-variant
+		rst->p_chi2 = contrast2(ma, rst->cmp);
 	return 0;
 }