Make sure that the GT genotype field is the first

[samtools.git] / bcftools / call1.c

diff --git a/bcftools/call1.c b/bcftools/call1.c
index 012c2b32b7d9c731b1c509559b66f94320ae9cbb..b913c9a4990e1f59bbdde8667d6496f842c02d21 100644 (file)
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -206,6 +206,7 @@ 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);
        bcf_t *bp, *bout = 0;
        bcf1_t *b, *blast;
        int c;
@@ -372,6 +373,7 @@ int bcfview(int argc, char *argv[])
                        b->n_gi = 0;
                        b->fmt[0] = '\0';
                }
+               bcf_fix_gt(b);
                vcf_write(bout, h, b);
        }
        if (vc.prior_file) free(vc.prior_file);