#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;
+ char *fn_list, *prior_file;
double theta, pref;
} viewconf_t;
p += 4;
for (i = 0; i < 4; ++i) {
d[i] = strtol(p, &p, 10);
- if (errno == EINVAL || errno == ERANGE) return -2.;
+ 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);
}
kputc('\0', &s); kputc('\0', &s);
kputs(b->info, &s);
- if (p_dp >= 0. && d[2] + d[3] > 0) { // has at least one non-reference base
- 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, ";HWE=%.3lf", p_hwe);
+ 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);
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; vc.pref = 0.9;
- while ((c = getopt(argc, argv, "l:cGvLbP:t:p:")) >= 0) {
+ 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 (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