--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Dotplot_Release/BaitCheck.pl	Fri Jan 29 09:56:02 2016 -0500
@@ -0,0 +1,45 @@
+#!/usr/bin/perl
+
+# 27/04/2014
+
+if($#ARGV==0){
+	print "This program checks the number of baits in a Saint Output File.\n";
+	print "\nusage:\n $0\n-i [csv saint output file]]\n\n";
+	die;
+}
+else{
+	$i=0;
+	$cutoff=0.01;
+	while($i<=$#ARGV){
+		if($ARGV[$i] eq '-i'){
+			$i++;
+			$ifile=$ARGV[$i];
+		}
+		else{
+			die "\Incorrect program usage\n\n";
+		}
+		$i++;
+	}
+}
+
+$file='';
+open(IFILE,"<$ifile") || die "$ifile can't be opened: $!";
+{ local $/=undef;  $file=<IFILE>; }
+@lines=split /[\r\n]+/, $file;
+foreach $line (@lines) {
+	if($line =~ /^Bait/){
+	}
+	elsif($line =~ /^([^\t]+)/){
+		if($1 ne $bait[$baitn]){
+			$baitn++;
+			$bait[$baitn]=$1;
+		}
+	}
+	else{
+	}
+}	
+close(IFILE);
+
+print $baitn;
+
+