Merge pull request #44 from peterjc/check_bins

[samtools.git] / bcftools / call1.c

diff --git a/bcftools/call1.c b/bcftools/call1.c
index 18805a03e7b76ab8db3040cc6e9d87a5e16dadaa..20083016e2814e51dd0fda5e8e4caa78248fe8bd 100644 (file)
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -258,8 +258,10 @@ static void write_header(bcf_hdr_t *h)
                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,"))
@@ -288,10 +290,8 @@ static void write_header(bcf_hdr_t *h)
         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,"))
@@ -349,7 +349,7 @@ 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); 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;