kputs("##INFO=<ID=AC1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first ALT allele count (no HWE assumption)\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=AN,"))
kputs("##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">\n", &str);
- if (!strstr(str.s, "##INFO=<ID=IS,"))
- kputs("##INFO=<ID=IS,Number=2,Type=Float,Description=\"Maximum number of reads supporting an indel and fraction of indel reads\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=IDV,"))
+ kputs("##INFO=<ID=IDV,Number=1,Type=Integer,Description=\"Maximum number of reads supporting an indel\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=IMF,"))
+ kputs("##INFO=<ID=IMF,Number=1,Type=Float,Description=\"Maximum fraction of reads supporting an indel\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=AC,"))
kputs("##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes for each ALT allele, in the same order as listed\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=G3,"))
kputs("##INFO=<ID=PR,Number=1,Type=Integer,Description=\"# permutations yielding a smaller PCHI2.\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=QBD,"))
kputs("##INFO=<ID=QBD,Number=1,Type=Float,Description=\"Quality by Depth: QUAL/#reads\">\n", &str);
- if (!strstr(str.s, "##INFO=<ID=QBDNR,"))
- kputs("##INFO=<ID=QBDNR,Number=1,Type=Float,Description=\"Quality by Depth: QUAL/#nref-reads\">\n", &str);
- if (!strstr(str.s, "##INFO=<ID=RPS,"))
- kputs("##INFO=<ID=RPS,Number=3,Type=Float,Description=\"Read Position Stats: depth, average, stddev\">\n", &str);
+ //if (!strstr(str.s, "##INFO=<ID=RPS,"))
+ // kputs("##INFO=<ID=RPS,Number=3,Type=Float,Description=\"Read Position Stats: depth, average, stddev\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=RPB,"))
kputs("##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Read Position Bias\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=MDV,"))
while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Ywm:K:")) >= 0) {
switch (c) {
case '1': vc.n1 = atoi(optarg); break;
- case 'l': vc.bed = bed_read(optarg); if (!vc.bed) fprintf(stderr,"Could not read \"%s\"\n", optarg); return 1; break;
+ case 'l': vc.bed = bed_read(optarg); if (!vc.bed) { fprintf(stderr,"Could not read \"%s\"\n", optarg); return 1; } 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;