* 0.1.16-dev (r969:252)

[samtools.git] / bcftools / vcfutils.pl

diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
index 3c962eccb5f52b54628090a4d6f47025b39e1f54..6ced66a2893e9b98884774e88607e9f2060af3d1 100755 (executable)
--- a/bcftools/vcfutils.pl
+++ b/bcftools/vcfutils.pl
@@ -512,7 +512,7 @@ Options: -d INT    minimum depth          [$opts{d}]
          $q = chr($q <= 126? $q : 126);
          $seq .= $b;
          $qual .= $q;
-       } else { # an INDEL
+       } elsif ($t[4] ne '.') { # an INDEL
          push(@gaps, [$t[1], length($t[3])]);
        }
        $last_pos = $t[1];