Fixed the VCF header to pass validation

[samtools.git] / bcftools / call1.c

diff --git a/bcftools/call1.c b/bcftools/call1.c
index adf7a52cf69ad371eb6ec2f76c2d76ff45565275..2308607ab6d9de176570282f32a4797a275b6f7c 100644 (file)
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -26,6 +26,7 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 #define VC_CALL_GT 2048
 #define VC_ADJLD   4096
 #define VC_NO_INDEL 8192
+#define VC_ANNO_MAX 16384
 
 typedef struct {
        int flag, prior_type, n1;
@@ -212,19 +213,27 @@ static void write_header(bcf_hdr_t *h)
        if (!strstr(str.s, "##INFO=<ID=MQ,"))
                kputs("##INFO=<ID=MQ,Number=1,Type=Integer,Description=\"Root-mean-square mapping quality of covering reads\">\n", &str);
        if (!strstr(str.s, "##INFO=<ID=FQ,"))
-               kputs("##INFO=<ID=FQ,Number=1,Type=Integer,Description=\"Phred probability that sample chromosomes are not all the same\">\n", &str);
+               kputs("##INFO=<ID=FQ,Number=1,Type=Float,Description=\"Phred probability that sample chromosomes are not all the same\">\n", &str);
        if (!strstr(str.s, "##INFO=<ID=AF1,"))
                kputs("##INFO=<ID=AF1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the site allele frequency of the first ALT allele\">\n", &str);
        if (!strstr(str.s, "##INFO=<ID=CI95,"))
                kputs("##INFO=<ID=CI95,Number=2,Type=Float,Description=\"Equal-tail Bayesian credible interval of the site allele frequency at the 95% level\">\n", &str);
        if (!strstr(str.s, "##INFO=<ID=PV4,"))
                kputs("##INFO=<ID=PV4,Number=4,Type=Float,Description=\"P-values for strand bias, baseQ bias, mapQ bias and tail distance bias\">\n", &str);
+    if (!strstr(str.s, "##INFO=<ID=INDEL,"))
+        kputs("##INFO=<ID=INDEL,Number=0,Type=Flag,Descriptin=\"Indicates that the variant is an INDEL.\">\n", &str);
+    if (!strstr(str.s, "##INFO=<ID=GT,"))
+        kputs("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n", &str);
+    if (!strstr(str.s, "##FORMAT=<ID=GQ,"))
+        kputs("##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\n", &str);
+    if (!strstr(str.s, "##FORMAT=<ID=GL,"))
+        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=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,"))
-               kputs("##FORMAT=<ID=PL,Number=(#ALT+1)*(#ALT+2)/2,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">\n", &str);
+               kputs("##FORMAT=<ID=PL,Number=-1,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2\">\n", &str);
        h->l_txt = str.l + 1; h->txt = str.s;
 }
 
@@ -235,6 +244,7 @@ int bcfview(int argc, char *argv[])
        extern int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b);
        extern void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x);
        extern int bcf_fix_gt(bcf1_t *b);
+       extern int bcf_anno_max(bcf1_t *b);
        bcf_t *bp, *bout = 0;
        bcf1_t *b, *blast;
        int c;
@@ -249,7 +259,7 @@ int bcfview(int argc, char *argv[])
        tid = begin = end = -1;
        memset(&vc, 0, sizeof(viewconf_t));
        vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.;
-       while ((c = getopt(argc, argv, "N1:l:cHAGvbSuP:t:p:QgLi:I")) >= 0) {
+       while ((c = getopt(argc, argv, "N1:l:cHAGvbSuP:t:p:QgLi:IM")) >= 0) {
                switch (c) {
                case '1': vc.n1 = atoi(optarg); break;
                case 'l': vc.fn_list = strdup(optarg); break;
@@ -264,6 +274,7 @@ int bcfview(int argc, char *argv[])
                case 'H': vc.flag |= VC_HWE; break;
                case 'g': vc.flag |= VC_CALL_GT | VC_CALL; break;
                case 'I': vc.flag |= VC_NO_INDEL; break;
+               case 'M': vc.flag |= VC_ANNO_MAX; break;
                case 't': vc.theta = atof(optarg); break;
                case 'p': vc.pref = atof(optarg); break;
                case 'i': vc.indel_frac = atof(optarg); break;
@@ -400,11 +411,12 @@ int bcfview(int argc, char *argv[])
                        }
                        bcf_cpy(blast, b);
                }
+               if (vc.flag & VC_ANNO_MAX) bcf_anno_max(b);
                if (vc.flag & VC_NO_GENO) { // do not output GENO fields
                        b->n_gi = 0;
                        b->fmt[0] = '\0';
-               }
-               bcf_fix_gt(b);
+                       b->l_str = b->fmt - b->str + 1;
+               } else bcf_fix_gt(b);
                vcf_write(bout, h, b);
        }
        if (vc.prior_file) free(vc.prior_file);