Unfinished

diff --git a/misc/samtools.pl b/misc/samtools.pl
index 39992b986edd5cb1a832193b6608ca6347f893e6..c014c52bcf0880d39ba23f567a31396017220142 100755 (executable)
--- a/misc/samtools.pl
+++ b/misc/samtools.pl
@@ -214,6 +214,30 @@ sub p2q_print_str {
   }
 }
 
+#
+# varStats
+#
+
+sub varStats {
+  my %opts = (d=>'', c=>5);
+  getopts('d:c:', \%opts);
+  die("Usage: samtools.pl varStats [-d dbSNP.snp] [-c $opts{c}] <in.plp.snp>\n") if (@ARGV == 0 && -t STDIN);
+  my (@cnt, %hash);
+  my $col = $opts{c} - 1;
+  while (<>) {
+       my @t = split;
+       if ($t[2] eq '*') {
+       } else {
+         my $q = $t[$col];
+         $q = 99 if ($q > 99);
+         $q = int($q/10);
+         my $is_het = ($t[3] =~ /^[ACGT]$/)? 0 : 1;
+         ++$cnt[$q][$is_het];
+         $hash{$t[0],$t[1]} = $q;
+       }
+  }
+}
+
 #
 # Usage
 #