z' and z'' can be calculated

diff --git a/bcftools/call1.c b/bcftools/call1.c
index 75483e921a9ee10c45bfe6e4acf8e2ad3261f42c..c722b355afd8752031044ef63f98e9eef7c2876e 100644 (file)
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -20,9 +20,10 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 #define VC_VARONLY 16
 #define VC_VCFIN   32
 #define VC_UNCOMP  64
+#define VC_HWE     128
 
 typedef struct {
-       int flag, prior_type;
+       int flag, prior_type, n1;
        char *fn_list, *prior_file;
        double theta, pref;
 } viewconf_t;
@@ -140,14 +141,14 @@ static void rm_info(int n_smpl, bcf1_t *b, const char *key)
        bcf_sync(n_smpl, b);
 }
 
-static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag)
+static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref)
 {
        kstring_t s;
        int is_var = (pr->p_ref < pref);
        double p_hwe, r = is_var? pr->p_ref : 1. - pr->p_ref;
        anno16_t a;
 
-       p_hwe = test_hwe(pr->g);
+       p_hwe = pr->g[0] >= 0.? test_hwe(pr->g) : 1.0; // only do HWE g[] is calculated
        test16(b, &a);
        rm_info(n_smpl, b, "I16=");
 
@@ -162,7 +163,8 @@ static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p
        ksprintf(&s, "AF1=%.3lf;AFE=%.3lf", 1.-pr->f_em, 1.-pr->f_exp);
        ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
        if (a.is_tested) ksprintf(&s, ";PV4=%.2lg,%.2lg,%.2lg,%.2lg", a.p[0], a.p[1], a.p[2], a.p[3]);
-       if (p_hwe <= .2) ksprintf(&s, ";GC=%.2lf,%.2lf,%.2lf;HWE=%.3lf", pr->g[2], pr->g[1], pr->g[0], p_hwe);
+       if (pr->g[0] >= 0. && p_hwe <= .2)
+               ksprintf(&s, ";GC=%.2lf,%.2lf,%.2lf;HWE=%.3lf", pr->g[2], pr->g[1], pr->g[0], p_hwe);
        kputc('\0', &s);
        kputs(b->fmt, &s); kputc('\0', &s);
        free(b->str);
@@ -188,9 +190,10 @@ int bcfview(int argc, char *argv[])
 
        tid = begin = end = -1;
        memset(&vc, 0, sizeof(viewconf_t));
-       vc.prior_type = -1; vc.theta = 1e-3; vc.pref = 0.9;
-       while ((c = getopt(argc, argv, "l:cGvLbSuP:t:p:")) >= 0) {
+       vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.9;
+       while ((c = getopt(argc, argv, "1:l:cHGvLbSuP:t:p:")) >= 0) {
                switch (c) {
+               case '1': vc.n1 = atoi(optarg); break;
                case 'l': vc.fn_list = strdup(optarg); break;
                case 'G': vc.flag |= VC_NO_GENO; break;
                case 'L': vc.flag |= VC_NO_PL; break;
@@ -199,6 +202,7 @@ int bcfview(int argc, char *argv[])
                case 'c': vc.flag |= VC_CALL; break;
                case 'v': vc.flag |= VC_VARONLY; break;
                case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
+               case 'H': vc.flag |= VC_HWE; break;
                case 't': vc.theta = atof(optarg); break;
                case 'p': vc.pref = atof(optarg); break;
                case 'P':
@@ -218,6 +222,7 @@ int bcfview(int argc, char *argv[])
                fprintf(stderr, "         -S        input is VCF\n");
                fprintf(stderr, "         -G        suppress all individual genotype information\n");
                fprintf(stderr, "         -L        discard the PL genotype field\n");
+               fprintf(stderr, "         -H        perform Hardy-Weinberg test (slower)\n");
                fprintf(stderr, "         -v        output potential variant sites only\n");
                fprintf(stderr, "         -l FILE   list of sites to output [all sites]\n");
                fprintf(stderr, "         -t FLOAT  scaled mutation rate [%.4lg]\n", vc.theta);
@@ -245,6 +250,7 @@ int bcfview(int argc, char *argv[])
                                return 1;
                        }
                } else bcf_p1_init_prior(p1, vc.prior_type, vc.theta);
+               if (vc.n1 > 0) bcf_p1_set_n1(p1, vc.n1);
        }
        if (vc.fn_list) hash = bcf_load_pos(vc.fn_list, h);
        if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
@@ -274,10 +280,11 @@ int bcfview(int argc, char *argv[])
                }
                if (vc.flag & VC_CALL) {
                        bcf_p1rst_t pr;
-                       bcf_p1_cal(b, p1, &pr);
+                       bcf_p1_cal(b, p1, &pr); // pr.g[3] is not calculated here
+                       if (vc.flag&VC_HWE) bcf_p1_cal_g3(p1, pr.g);
                        if ((n_processed + 1) % 50000 == 0) bcf_p1_dump_afs(p1);
                        if (pr.p_ref >= vc.pref && (vc.flag & VC_VARONLY)) continue;
-                       update_bcf1(h->n_smpl, b, p1, &pr, vc.pref, vc.flag);
+                       update_bcf1(h->n_smpl, b, p1, &pr, vc.pref);
                }
                if (vc.flag & VC_NO_GENO) {
                        b->n_gi = 0;

diff --git a/bcftools/prob1.c b/bcftools/prob1.c
index e124b0f8f7810114f47c5d7eed3178681849877c..afbbd419cd0242aeefd1e31776e45fecdf36a981 100644 (file)
--- a/bcftools/prob1.c
+++ b/bcftools/prob1.c
@@ -36,6 +36,8 @@ struct __bcf_p1aux_t {
        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
        const uint8_t *PL; // point to PL
        int PL_len;
@@ -107,6 +109,8 @@ bcf_p1aux_t *bcf_p1_init(int n) // FIXME: assuming diploid
        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)
@@ -127,7 +131,7 @@ 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);
        }
@@ -195,10 +199,10 @@ int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k)
 
 #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;
@@ -206,10 +210,11 @@ 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.;
@@ -223,16 +228,56 @@ 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;
+               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 = exp(ma->t - (ma->t1 + ma->t2));
+               for (k = 0; k <= ma->M; ++k) ma->z[k] *= x;
+       } else mc_cal_y_core(ma, 0);
+/*
+       if (ma->n1 > 0 && ma->n1 < ma->n) {
+               int i;
+               double y[5];
+               printf("*****\n");
+               for (i = 0; i <= 2; ++i)
+                       printf("(%lf,%lf) ", ma->z1[i], ma->z2[i]);
+               printf("\n");
+               y[0] = ma->z1[0] * ma->z2[0];
+               y[1] = 1./2. * (ma->z1[0] * ma->z2[1] + ma->z1[1] * ma->z2[0]);
+               y[2] = 1./6. * (ma->z1[0] * ma->z2[2] + ma->z1[2] * ma->z2[0]) + 4./6. * ma->z1[1] * ma->z2[1];
+               y[3] = 1./2. * (ma->z1[1] * ma->z2[2] + ma->z1[2] * ma->z2[1]);
+               y[4] = ma->z1[2] * ma->z2[2];
+               for (i = 0; i <= 4; ++i) printf("(%lf,%lf) ", ma->z[i], y[i]);
+               printf("\n");
+       }
+*/
+}
+
 static double mc_cal_afs(bcf_p1aux_t *ma)
 {
        int k;
@@ -252,7 +297,7 @@ 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;
@@ -312,7 +357,8 @@ 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.;
+//     bcf_p1_cal_g3(ma, rst->g);
        return 0;
 }
 

diff --git a/bcftools/prob1.h b/bcftools/prob1.h
index 358f551b4f4bde25a591de96a67a013941a18416..6bb7440efde77043476de22ca922d590ebf2cf66 100644 (file)
--- a/bcftools/prob1.h
+++ b/bcftools/prob1.h
@@ -26,6 +26,8 @@ extern "C" {
        int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k);
        void bcf_p1_dump_afs(bcf_p1aux_t *ma);
        int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
+       long double bcf_p1_cal_g3(bcf_p1aux_t *p1a, double g[3]);
+       int bcf_p1_set_n1(bcf_p1aux_t *b, int n1);
 
 #ifdef __cplusplus
 }