#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;
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=DV,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,"))
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;