X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fcall1.c;h=bc1cd407e7967290051b4ffbf4c73938468a43dd;hb=496174d0b1c432375fd71b46ebdbecff78ef3f1a;hp=14a1570a13d6820152359e583c9c69d42d1021dd;hpb=4773f0ea85f278fc544d762d707e92673232f1e4;p=samtools.git diff --git a/bcftools/call1.c b/bcftools/call1.c index 14a1570..bc1cd40 100644 --- a/bcftools/call1.c +++ b/bcftools/call1.c @@ -319,7 +319,7 @@ int bcfview(int argc, char *argv[]) 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); 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; @@ -436,7 +436,7 @@ int bcfview(int argc, char *argv[]) vc.sublist = calloc(vc.n_sub, sizeof(int)); hout = bcf_hdr_subsam(hin, vc.n_sub, vc.subsam, vc.sublist); } - if (vc.flag & VC_CALL) write_header(hout); + write_header(hout); // always print the header vcf_hdr_write(bout, hout); } if (vc.flag & VC_CALL) {