#include "kseq.h"
KSTREAM_INIT(gzFile, gzread, 16384)
-#define VC_NO_PL 1
#define VC_NO_GENO 2
#define VC_BCFOUT 4
#define VC_CALL 8
#define VC_VCFIN 32
#define VC_UNCOMP 64
#define VC_HWE 128
+#define VC_KEEPALT 256
+#define VC_ACGT_ONLY 512
+#define VC_QCALL 1024
+#define VC_CALL_GT 2048
+#define VC_ADJLD 4096
typedef struct {
int flag, prior_type, n1;
return test16_core(anno, a);
}
-static void rm_info(int n_smpl, bcf1_t *b, const char *key)
+static void rm_info(bcf1_t *b, const char *key)
{
char *p, *q;
if ((p = strstr(b->info, key)) == 0) return;
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);
+ bcf_sync(b);
}
-static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref)
+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 is_var = (pr->p_ref < pref);
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=");
+ rm_info(b, "I16=");
memset(&s, 0, sizeof(kstring_t));
kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s);
- if (is_var) {
- kputs(b->alt, &s);
- }
- kputc('\0', &s); kputc('\0', &s);
+ kputs(b->alt, &s); kputc('\0', &s); kputc('\0', &s);
kputs(b->info, &s);
if (b->info[0]) kputc(';', &s);
- ksprintf(&s, "AF1=%.3lf;AFE=%.3lf", 1.-pr->f_em, 1.-pr->f_exp);
+// ksprintf(&s, "AF1=%.4lg;AFE=%.4lg;CI95=%.4lg,%.4lg", 1.-pr->f_em, 1.-pr->f_exp, pr->cil, pr->cih);
+ ksprintf(&s, "AF1=%.4lg;CI95=%.4lg,%.4lg", 1.-pr->f_em, pr->cil, pr->cih);
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 (a.is_tested) {
+ if (pr->pc[0] >= 0.) ksprintf(&s, ";PC4=%lg,%lg,%lg,%lg", pr->pc[0], pr->pc[1], pr->pc[2], pr->pc[3]);
+ ksprintf(&s, ";PV4=%.2lg,%.2lg,%.2lg,%.2lg", a.p[0], a.p[1], a.p[2], a.p[3]);
+ }
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);
b->m_str = s.m; b->l_str = s.l; b->str = s.s;
- b->qual = r < 1e-100? 99 : -3.434 * log(r);
+ b->qual = r < 1e-100? 99 : -4.343 * log(r);
if (b->qual > 99) b->qual = 99;
- bcf_sync(n_smpl, b);
+ bcf_sync(b);
+ if (!is_var) bcf_shrink_alt(b, 1);
+ else if (!(flag&VC_KEEPALT))
+ bcf_shrink_alt(b, pr->rank0 < 2? 2 : pr->rank0+1);
+ if (is_var && (flag&VC_CALL_GT)) { // call individual genotype
+ int i, x, old_n_gi = b->n_gi;
+ s.m = b->m_str; s.l = b->l_str - 1; s.s = b->str;
+ kputs(":GT:GQ", &s); kputc('\0', &s);
+ b->m_str = s.m; b->l_str = s.l; b->str = s.s;
+ bcf_sync(b);
+ for (i = 0; i < b->n_smpl; ++i) {
+ x = bcf_p1_call_gt(pa, pr->f_em, i);
+ ((uint8_t*)b->gi[old_n_gi].data)[i] = (x&3) == 0? 1<<3|1 : (x&3) == 1? 1 : 0;
+ ((uint8_t*)b->gi[old_n_gi+1].data)[i] = x>>2;
+ }
+ }
return is_var;
}
+double bcf_ld_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]);
+
int bcfview(int argc, char *argv[])
{
+ extern int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b);
bcf_t *bp, *bout = 0;
- bcf1_t *b;
+ bcf1_t *b, *blast;
int c;
uint64_t n_processed = 0;
viewconf_t vc;
tid = begin = end = -1;
memset(&vc, 0, sizeof(viewconf_t));
- 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) {
+ vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5;
+ while ((c = getopt(argc, argv, "N1:l:cHAGvbSuP:t:p:QgL")) >= 0) {
switch (c) {
case '1': vc.n1 = atoi(optarg); break;
case 'l': vc.fn_list = strdup(optarg); break;
+ case 'N': vc.flag |= VC_ACGT_ONLY; break;
case 'G': vc.flag |= VC_NO_GENO; break;
- case 'L': vc.flag |= VC_NO_PL; break;
+ case 'A': vc.flag |= VC_KEEPALT; 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 'v': vc.flag |= VC_VARONLY | VC_CALL; break;
case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
case 'H': vc.flag |= VC_HWE; break;
+ case 'g': vc.flag |= VC_CALL_GT | VC_CALL; break;
case 't': vc.theta = atof(optarg); break;
case 'p': vc.pref = atof(optarg); break;
+ case 'Q': vc.flag |= VC_QCALL; break;
+ case 'L': vc.flag |= VC_ADJLD; 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;
fprintf(stderr, "\n");
fprintf(stderr, "Usage: bcftools view [options] <in.bcf> [reg]\n\n");
fprintf(stderr, "Options: -c SNP calling\n");
+ fprintf(stderr, " -v output potential variant sites only (force -c)\n");
+ fprintf(stderr, " -g call genotypes at variant sites (force -c)\n");
fprintf(stderr, " -b output BCF instead of VCF\n");
- fprintf(stderr, " -u uncompressed BCF output\n");
+ fprintf(stderr, " -u uncompressed BCF output (force -b)\n");
fprintf(stderr, " -S input is VCF\n");
+ fprintf(stderr, " -A keep all possible alternate alleles at variant sites\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, " -N skip sites where REF is not A/C/G/T\n");
+ fprintf(stderr, " -Q output the QCALL likelihood format\n");
+ fprintf(stderr, " -L calculate LD for adjacent sites\n");
+ fprintf(stderr, " -1 INT number of group-1 samples [0]\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);
}
b = calloc(1, sizeof(bcf1_t));
+ blast = calloc(1, sizeof(bcf1_t));
strcpy(moder, "r");
if (!(vc.flag & VC_VCFIN)) strcat(moder, "b");
strcpy(modew, "w");
bp = vcf_open(argv[optind], moder);
h = vcf_hdr_read(bp);
bout = vcf_open("-", modew);
- vcf_hdr_write(bout, h);
+ if (!(vc.flag & VC_QCALL)) vcf_hdr_write(bout, h);
if (vc.flag & VC_CALL) {
p1 = bcf_p1_init(h->n_smpl);
if (vc.prior_file) {
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.n1 > 0) {
+ bcf_p1_set_n1(p1, vc.n1);
+ bcf_p1_init_subprior(p1, vc.prior_type, vc.theta);
+ }
}
if (vc.fn_list) hash = bcf_load_pos(vc.fn_list, h);
if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
idx = bcf_idx_load(argv[optind]);
if (idx) {
uint64_t off;
- off = bcf_idx_query(idx, tid, begin, end);
+ off = bcf_idx_query(idx, tid, begin);
+ if (off == 0) {
+ fprintf(stderr, "[%s] no records in the query region.\n", __func__);
+ return 1; // FIXME: a lot of memory leaks...
+ }
bgzf_seek(bp->fp, off, SEEK_SET);
bcf_idx_destroy(idx);
}
}
}
while (vcf_read(bp, h, b) > 0) {
+ if (vc.flag & VC_ACGT_ONLY) {
+ int x;
+ if (b->ref[0] == 0 || b->ref[1] != 0) continue;
+ x = toupper(b->ref[0]);
+ if (x != 'A' && x != 'C' && x != 'G' && x != 'T') continue;
+ }
if (hash) {
uint64_t x = (uint64_t)b->tid<<32 | b->pos;
khint_t k = kh_get(set64, hash, x);
+ if (kh_size(hash) == 0) break;
if (k == kh_end(hash)) continue;
+ kh_del(set64, hash, k);
}
if (tid >= 0) {
int l = strlen(b->ref);
if (b->tid != tid || b->pos >= end) break;
if (!(l > begin && end > b->pos)) continue;
}
- if (vc.flag & VC_CALL) {
+ ++n_processed;
+ if (vc.flag & VC_QCALL) { // output QCALL format; STOP here
+ bcf_2qcall(h, b);
+ continue;
+ }
+ if (vc.flag & (VC_CALL|VC_ADJLD)) bcf_gl2pl(b);
+ if (vc.flag & VC_CALL) { // call variants
bcf_p1rst_t 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 (n_processed % 100000 == 0) {
+ fprintf(stderr, "[%s] %ld sites processed.\n", __func__, (long)n_processed);
+ 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);
+ update_bcf1(h->n_smpl, b, p1, &pr, vc.pref, vc.flag);
}
- if (vc.flag & VC_NO_GENO) {
+ if (vc.flag & VC_ADJLD) { // compute LD
+ double f[4], r2;
+ if ((r2 = bcf_ld_freq(blast, b, f)) >= 0) {
+ kstring_t s;
+ s.m = s.l = 0; s.s = 0;
+ if (*b->info) kputc(';', &s);
+ ksprintf(&s, "NEIR=%.3lf;NEIF=%.3lf,%.3lf", r2, f[0]+f[2], f[0]+f[1]);
+ bcf_append_info(b, s.s, s.l);
+ free(s.s);
+ }
+ bcf_cpy(blast, b);
+ }
+ if (vc.flag & VC_NO_GENO) { // do not output GENO fields
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_destroy(b);
+ bcf_destroy(b); bcf_destroy(blast);
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);
return 0;
}
-
projects / samtools.git / blobdiff