#include "bcf.h"
#include "prob1.h"
#include "kstring.h"
+#include "time.h"
#include "khash.h"
KHASH_SET_INIT_INT64(set64)
#define VC_VARONLY 16
#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_ADJLD 4096
#define VC_NO_INDEL 8192
#define VC_ANNO_MAX 16384
+#define VC_FIX_PL 32768
typedef struct {
- int flag, prior_type, n1, n_sub, *sublist;
+ int flag, prior_type, n1, n_sub, *sublist, n_perm;
char *fn_list, *prior_file, **subsam, *fn_dict;
- double theta, pref, indel_frac;
+ uint8_t *ploidy;
+ double theta, pref, indel_frac, min_perm_p, min_smpl_frac;
} viewconf_t;
khash_t(set64) *bcf_load_pos(const char *fn, bcf_hdr_t *_h)
return hash;
}
-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];
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);
- double p_hwe, r = is_var? pr->p_ref : pr->p_var, fq;
+ int has_I16, is_var = (pr->p_ref < pref);
+ double fq, r = is_var? pr->p_ref : pr->p_var;
anno16_t a;
- p_hwe = pr->g[0] >= 0.? test_hwe(pr->g) : 1.0; // only do HWE g[] is calculated
- test16(b, &a);
+ has_I16 = test16(b, &a) >= 0? 1 : 0;
rm_info(b, "I16=");
memset(&s, 0, sizeof(kstring_t));
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);
- ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
+ 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 (a.is_tested) {
- if (pr->pc[0] >= 0.) ksprintf(&s, ";PC4=%g,%g,%g,%g", pr->pc[0], pr->pc[1], pr->pc[2], pr->pc[3]);
- ksprintf(&s, ";PV4=%.2g,%.2g,%.2g,%.2g", a.p[0], a.p[1], a.p[2], a.p[3]);
+ if (pr->cmp[0] >= 0.) {
+ int i, q[3], pq;
+ 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]);
}
- if (pr->g[0] >= 0. && p_hwe <= .2)
- ksprintf(&s, ";GC=%.2f,%.2f,%.2f;HWE=%.3f", pr->g[2], pr->g[1], pr->g[0], p_hwe);
+ 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);
kputs(b->fmt, &s); kputc('\0', &s);
free(b->str);
if (fp == 0) return 0; // fail to open file
ks = ks_init(fp);
while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
+ int l;
if (max == n) {
max = max? max<<1 : 4;
sam = realloc(sam, sizeof(void*)*max);
}
- sam[n++] = strdup(s.s);
+ l = s.l;
+ sam[n] = malloc(s.l + 2);
+ strcpy(sam[n], s.s);
+ sam[n][l+1] = 2; // by default, diploid
+ if (dret != '\n') {
+ if (ks_getuntil(ks, 0, &s, &dret) >= 0) { // read ploidy, 1 or 2
+ int x = (int)s.s[0] - '0';
+ if (x == 1 || x == 2) sam[n][l+1] = x;
+ else fprintf(stderr, "(%s) ploidy can only be 1 or 2; assume diploid\n", __func__);
+ }
+ if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+ }
+ ++n;
}
ks_destroy(ks);
gzclose(fp);
if (!strstr(str.s, "##INFO=<ID=MQ,"))
kputs("##INFO=<ID=MQ,Number=1,Type=Integer,Description=\"Root-mean-square mapping quality of covering reads\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=FQ,"))
- kputs("##INFO=<ID=FQ,Number=1,Type=Float,Description=\"Phred probability that sample chromosomes are not all the same\">\n", &str);
+ 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=CI95,"))
kputs("##INFO=<ID=PV4,Number=4,Type=Float,Description=\"P-values for strand bias, baseQ bias, mapQ bias and tail distance bias\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=INDEL,"))
kputs("##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">\n", &str);
- if (!strstr(str.s, "##INFO=<ID=GT,"))
+ if (!strstr(str.s, "##INFO=<ID=PC2,"))
+ kputs("##INFO=<ID=PC2,Number=2,Type=Integer,Description=\"Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=PCHI2,"))
+ kputs("##INFO=<ID=PCHI2,Number=1,Type=Float,Description=\"Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.\">\n", &str);
+ 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);
+ 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,"))
kputs("##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\n", &str);
extern void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x);
extern int bcf_fix_gt(bcf1_t *b);
extern int bcf_anno_max(bcf1_t *b);
+ extern int bcf_shuffle(bcf1_t *b, int seed);
bcf_t *bp, *bout = 0;
bcf1_t *b, *blast;
- int c;
+ int c, *seeds = 0;
uint64_t n_processed = 0;
viewconf_t vc;
bcf_p1aux_t *p1 = 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_sub = 0; vc.subsam = 0; vc.sublist = 0;
- while ((c = getopt(argc, argv, "N1:l:cHAGvbSuP:t:p:QgLi:IMs: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;
+ while ((c = getopt(argc, argv, "FN1:l:cHAGvbSuP: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 'D': vc.fn_dict = strdup(optarg); break;
+ case 'F': vc.flag |= VC_FIX_PL; break;
case 'N': vc.flag |= VC_ACGT_ONLY; break;
case 'G': vc.flag |= VC_NO_GENO; break;
case 'A': vc.flag |= VC_KEEPALT; break;
case 'c': vc.flag |= VC_CALL; 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 'I': vc.flag |= VC_NO_INDEL; break;
case 'M': vc.flag |= VC_ANNO_MAX; break;
case 'i': vc.indel_frac = atof(optarg); break;
case 'Q': vc.flag |= VC_QCALL; break;
case 'L': vc.flag |= VC_ADJLD; break;
- case 's': vc.subsam = read_samples(optarg, &vc.n_sub); break;
+ case 'U': vc.n_perm = atoi(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);
+ vc.ploidy = calloc(vc.n_sub + 1, 1);
+ for (tid = 0; tid < vc.n_sub; ++tid) vc.ploidy[tid] = vc.subsam[tid][strlen(vc.subsam[tid]) + 1];
+ tid = -1;
+ 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, " -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, " -H perform Hardy-Weinberg test (slower)\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, " -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 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, "\n");
return 1;
}
fprintf(stderr, "[%s] For VCF->BCF conversion please specify the sequence dictionary with -D\n", __func__);
return 1;
}
+ if (vc.n1 <= 0) vc.n_perm = 0; // TODO: give a warning here!
+ if (vc.n_perm > 0) {
+ seeds = malloc(vc.n_perm * sizeof(int));
+ srand48(time(0));
+ for (c = 0; c < vc.n_perm; ++c) seeds[c] = lrand48();
+ }
b = calloc(1, sizeof(bcf1_t));
blast = calloc(1, sizeof(bcf1_t));
strcpy(moder, "r");
vcf_hdr_write(bout, hout);
}
if (vc.flag & VC_CALL) {
- p1 = bcf_p1_init(hout->n_smpl);
+ p1 = bcf_p1_init(hout->n_smpl, vc.ploidy);
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__);
}
while (vcf_read(bp, hin, b) > 0) {
int is_indel;
+ 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);
+ int n = bcf_smpl_covered(b);
+ if ((double)n / b->n_smpl < vc.min_smpl_frac) continue;
+ }
if (vc.n_sub) bcf_subsam(vc.n_sub, vc.sublist, b);
+ if (vc.flag & VC_FIX_PL) bcf_fix_pl(b);
is_indel = bcf_is_indel(b);
if ((vc.flag & VC_NO_INDEL) && is_indel) continue;
if ((vc.flag & VC_ACGT_ONLY) && !is_indel) {
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 % 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;
+ if (vc.n_perm && vc.n1 > 0 && pr.p_chi2 < vc.min_perm_p) { // permutation test
+ bcf_p1rst_t r;
+ int i, n = 0;
+ for (i = 0; i < vc.n_perm; ++i) {
+ bcf_shuffle(b, seeds[i]);
+ bcf_p1_cal(b, p1, &r);
+ if (pr.p_chi2 >= r.p_chi2) ++n;
+ }
+ pr.perm_rank = n;
+ }
update_bcf1(hout->n_smpl, b, p1, &pr, vc.pref, vc.flag);
}
if (vc.flag & VC_ADJLD) { // compute LD
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) {
int i;
for (i = 0; i < vc.n_sub; ++i) free(vc.subsam[i]);
free(vc.subsam); free(vc.sublist);
}
+ if (seeds) free(seeds);
if (p1) bcf_p1_destroy(p1);
return 0;
}
projects / samtools.git / blobdiff