--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/human_genome_variation/gpass.pl	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,79 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::Basename;
+use File::Temp qw/ tempfile /;
+
+$ENV{'PATH'} .= ':' . dirname($0);
+
+#this is a wrapper for gpass that converts a linkage pedigree file to input 
+#for this program
+
+my($map, $ped, $out, $fdr) = @ARGV;
+
+if (!$map or !$ped or !$out or !$fdr) { die "missing args\n"; }
+
+my($fh, $name) = tempfile();
+#by default this file is removed when these variable go out of scope
+print $fh "map=$map ped=$ped\n";
+close $fh;  #converter will overwrite, just keep name
+
+#run converter 
+system("lped_to_geno.pl $map $ped > $name") == 0
+	or die "system lped_to_geno.pl $map $ped > $name failed\n";
+
+#system("cp $name tmp.middle");
+
+#run GPASS
+system("gpass $name -o $out -fdr $fdr 1>/dev/null") == 0
+	or die "system gpass $name -o $out -fdr $fdr, failed\n";
+
+#merge SNP data with results
+merge();
+
+exit;
+
+########################################
+
+#merge the input and output files so have SNP data with result
+sub merge {
+   open(FH, $out) or die "Couldn't open $out, $!\n";
+   my %res;
+   my @ind;
+   while (<FH>) {
+      chomp;
+      my $line = $_;
+      if ($line =~ /^(\d+)/) { $res{$1} = $line; push(@ind, $1); }
+      else { $res{'index'} = $line; }
+   }
+   close FH;
+   if (!@ind) { return; } #no results, leave alone
+   @ind = sort { $a <=> $b } @ind;
+   $res{'index'} =~ s/Index/#ID\tchr\tposition/;
+   #read input file to get SNP data
+   open(FH, $name) or die "Couldn't open $name, $!\n";
+   my $i = 0; #index is 0 based not counting header line
+   my $c = shift @ind;
+   while (<FH>) {
+      chomp; 
+      if (/^ID/) { next; }
+      my @f = split(/\s+/);
+      if ($i == $c) { 
+         $res{$i} =~ s/^$i/$f[0]\t$f[1]\t$f[2]/;
+         if (!@ind) { last; }
+         $c = shift @ind;
+      }
+      $i++;      
+   }
+   close FH;
+   #now reprint results with SNP data included
+   open(FH, ">", $out) or die "Couldn't write to $out, $!\n";
+   print FH $res{'index'}, "\n";
+   delete $res{'index'};
+   foreach $i (keys %res) {
+      print FH $res{$i}, "\n";
+   }
+   close FH;
+}
+