#define VC_CALL_GT 2048
#define VC_ADJLD 4096
#define VC_NO_INDEL 8192
-#define VC_FOLDED 16384
+#define VC_ANNO_MAX 16384
typedef struct {
int flag, prior_type, n1;
if ((p = strstr(b->info, "I16=")) == 0) return -1;
p += 4;
for (i = 0; i < 16; ++i) {
- anno[i] = strtol(p, &p, 10);
+ errno = 0; anno[i] = strtol(p, &p, 10);
if (anno[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2;
++p;
}
{
kstring_t s;
int is_var = (pr->p_ref < pref);
- double p_hwe, r = is_var? pr->p_ref : 1. - pr->p_ref;
+ double p_hwe, r = is_var? pr->p_ref : pr->p_var, fq;
anno16_t a;
p_hwe = pr->g[0] >= 0.? test_hwe(pr->g) : 1.0; // only do HWE g[] is calculated
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=%.4lg;CI95=%.4lg,%.4lg", 1.-pr->f_em, 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);
+ 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=%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->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->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);
+ ksprintf(&s, ";GC=%.2f,%.2f,%.2f;HWE=%.3f", 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 : -4.343 * log(r);
- if (b->qual > 99) b->qual = 99;
+ b->qual = r < 1e-100? 999 : -4.343 * log(r);
+ if (b->qual > 999) b->qual = 999;
bcf_sync(b);
if (!is_var) bcf_shrink_alt(b, 1);
else if (!(flag&VC_KEEPALT))
return is_var;
}
+static void write_header(bcf_hdr_t *h)
+{
+ kstring_t str;
+ str.l = h->l_txt? h->l_txt - 1 : 0;
+ str.m = str.l + 1; str.s = h->txt;
+ if (!strstr(str.s, "##INFO=<ID=DP,"))
+ kputs("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=DP4,"))
+ kputs("##INFO=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\n", &str);
+ 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);
+ 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=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,"))
+ 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,Descriptin=\"Indicates that the variant is an INDEL.\">\n", &str);
+ if (!strstr(str.s, "##INFO=<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);
+ if (!strstr(str.s, "##FORMAT=<ID=GL,"))
+ kputs("##FORMAT=<ID=GL,Number=3,Type=Float,Description=\"Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=DP,"))
+ kputs("##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"# high-quality bases\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=SP,"))
+ kputs("##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=PL,"))
+ kputs("##FORMAT=<ID=PL,Number=-1,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2\">\n", &str);
+ 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]);
int bcfview(int argc, char *argv[])
{
extern int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b);
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);
bcf_t *bp, *bout = 0;
bcf1_t *b, *blast;
int c;
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.;
- while ((c = getopt(argc, argv, "fN1:l:cHAGvbSuP:t:p:QgLi:I")) >= 0) {
+ while ((c = getopt(argc, argv, "N1:l:cHAGvbSuP:t:p:QgLi:IM")) >= 0) {
switch (c) {
- case 'f': vc.flag |= VC_FOLDED; break;
case '1': vc.n1 = atoi(optarg); break;
case 'l': vc.fn_list = strdup(optarg); break;
case 'N': vc.flag |= VC_ACGT_ONLY; 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 't': vc.theta = atof(optarg); break;
case 'p': vc.pref = atof(optarg); break;
case 'i': vc.indel_frac = atof(optarg); break;
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 reference-free variant calling\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 [%.4lg]\n", vc.theta);
- fprintf(stderr, " -i FLOAT indel-to-substitution ratio [%.4lg]\n", vc.indel_frac);
- fprintf(stderr, " -p FLOAT variant if P(ref|D)<FLOAT [%.3lg]\n", vc.pref);
+ 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, "\n");
return 1;
bp = vcf_open(argv[optind], moder);
h = vcf_hdr_read(bp);
bout = vcf_open("-", modew);
- if (!(vc.flag & VC_QCALL)) vcf_hdr_write(bout, h);
+ if (!(vc.flag & VC_QCALL)) {
+ if (vc.flag & VC_CALL) write_header(h);
+ vcf_hdr_write(bout, h);
+ }
if (vc.flag & VC_CALL) {
p1 = bcf_p1_init(h->n_smpl);
if (vc.prior_file) {
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.flag & VC_FOLDED) bcf_p1_set_folded(p1);
}
if (vc.fn_list) hash = bcf_load_pos(vc.fn_list, h);
if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
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]);
+ ksprintf(&s, "NEIR=%.3f;NEIF=%.3f,%.3f", 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_ANNO_MAX) bcf_anno_max(b);
if (vc.flag & VC_NO_GENO) { // do not output GENO fields
b->n_gi = 0;
b->fmt[0] = '\0';
- }
+ b->l_str = b->fmt - b->str + 1;
+ } else bcf_fix_gt(b);
vcf_write(bout, h, b);
}
if (vc.prior_file) free(vc.prior_file);
projects / samtools.git / blobdiff