Merge branch 'master' of github.com:samtools/samtools

[samtools.git] / bcftools / call1.c

diff --git a/bcftools/call1.c b/bcftools/call1.c
index 14a1570a13d6820152359e583c9c69d42d1021dd..bc1cd407e7967290051b4ffbf4c73938468a43dd 100644 (file)
--- 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) {