#include "kstring.h"
#include "time.h"
-#include "khash.h"
-KHASH_SET_INIT_INT64(set64)
-
#include "kseq.h"
KSTREAM_INIT(gzFile, gzread, 16384)
#define VC_NO_INDEL 8192
#define VC_ANNO_MAX 16384
#define VC_FIX_PL 32768
+#define VC_EM 0x10000
typedef struct {
int flag, prior_type, n1, n_sub, *sublist, n_perm;
- char *fn_list, *prior_file, **subsam, *fn_dict;
+ char *prior_file, **subsam, *fn_dict;
uint8_t *ploidy;
- double theta, pref, indel_frac, min_perm_p, min_smpl_frac;
+ double theta, pref, indel_frac, min_perm_p, min_smpl_frac, min_lrt;
+ void *bed;
} viewconf_t;
-khash_t(set64) *bcf_load_pos(const char *fn, bcf_hdr_t *_h)
-{
- void *str2id;
- gzFile fp;
- kstream_t *ks;
- int ret, dret, lineno = 1;
- kstring_t *str;
- khash_t(set64) *hash = 0;
-
- hash = kh_init(set64);
- str2id = bcf_build_refhash(_h);
- str = calloc(1, sizeof(kstring_t));
- fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
- ks = ks_init(fp);
- while (ks_getuntil(ks, 0, str, &dret) >= 0) {
- int tid = bcf_str2id(str2id, str->s);
- if (tid >= 0 && dret != '\n') {
- if (ks_getuntil(ks, 0, str, &dret) >= 0) {
- uint64_t x = (uint64_t)tid<<32 | (atoi(str->s) - 1);
- kh_put(set64, hash, x, &ret);
- } else break;
- } else fprintf(stderr, "[%s] %s is not a reference name (line %d).\n", __func__, str->s, lineno);
- if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
- if (dret < 0) break;
- ++lineno;
- }
- bcf_str2id_destroy(str2id);
- ks_destroy(ks);
- gzclose(fp);
- free(str->s); free(str);
- return hash;
-}
+void *bed_read(const char *fn);
+void bed_destroy(void *_h);
+int bed_overlap(const void *_h, const char *chr, int beg, int end);
typedef struct {
double p[4];
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, int flag)
+static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag, double em[9])
{
kstring_t s;
- int has_I16, is_var = (pr->p_ref < pref);
- double fq, r = is_var? pr->p_ref : pr->p_var;
+ int has_I16, is_var;
+ double fq, r;
anno16_t a;
has_I16 = test16(b, &a) >= 0? 1 : 0;
- rm_info(b, "I16=");
+ rm_info(b, "I16="); // FIXME: probably this function has a bug. If I move it below, I16 will not be removed!
memset(&s, 0, sizeof(kstring_t));
kputc('\0', &s); kputs(b->ref, &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=%.4lg;AFE=%.4lg;CI95=%.4lg,%.4lg", 1.-pr->f_em, 1.-pr->f_exp, pr->cil, pr->cih);
- ksprintf(&s, "AF1=%.4g;CI95=%.4g,%.4g", 1.-pr->f_em, pr->cil, pr->cih);
+ { // print EM
+ if (em[0] >= 0) ksprintf(&s, "AF1=%.4g", 1 - em[0]);
+ if (em[4] >= 0 && em[4] <= 0.05) ksprintf(&s, ";G3=%.4g,%.4g,%.4g;HWE=%.3g", em[3], em[2], em[1], em[4]);
+ if (em[5] >= 0 && em[6] >= 0) ksprintf(&s, ";AF2=%.4g,%.4g", 1 - em[5], 1 - em[6]);
+ if (em[7] >= 0) ksprintf(&s, ";LRT=%.3g", em[7]);
+ }
+ if (pr == 0) { // if pr is unset, return
+ 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;
+ bcf_sync(b);
+ return 1;
+ }
+
+ is_var = (pr->p_ref < pref);
+ r = is_var? pr->p_ref : pr->p_var;
+
+ ksprintf(&s, ";CI95=%.4g,%.4g", pr->cil, pr->cih); // FIXME: when EM is not used, ";" should be omitted!
if (has_I16) ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
fq = pr->p_ref_folded < 0.5? -4.343 * log(pr->p_ref_folded) : 4.343 * log(pr->p_var_folded);
if (fq < -999) fq = -999;
if (fq > 999) fq = 999;
ksprintf(&s, ";FQ=%.3g", fq);
- if (pr->cmp[0] >= 0.) {
- int i, q[3], pq;
+ if (pr->cmp[0] >= 0.) { // two sample groups
+ int i, q[3];
for (i = 1; i < 3; ++i) {
double x = pr->cmp[i] + pr->cmp[0]/2.;
q[i] = x == 0? 255 : (int)(-4.343 * log(x) + .499);
if (q[i] > 255) q[i] = 255;
}
- pq = (int)(-4.343 * log(pr->p_chi2) + .499);
if (pr->perm_rank >= 0) ksprintf(&s, ";PR=%d", pr->perm_rank);
- ksprintf(&s, ";QCHI2=%d;PCHI2=%.3g;PC2=%d,%d", pq, q[1], q[2], pr->p_chi2);
-// ksprintf(&s, ",%g,%g,%g", pr->cmp[0], pr->cmp[1], pr->cmp[2]);
+ ksprintf(&s, ";PCHI2=%.3g;PC2=%d,%d", q[1], q[2], pr->p_chi2);
}
if (has_I16 && a.is_tested) ksprintf(&s, ";PV4=%.2g,%.2g,%.2g,%.2g", a.p[0], a.p[1], a.p[2], a.p[3]);
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);
+ x = bcf_p1_call_gt(pa, pr->f_exp, 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;
}
kputs("##INFO=<ID=FQ,Number=1,Type=Float,Description=\"Phred probability of all samples being the same\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=AF1,"))
kputs("##INFO=<ID=AF1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the site allele frequency of the first ALT allele\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=G3,"))
+ kputs("##INFO=<ID=G3,Number=3,Type=Float,Description=\"ML estimate of genotype frequencies\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=HWE,"))
+ kputs("##INFO=<ID=HWE,Number=1,Type=Float,Description=\"Chi^2 based HWE test P-value based on G3\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=CI95,"))
kputs("##INFO=<ID=CI95,Number=2,Type=Float,Description=\"Equal-tail Bayesian credible interval of the site allele frequency at the 95% level\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=PV4,"))
if (!strstr(str.s, "##INFO=<ID=QCHI2,"))
kputs("##INFO=<ID=QCHI2,Number=1,Type=Integer,Description=\"Phred scaled PCHI2.\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=RP,"))
- kputs("##INFO=<ID=RP,Number=1,Type=Integer,Description=\"# permutations yielding a smaller PCHI2.\">\n", &str);
+ kputs("##INFO=<ID=PR,Number=1,Type=Integer,Description=\"# permutations yielding a smaller PCHI2.\">\n", &str);
if (!strstr(str.s, "##FORMAT=<ID=GT,"))
kputs("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n", &str);
if (!strstr(str.s, "##FORMAT=<ID=GQ,"))
h->l_txt = str.l + 1; h->txt = str.s;
}
-double bcf_ld_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]);
+double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]);
int bcfview(int argc, char *argv[])
{
bcf_hdr_t *hin, *hout;
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 = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.; vc.n_perm = 0; vc.min_perm_p = 0.01; vc.min_smpl_frac = 0;
- while ((c = getopt(argc, argv, "FN1:l:cHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:")) >= 0) {
+ vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.; vc.n_perm = 0; vc.min_perm_p = 0.01; vc.min_smpl_frac = 0; vc.min_lrt = 1;
+ while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:")) >= 0) {
switch (c) {
case '1': vc.n1 = atoi(optarg); break;
- case 'l': vc.fn_list = strdup(optarg); break;
+ case 'l': vc.bed = bed_read(optarg); break;
case 'D': vc.fn_dict = strdup(optarg); break;
case 'F': vc.flag |= VC_FIX_PL; break;
case 'N': vc.flag |= VC_ACGT_ONLY; break;
case 'b': vc.flag |= VC_BCFOUT; break;
case 'S': vc.flag |= VC_VCFIN; break;
case 'c': vc.flag |= VC_CALL; break;
+ case 'e': vc.flag |= VC_EM; break;
case 'v': vc.flag |= VC_VARONLY | VC_CALL; break;
case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
case 'g': vc.flag |= VC_CALL_GT | VC_CALL; break;
case 'Q': vc.flag |= VC_QCALL; break;
case 'L': vc.flag |= VC_ADJLD; break;
case 'U': vc.n_perm = atoi(optarg); break;
+ case 'C': vc.min_lrt = atof(optarg); break;
case 'X': vc.min_perm_p = atof(optarg); break;
case 'd': vc.min_smpl_frac = atof(optarg); break;
case 's': vc.subsam = read_samples(optarg, &vc.n_sub);
}
if (argc == optind) {
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 (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, " -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, " -I skip indels\n");
- fprintf(stderr, " -F PL generated by r921 or before\n");
- fprintf(stderr, " -d FLOAT skip loci where less than FLOAT fraction of samples covered [0]\n");
- fprintf(stderr, " -D FILE sequence dictionary for VCF->BCF conversion [null]\n");
- fprintf(stderr, " -l FILE list of sites to output [all sites]\n");
- fprintf(stderr, " -t FLOAT scaled substitution mutation rate [%.4g]\n", vc.theta);
- fprintf(stderr, " -i FLOAT indel-to-substitution ratio [%.4g]\n", vc.indel_frac);
- fprintf(stderr, " -p FLOAT variant if P(ref|D)<FLOAT [%.3g]\n", vc.pref);
- fprintf(stderr, " -P STR type of prior: full, cond2, flat [full]\n");
- fprintf(stderr, " -s FILE list of samples to use [all samples]\n");
- fprintf(stderr, " -1 INT number of group-1 samples [0]\n");
- fprintf(stderr, " -U INT number of permutations for association testing (effective with -1) [0]\n");
- fprintf(stderr, " -X FLOAT only perform permutations for P(chi^2)<FLOAT [%g]\n", vc.min_perm_p);
+ fprintf(stderr, "Usage: bcftools view [options] <in.bcf> [reg]\n\n");
+ fprintf(stderr, "Input/output options:\n\n");
+ fprintf(stderr, " -A keep all possible alternate alleles at variant sites\n");
+ fprintf(stderr, " -b output BCF instead of VCF\n");
+ fprintf(stderr, " -D FILE sequence dictionary for VCF->BCF conversion [null]\n");
+ fprintf(stderr, " -F PL generated by r921 or before (which generate old ordering)\n");
+ fprintf(stderr, " -G suppress all individual genotype information\n");
+ fprintf(stderr, " -l FILE list of sites (chr pos) or regions (BED) to output [all sites]\n");
+ fprintf(stderr, " -L calculate LD for adjacent sites\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, " -s FILE list of samples to use [all samples]\n");
+ fprintf(stderr, " -S input is VCF\n");
+ fprintf(stderr, " -u uncompressed BCF output (force -b)\n");
+ fprintf(stderr, "\nConsensus/variant calling options:\n\n");
+ fprintf(stderr, " -c SNP calling (force -e)\n");
+ fprintf(stderr, " -d FLOAT skip loci where less than FLOAT fraction of samples covered [0]\n");
+ fprintf(stderr, " -e likelihood based analyses\n");
+ fprintf(stderr, " -g call genotypes at variant sites (force -c)\n");
+ fprintf(stderr, " -i FLOAT indel-to-substitution ratio [%.4g]\n", vc.indel_frac);
+ fprintf(stderr, " -I skip indels\n");
+ fprintf(stderr, " -p FLOAT variant if P(ref|D)<FLOAT [%.3g]\n", vc.pref);
+ fprintf(stderr, " -P STR type of prior: full, cond2, flat [full]\n");
+ fprintf(stderr, " -t FLOAT scaled substitution mutation rate [%.4g]\n", vc.theta);
+ fprintf(stderr, " -v output potential variant sites only (force -c)\n");
+ fprintf(stderr, "\nContrast calling and association test options:\n\n");
+ fprintf(stderr, " -1 INT number of group-1 samples [0]\n");
+ fprintf(stderr, " -C FLOAT posterior constrast for LRT<FLOAT and P(ref|D)<0.5 [%g]\n", vc.min_lrt);
+ fprintf(stderr, " -U INT number of permutations for association testing (effective with -1) [0]\n");
+ fprintf(stderr, " -X FLOAT only perform permutations for P(chi^2)<FLOAT [%g]\n", vc.min_perm_p);
fprintf(stderr, "\n");
return 1;
}
+ if (vc.flag & VC_CALL) vc.flag |= VC_EM;
if ((vc.flag & VC_VCFIN) && (vc.flag & VC_BCFOUT) && vc.fn_dict == 0) {
fprintf(stderr, "[%s] For VCF->BCF conversion please specify the sequence dictionary with -D\n", __func__);
return 1;
return 1;
}
} else bcf_p1_init_prior(p1, vc.prior_type, vc.theta);
- if (vc.n1 > 0) {
+ if (vc.n1 > 0 && vc.min_lrt > 0.) { // set n1
bcf_p1_set_n1(p1, vc.n1);
bcf_p1_init_subprior(p1, vc.prior_type, vc.theta);
}
if (vc.indel_frac > 0.) bcf_p1_indel_prior(p1, vc.indel_frac); // otherwise use the default indel_frac
}
- if (vc.fn_list) hash = bcf_load_pos(vc.fn_list, hin);
if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
void *str2id = bcf_build_refhash(hout);
if (bcf_parse_region(str2id, argv[optind+1], &tid, &begin, &end) >= 0) {
}
while (vcf_read(bp, hin, b) > 0) {
int is_indel;
+ double em[9];
if ((vc.flag & VC_VARONLY) && strcmp(b->alt, "X") == 0) continue;
if ((vc.flag & VC_VARONLY) && vc.min_smpl_frac > 0.) {
extern int bcf_smpl_covered(const bcf1_t *b);
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 (vc.bed && !bed_overlap(vc.bed, hin->ns[b->tid], b->pos, b->pos + strlen(b->ref))) continue;
if (tid >= 0) {
int l = strlen(b->ref);
l = b->pos + (l > 0? l : 1);
bcf_2qcall(hout, b);
continue;
}
+ if (vc.flag & VC_EM) bcf_em1(b, vc.n1, 0xff, em);
+ else {
+ int i;
+ for (i = 0; i < 9; ++i) em[i] = -1.;
+ }
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
+ int calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
if (n_processed % 100000 == 0) {
fprintf(stderr, "[%s] %ld sites processed.\n", __func__, (long)n_processed);
bcf_p1_dump_afs(p1);
bcf_p1rst_t r;
int i, n = 0;
for (i = 0; i < vc.n_perm; ++i) {
+#ifdef BCF_PERM_LRT // LRT based permutation is much faster but less robust to artifacts
+ double x[9];
bcf_shuffle(b, seeds[i]);
- bcf_p1_cal(b, p1, &r);
+ bcf_em1(b, vc.n1, 1<<7, x);
+ if (x[7] < em[7]) ++n;
+#else
+ bcf_shuffle(b, seeds[i]);
+ bcf_p1_cal(b, 1, p1, &r);
if (pr.p_chi2 >= r.p_chi2) ++n;
+#endif
}
pr.perm_rank = n;
}
- update_bcf1(hout->n_smpl, b, p1, &pr, vc.pref, vc.flag);
- }
+ if (calret >= 0) update_bcf1(b, p1, &pr, vc.pref, vc.flag, em);
+ } else if (vc.flag & VC_EM) update_bcf1(b, 0, 0, 0, vc.flag, em);
if (vc.flag & VC_ADJLD) { // compute LD
double f[4], r2;
- if ((r2 = bcf_ld_freq(blast, b, f)) >= 0) {
+ if ((r2 = bcf_pair_freq(blast, b, f)) >= 0) {
kstring_t s;
s.m = s.l = 0; s.s = 0;
if (*b->info) kputc(';', &s);
- ksprintf(&s, "NEIR=%.3f;NEIF=%.3f,%.3f", r2, f[0]+f[2], f[0]+f[1]);
+ ksprintf(&s, "NEIR=%.3f;NEIF4=%.3f,%.3f,%.3f,%.3f", r2, f[0], f[1], f[2], f[3]);
bcf_append_info(b, s.s, s.l);
free(s.s);
}
bcf_hdr_destroy(hin);
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 (vc.fn_dict) free(vc.fn_dict);
if (vc.ploidy) free(vc.ploidy);
if (vc.n_sub) {
for (i = 0; i < vc.n_sub; ++i) free(vc.subsam[i]);
free(vc.subsam); free(vc.sublist);
}
+ if (vc.bed) bed_destroy(vc.bed);
if (seeds) free(seeds);
if (p1) bcf_p1_destroy(p1);
return 0;
projects / samtools.git / blobdiff