* changed 3.434 to 4.343 (typo!)

[samtools.git] / bcftools / vcfutils.pl

diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
index 0fe1af88014c8b94e9b761e96f2da57be3be545e..ee9e998e5a65d5c85bd81c3801571f0c83b7b352 100755 (executable)
--- a/bcftools/vcfutils.pl
+++ b/bcftools/vcfutils.pl
@@ -116,6 +116,7 @@ Note: This command discards indels. Output: QUAL #non-indel #SNPs #transitions #
        my @t = split;
        next if (length($t[3]) != 1 || uc($t[3]) eq 'N');
        my @s = split(',', $t[4]);
+       $t[5] = 3 if ($t[5] < 0);
        $t[3] = uc($t[3]); $t[4] = uc($t[4]);
        next if (length($s[0]) != 1);
        push(@a, [$t[5], ($t[4] eq '.' || $t[4] eq $t[3])? 0 : 1, $ts{$t[3].$s[0]}? 1 : 0, $h{$t[0],$t[1]}? 1 : 0]);
@@ -131,7 +132,7 @@ Note: This command discards indels. Output: QUAL #non-indel #SNPs #transitions #
          my @x;
          $x[0] = sprintf("%.3f", $c[1]-$c[2]? $c[2] / ($c[1] - $c[2]) : 100);
          $x[1] = sprintf("%.3f", $hsize? $c[3] / $hsize : 0);
-         $x[2] = sprintf("%.3f", $c[3] / $c[0]);
+         $x[2] = sprintf("%.3f", $c[3] / $c[1]);
          print join("\t", $last, @c, @x), "\n";
          $next = $c[0]/@a + $opts{s};
        }