--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/human_genome_variation/mergeSnps.pl	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,57 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+#this merges the significance output with the SNPs so users get more than an index
+
+my($out, $snp) = @ARGV;
+
+if (!$out or !$snp) { die "missing args\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 = $_;
+      #0:      10 score= 14.224153 , df= 2 , p= 0.040760 , N=50
+      if ($line =~ /^(\d+):\s+(.*)/) { $res{$1} = $2; push(@ind, $1); }
+   }
+   close FH;
+   if (!@ind) { return; } #no results, leave alone
+   @ind = sort { $a <=> $b } @ind;
+   #read input file to get SNP data
+   open(FH, $snp) or die "Couldn't open $snp, $!\n";
+   my $i = 0; #0 based, not counting ID line
+   my $c = shift @ind;
+   while (<FH>) {
+      chomp; 
+      if (/^ID/) { next; }
+      my @f = split(/\s+/);
+      if ($i == $c) { 
+         $res{$i} = "$f[0]\t$f[1]\t$f[2]\t$res{$i}";
+         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 "ID\tchr\tposition\tresults\n";
+   foreach $i (keys %res) {
+      print FH $res{$i}, "\n";
+   }
+   close FH;
+}
+