#define VC_QCALL 1024
#define VC_CALL_GT 2048
#define VC_ADJLD 4096
+#define VC_NO_INDEL 8192
+#define VC_FOLDED 16384
typedef struct {
int flag, prior_type, n1;
char *fn_list, *prior_file;
- double theta, pref;
+ double theta, pref, indel_frac;
} viewconf_t;
khash_t(set64) *bcf_load_pos(const char *fn, bcf_hdr_t *_h)
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;
}
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) {
if (pr->pc[0] >= 0.) ksprintf(&s, ";PC4=%lg,%lg,%lg,%lg", pr->pc[0], pr->pc[1], pr->pc[2], pr->pc[3]);
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);
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;
- while ((c = getopt(argc, argv, "N1:l:cHAGvbSuP:t:p:QgL")) >= 0) {
+ 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) {
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 '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 't': vc.theta = atof(optarg); break;
case 'p': vc.pref = atof(optarg); break;
+ case 'i': vc.indel_frac = atof(optarg); break;
case 'Q': vc.flag |= VC_QCALL; break;
case 'L': vc.flag |= VC_ADJLD; break;
case 'P':
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 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 mutation rate [%.4lg]\n", vc.theta);
+ 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, " -P STR type of prior: full, cond2, flat [full]\n");
fprintf(stderr, "\n");
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.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)) {
}
}
while (vcf_read(bp, h, b) > 0) {
- if (vc.flag & VC_ACGT_ONLY) {
+ int is_indel = bcf_is_indel(b);
+ if ((vc.flag & VC_NO_INDEL) && is_indel) continue;
+ if ((vc.flag & VC_ACGT_ONLY) && !is_indel) {
int x;
if (b->ref[0] == 0 || b->ref[1] != 0) continue;
x = toupper(b->ref[0]);