* removed a comment line in kaln.c

[samtools.git] / bcftools / vcfutils.pl

diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
index 371e8d84181dd5bc55aa5cfa0777ae7535ff4f69..cdb96cb53ee287fbbc3b541baa50c7778ec176bb 100755 (executable)
--- a/bcftools/vcfutils.pl
+++ b/bcftools/vcfutils.pl
@@ -70,12 +70,21 @@ sub fillac {
          print;
        } else {
          my @t = split;
-         my @c;
+         my @c = (0);
          my $n = 0;
-         $c[1] = 0;
+         my $s = -1;
+         @_ = split(":", $t[8]);
+         for (0 .. $#_) {
+               if ($_[$_] eq 'GT') { $s = $_; last; }
+         }
+         if ($s < 0) {
+               print join("\t", @t), "\n";
+               next;
+         }
          for (9 .. $#t) {
-               if ($t[$_] =~ /^(\d+).(\d+)/) {
-                 ++$c[$1]; ++$c[$2];
+               if ($t[$_] =~ /^0,0,0/) {
+               } elsif ($t[$_] =~ /^([^\s:]+:){$s}(\d+).(\d+)/) {
+                 ++$c[$2]; ++$c[$3];
                  $n += 2;
                }
          }