#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.);
+}
+
+typedef struct {
+ double p[4];
+ int mq, depth, is_tested, d[4];
+} anno16_t;
+
+static double ttest(int n1, int n2, int a[4])
+{
+ extern double kf_betai(double a, double b, double x);
+ double t, v, u1, u2;
+ if (n1 == 0 || n2 == 0 || n1 + n2 < 3) return 1.0;
+ u1 = (double)a[0] / n1; u2 = (double)a[2] / n2;
+ if (u1 <= u2) return 1.;
+ t = (u1 - u2) / sqrt(((a[1] - n1 * u1 * u1) + (a[3] - n2 * u2 * u2)) / (n1 + n2 - 2) * (1./n1 + 1./n2));
+ v = n1 + n2 - 2;
+// printf("%d,%d,%d,%d,%lf,%lf,%lf\n", a[0], a[1], a[2], a[3], t, u1, u2);
+ return t < 0.? 1. : .5 * kf_betai(.5*v, .5, v/(v+t*t));
+}
+
+static int test16_core(int anno[16], anno16_t *a)
+{
+ extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
+ double left, right;
+ int i;
+ a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
+ memcpy(a->d, anno, 4 * sizeof(int));
+ a->depth = anno[0] + anno[1] + anno[2] + anno[3];
+ a->is_tested = (anno[0] + anno[1] > 0 && anno[2] + anno[3] > 0);
+ if (a->depth == 0) return -1;
+ a->mq = (int)(sqrt((anno[9] + anno[11]) / a->depth) + .499);
+ kt_fisher_exact(anno[0], anno[1], anno[2], anno[3], &left, &right, &a->p[0]);
+ for (i = 1; i < 4; ++i)
+ a->p[i] = ttest(anno[0] + anno[1], anno[2] + anno[3], anno+4*i);
+ return 0;
+}
+
+static int test16(bcf1_t *b, anno16_t *a)
+{
+ char *p;
+ int i, anno[16];
+ a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
+ a->d[0] = a->d[1] = a->d[2] = a->d[3] = 0.;
+ a->mq = a->depth = a->is_tested = 0;
+ if ((p = strstr(b->info, "I16=")) == 0) return -1;
+ p += 4;
+ for (i = 0; i < 16; ++i) {
+ anno[i] = strtol(p, &p, 10);
+ if (anno[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2;
+ ++p;
+ }
+ return test16_core(anno, a);
+}
+
+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 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);
+ test16(b, &a);
+ rm_info(n_smpl, b, "I16=");
+
memset(&s, 0, sizeof(kstring_t));
kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s);
if (is_var) {
kputc('\0', &s); kputc('\0', &s);
kputs(b->info, &s);
if (b->info[0]) kputc(';', &s);
- ksprintf(&s, "AF1=%.3lf;AFE=%.3lf;HWE=%.3lf,%.3lf,%.3lf", 1.-pr->f_em, 1.-pr->f_exp, pr->g[0], pr->g[1], pr->g[2]);
+ 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);
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;
+ b->qual = r < 1e-100? 99 : -3.434 * log(r);
+ if (b->qual > 99) b->qual = 99;
+ 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);
projects / samtools.git / blobdiff