#define VC_EM 0x10000
#define VC_PAIRCALL 0x20000
#define VC_QCNT 0x40000
+#define VC_INDEL_ONLY 0x80000
typedef struct {
int flag, prior_type, n1, n_sub, *sublist, n_perm;
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 (em[8] >= 0) ksprintf(&s, ";LRT2=%.3g", em[8]);
- //if (em[9] >= 0) ksprintf(&s, ";LRT1=%.3g", em[9]);
}
if (cons_llr > 0) {
ksprintf(&s, ";CLR=%d", cons_llr);
kputs("##INFO=<ID=QCHI2,Number=1,Type=Integer,Description=\"Phred scaled PCHI2.\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=RP,"))
kputs("##INFO=<ID=PR,Number=1,Type=Integer,Description=\"# permutations yielding a smaller PCHI2.\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=VDB,"))
+ kputs("##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias\">\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=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=DV,"))
+ kputs("##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"# high-quality non-reference 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);
+ kputs("##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">\n", &str);
h->l_txt = str.l + 1; h->txt = str.s;
}
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; vc.min_lrt = 1;
memset(qcnt, 0, 8 * 256);
- while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Y")) >= 0) {
+ while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Yw")) >= 0) {
switch (c) {
case '1': vc.n1 = atoi(optarg); break;
case 'l': vc.bed = bed_read(optarg); break;
case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
case 'g': vc.flag |= VC_CALL_GT | VC_CALL; break;
case 'I': vc.flag |= VC_NO_INDEL; break;
+ case 'w': vc.flag |= VC_INDEL_ONLY; break;
case 'M': vc.flag |= VC_ANNO_MAX; break;
case 'Y': vc.flag |= VC_QCNT; break;
case 't': vc.theta = atof(optarg); break;
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_INDEL_ONLY) && !is_indel) continue;
if ((vc.flag & VC_ACGT_ONLY) && !is_indel) {
int x;
if (b->ref[0] == 0 || b->ref[1] != 0) continue;
if (!(l > begin && end > b->pos)) continue;
}
++n_processed;
- if (vc.flag & VC_QCNT) { // summarize the difference
+ if ((vc.flag & VC_QCNT) && !is_indel) { // summarize the difference
int x = bcf_min_diff(b);
if (x > 255) x = 255;
if (x >= 0) ++qcnt[x];