compute max SP and max GQ from sample genotypes

[samtools.git] / bcftools / call1.c

diff --git a/bcftools/call1.c b/bcftools/call1.c
index adf7a52cf69ad371eb6ec2f76c2d76ff45565275..76eabf5bc7d638c0c7359559715e6baa68abd8ef 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;
@@ -235,6 +236,7 @@ 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 +251,7 @@ 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 +266,7 @@ 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 +403,12 @@ 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);