#include <stdlib.h>
#include <math.h>
#include <zlib.h>
+#include <errno.h>
#include "bcf.h"
#include "prob1.h"
#include "kstring.h"
#define VC_NO_PL 1
#define VC_NO_GENO 2
-#define VC_BCF 4
+#define VC_BCFOUT 4
#define VC_CALL 8
#define VC_VARONLY 16
+#define VC_VCFIN 32
+#define VC_UNCOMP 64
typedef struct {
int flag, prior_type;
- char *fn_list;
- double theta;
+ char *fn_list, *prior_file;
+ double theta, pref;
} viewconf_t;
khash_t(set64) *bcf_load_pos(const char *fn, bcf_hdr_t *_h)
return hash;
}
-static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, int flag)
+static double test_hwe(const double g[3])
+{
+ extern double kf_gammaq(double p, double x);
+ double fexp, chi2, f[3], n;
+ int i;
+ n = g[0] + g[1] + g[2];
+ fexp = (2. * g[2] + g[1]) / (2. * n);
+ if (fexp > 1. - 1e-10) fexp = 1. - 1e-10;
+ if (fexp < 1e-10) fexp = 1e-10;
+ f[0] = n * (1. - fexp) * (1. - fexp);
+ f[1] = n * 2. * fexp * (1. - fexp);
+ f[2] = n * fexp * fexp;
+ for (i = 0, chi2 = 0.; i < 3; ++i)
+ chi2 += (g[i] - f[i]) * (g[i] - f[i]) / f[i];
+ return kf_gammaq(.5, chi2 / 2.);
+}
+
+extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
+
+static double test_fisher(bcf1_t *b, const char *key, int d[4], int is_single)
+{
+ double left, right, two;
+ char *p;
+ int i;
+ if ((p = strstr(b->info, key)) == 0) return -1.;
+ p += 4;
+ for (i = 0; i < 4; ++i) {
+ d[i] = strtol(p, &p, 10);
+ if (d[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2.;
+ ++p;
+ }
+ kt_fisher_exact(d[0], d[1], d[2], d[3], &left, &right, &two);
+ return is_single? right : two;
+}
+
+static void rm_info(int n_smpl, bcf1_t *b, const char *key)
+{
+ char *p, *q;
+ if ((p = strstr(b->info, key)) == 0) return;
+ for (q = p; *q && *q != ';'; ++q);
+ if (p > b->info && *(p-1) == ';') --p;
+ memmove(p, q, b->l_str - (q - b->str));
+ b->l_str -= q - p;
+ 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)
{
kstring_t s;
- int x, is_var = (pr->p_ref < .5);
- double r = is_var? pr->p_ref : 1. - pr->p_ref;
+ int d[4], x, is_var = (pr->p_ref < pref);
+ double p_hwe, p_dp, p_ed, r = is_var? pr->p_ref : 1. - pr->p_ref;
+
+ p_hwe = test_hwe(pr->g);
+ p_ed = test_fisher(b, "ED4=", d, 1);
+ p_dp = test_fisher(b, "DP4=", d, 0);
+ rm_info(n_smpl, b, "ED4=");
+
memset(&s, 0, sizeof(kstring_t));
kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s);
if (is_var) {
kputs(b->info, &s);
if (b->info[0]) kputc(';', &s);
ksprintf(&s, "AF1=%.3lf;AFE=%.3lf", 1.-pr->f_em, 1.-pr->f_exp);
+ if (p_hwe <= .2) ksprintf(&s, ";GC=%.2lf,%.2lf,%.2lf;HWE=%.3lf", pr->g[2], pr->g[1], pr->g[0], p_hwe);
+ if (p_dp >= 0. && p_dp <= .2) ksprintf(&s, ";TDP=%.3lf", p_dp);
+ if (p_ed >= 0. && p_ed <= .2) ksprintf(&s, ";TED=%.3lf", p_ed);
kputc('\0', &s);
kputs(b->fmt, &s); kputc('\0', &s);
free(b->str);
b->m_str = s.m; b->l_str = s.l; b->str = s.s;
x = (int)(r < 1e-100? 99 : -3.434 * log(r) + .499);
b->qual = x > 99? 99 : x;
+ bcf_sync(n_smpl, b);
return is_var;
}
bcf_p1aux_t *p1 = 0;
bcf_hdr_t *h;
int tid, begin, end;
+ char moder[4], modew[4];
khash_t(set64) *hash = 0;
tid = begin = end = -1;
memset(&vc, 0, sizeof(viewconf_t));
- vc.prior_type = -1; vc.theta = 1e-3;
- while ((c = getopt(argc, argv, "l:cGvLbP:t:")) >= 0) {
+ vc.prior_type = -1; vc.theta = 1e-3; vc.pref = 0.9;
+ while ((c = getopt(argc, argv, "l:cGvLbSuP:t:p:")) >= 0) {
switch (c) {
case 'l': vc.fn_list = strdup(optarg); break;
case 'G': vc.flag |= VC_NO_GENO; break;
case 'L': vc.flag |= VC_NO_PL; break;
- case 'b': vc.flag |= VC_BCF; break;
+ case 'b': vc.flag |= VC_BCFOUT; break;
+ case 'S': vc.flag |= VC_VCFIN; break;
case 'c': vc.flag |= VC_CALL; break;
case 'v': vc.flag |= VC_VARONLY; break;
+ case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
case 't': vc.theta = atof(optarg); break;
+ case 'p': vc.pref = atof(optarg); break;
case 'P':
if (strcmp(optarg, "full") == 0) vc.prior_type = MC_PTYPE_FULL;
else if (strcmp(optarg, "cond2") == 0) vc.prior_type = MC_PTYPE_COND2;
else if (strcmp(optarg, "flat") == 0) vc.prior_type = MC_PTYPE_FLAT;
+ else vc.prior_file = strdup(optarg);
break;
}
}
if (argc == optind) {
- fprintf(stderr, "Usage: bcftools view [-cGPb] [-l list] <in.bcf> [reg]\n");
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: bcftools view [options] <in.bcf> [reg]\n\n");
+ fprintf(stderr, "Options: -c SNP calling\n");
+ fprintf(stderr, " -b output BCF instead of VCF\n");
+ fprintf(stderr, " -u uncompressed BCF output\n");
+ 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, " -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);
+ fprintf(stderr, " -p FLOAT variant if P(ref|D)<FLOAT [%.3lg]\n", vc.pref);
+ fprintf(stderr, " -P STR type of prior: full, cond2, flat [full]\n");
+ fprintf(stderr, "\n");
return 1;
}
b = calloc(1, sizeof(bcf1_t));
- bp = bcf_open(argv[optind], "r");
- h = bcf_hdr_read(bp);
- if (vc.flag & VC_BCF) {
- bout = bcf_open("-", "w");
- bcf_hdr_write(bout, h);
- }
+ strcpy(moder, "r");
+ if (!(vc.flag & VC_VCFIN)) strcat(moder, "b");
+ strcpy(modew, "w");
+ if (vc.flag & VC_BCFOUT) strcat(modew, "b");
+ if (vc.flag & VC_UNCOMP) strcat(modew, "u");
+ bp = vcf_open(argv[optind], moder);
+ h = vcf_hdr_read(bp);
+ bout = vcf_open("-", modew);
+ vcf_hdr_write(bout, h);
if (vc.flag & VC_CALL) {
p1 = bcf_p1_init(h->n_smpl);
- bcf_p1_init_prior(p1, vc.prior_type, vc.theta);
+ if (vc.prior_file) {
+ if (bcf_p1_read_prior(p1, vc.prior_file) < 0) {
+ fprintf(stderr, "[%s] fail to read the prior AFS.\n", __func__);
+ return 1;
+ }
+ } else bcf_p1_init_prior(p1, vc.prior_type, vc.theta);
}
if (vc.fn_list) hash = bcf_load_pos(vc.fn_list, h);
- if (optind + 1 < argc) {
+ if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
void *str2id = bcf_build_refhash(h);
if (bcf_parse_region(str2id, argv[optind+1], &tid, &begin, &end) >= 0) {
bcf_idx_t *idx;
}
}
}
- while (bcf_read(bp, h, b) > 0) {
+ while (vcf_read(bp, h, b) > 0) {
if (hash) {
uint64_t x = (uint64_t)b->tid<<32 | b->pos;
khint_t k = kh_get(set64, hash, x);
}
if (vc.flag & VC_CALL) {
bcf_p1rst_t pr;
- int is_var;
bcf_p1_cal(b, p1, &pr);
- is_var = update_bcf1(b, p1, &pr, vc.flag);
- bcf_sync(h->n_smpl, b);
if ((n_processed + 1) % 50000 == 0) bcf_p1_dump_afs(p1);
- if ((vc.flag & VC_VARONLY) && !is_var) continue;
+ if (pr.p_ref >= vc.pref && (vc.flag & VC_VARONLY)) continue;
+ update_bcf1(h->n_smpl, b, p1, &pr, vc.pref, vc.flag);
}
- if (vc.flag & VC_BCF) bcf_write(bout, h, b);
- else {
- char *vcf;
- if (vc.flag & VC_NO_GENO) {
- b->n_gi = 0;
- b->fmt[0] = '\0';
- }
- vcf = bcf_fmt(h, b);
- puts(vcf);
- free(vcf);
+ if (vc.flag & VC_NO_GENO) {
+ b->n_gi = 0;
+ b->fmt[0] = '\0';
}
+ vcf_write(bout, h, b);
++n_processed;
}
+ if (vc.prior_file) free(vc.prior_file);
if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);
bcf_hdr_destroy(h);
- bcf_close(bp); bcf_close(bout);
bcf_destroy(b);
+ vcf_close(bp); vcf_close(bout);
if (hash) kh_destroy(set64, hash);
if (vc.fn_list) free(vc.fn_list);
if (p1) bcf_p1_destroy(p1);
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