X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fprob1.c;h=1d0328f936c180ebb447e4006631fa2c018363b6;hb=b62e611309f1aab8113ae4f0f74b0a61113f3cda;hp=6afd664f397b32d62aedad0774849d2e698f5bb7;hpb=f27c5d351576e00cece3708adcb386da61fe7b7f;p=samtools.git

diff --git a/bcftools/prob1.c b/bcftools/prob1.c
index 6afd664..1d0328f 100644
--- a/bcftools/prob1.c
+++ b/bcftools/prob1.c
@@ -2,12 +2,18 @@
 #include <stdlib.h>
 #include <string.h>
 #include <stdio.h>
+#include <errno.h>
 #include "prob1.h"
 
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
 #define MC_AVG_ERR 0.007
 #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, 
@@ -28,11 +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, *CMk; // CMk=\binom{M}{k}
+	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;
 };
@@ -54,35 +63,96 @@ void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta)
 	}
 }
 
-bcf_p1aux_t *bcf_p1_init(int n) // FIXME: assuming diploid
+int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn)
+{
+	gzFile fp;
+	kstring_t s;
+	kstream_t *ks;
+	long double sum;
+	int dret, k;
+	memset(&s, 0, sizeof(kstring_t));
+	fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+	ks = ks_init(fp);
+	memset(ma->phi, 0, sizeof(double) * (ma->M + 1));
+	while (ks_getuntil(ks, '\n', &s, &dret) >= 0) {
+		if (strstr(s.s, "[afs] ") == s.s) {
+			char *p = s.s + 6;
+			for (k = 0; k <= ma->M; ++k) {
+				int x;
+				double y;
+				x = strtol(p, &p, 10);
+				if (x != k && (errno == EINVAL || errno == ERANGE)) return -1;
+				++p;
+				y = strtod(p, &p);
+				if (y == 0. && (errno == EINVAL || errno == ERANGE)) return -1;
+				ma->phi[ma->M - k] += y;
+			}
+		}
+	}
+	ks_destroy(ks);
+	gzclose(fp);
+	free(s.s);
+	for (sum = 0., k = 0; k <= ma->M; ++k) sum += ma->phi[k];
+	fprintf(stderr, "[prior]");
+	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);
+	return 0;
+}
+
+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->CMk = 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)
 		ma->q2p[i] = pow(10., -i / 10.);
-	for (i = 0; i <= ma->M; ++i)
-		ma->CMk[i] = exp(lgamma(ma->M + 1) - lgamma(i + 1) - lgamma(ma->M - i + 1));
 	bcf_p1_init_prior(ma, MC_PTYPE_FULL, 1e-3); // the simplest prior
 	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->CMk);
-		free(ma->z); free(ma->zswap);
+		free(ma->phi);
+		free(ma->z); free(ma->zswap); free(ma->z1); free(ma->z2);
 		free(ma->afs); free(ma->afs1);
+		free(ma->k1k2);
 		free(ma);
 	}
 }
@@ -147,39 +217,141 @@ int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k)
 	return q<<2|max_i;
 }
 
-static void mc_cal_z(bcf_p1aux_t *ma)
+#define TINY 1e-20
+
+static void mc_cal_y_core(bcf_p1aux_t *ma, int beg)
 {
 	double *z[2], *tmp, *pdg;
-	int i, j;
+	int _j, last_min, last_max;
 	z[0] = ma->z;
 	z[1] = ma->zswap;
 	pdg = ma->pdg;
-	z[0][0] = 1.; z[0][1] = z[0][2] = 0.;
-	for (j = 0; j < ma->n; ++j) {
-		int max = (j + 1) * 2;
-		double p[3];
-		pdg = ma->pdg + j * 3;
+	memset(z[0], 0, sizeof(double) * (ma->M + 1));
+	memset(z[1], 0, sizeof(double) * (ma->M + 1));
+	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];
-		z[1][0] = p[0] * z[0][0];
-		z[1][1] = p[0] * z[0][1] + p[1] * z[0][0];
-		for (i = 2; i <= max; ++i)
-			z[1][i] = p[0] * z[0][i] + p[1] * z[0][i-1] + p[2] * z[0][i-2];
-		if (j < ma->n - 1) z[1][max+1] = z[1][max+2] = 0.;
+		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));
+		}
 		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;
+	y = lgamma(2*n1 + 1) - lgamma(ma->M + 1);
+	for (k = 1, x = 0.; k <= 2 * n2; ++k)
+		x += ma->phi[k] * ma->z2[k] * exp(lgamma(ma->M - k + 1) - lgamma(2*n2 - k + 1) + y);
+	pc[0] = ma->z1[0] * x / sum;
+	y = lgamma(2*n2 + 1) - lgamma(ma->M + 1);
+	for (k = 1, x = 0.; k <= 2 * n1; ++k)
+		x += ma->phi[k] * ma->z1[k] * exp(lgamma(ma->M - k + 1) - lgamma(2*n1 - k + 1) + y);
+	pc[1] = ma->z2[0] * x / sum;
+	for (k = 0; k < 4; ++k) {
+		y = 1. - pc[k];
+		if (y <= 0.) y = 1e-100;
+		pc[k] = (int)(-3.434 * log(y) + .499);
+		if (pc[k] > 99.) pc[k] = 99.;
+	}
+}
+
 static double mc_cal_afs(bcf_p1aux_t *ma)
 {
 	int k;
 	long double sum = 0.;
 	memset(ma->afs1, 0, sizeof(double) * (ma->M + 1));
-	mc_cal_z(ma);
+	mc_cal_y(ma);
 	for (k = 0, sum = 0.; k <= ma->M; ++k)
-		sum += (long double)ma->phi[k] * ma->z[k] / ma->CMk[k];
+		sum += (long double)ma->phi[k] * ma->z[k];
 	for (k = 0; k <= ma->M; ++k) {
-		ma->afs1[k] = ma->phi[k] * ma->z[k] / ma->CMk[k] / sum;
+		ma->afs1[k] = ma->phi[k] * ma->z[k] / sum;
 		if (isnan(ma->afs1[k]) || isinf(ma->afs1[k])) return -1.;
 	}
 	for (k = 0, sum = 0.; k <= ma->M; ++k) {
@@ -189,7 +361,7 @@ 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;
@@ -234,10 +406,10 @@ int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
 	rst->p_ref = ma->afs1[ma->M];
 	// calculate f_flat and f_em
 	for (k = 0, sum = 0.; k <= ma->M; ++k)
-		sum += (long double)ma->z[k] / ma->CMk[k];
+		sum += (long double)ma->z[k];
 	rst->f_flat = 0.;
 	for (k = 0; k <= ma->M; ++k) {
-		double p = ma->z[k] / ma->CMk[k] / sum;
+		double p = ma->z[k] / sum;
 		rst->f_flat += k * p;
 	}
 	rst->f_flat /= ma->M;
@@ -249,7 +421,9 @@ 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;
 }