--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/get.frag.size.pl	Thu Sep 07 15:06:58 2017 -0400
@@ -0,0 +1,55 @@
+#for the results from paired end
+#The two inputs are the results from the two ends
+use strict;
+my $read_size = $ARGV[2];
+open(input1, $ARGV[0]);
+open(input2, $ARGV[1]);
+open(output, ">$ARGV[0].fragsize");
+#open(fusefile,">$ARGV[0].fuse");
+
+#my $LongMarker="L";
+#my $ShortMarker="S";
+
+while(my $line1=<input1>)
+{
+	my $line2=<input2>;
+	chomp($line1);
+	chomp($line2);
+	next if($line1=~/$\NM/ or $line2=~/$\NM/ or $line1=~/$\MT/ or $line2=~/$\MT/);
+	my @array1 = split("\t",$line1);
+	#my $read_size=length($array1[1]);
+	my @array2 = split("\t",$line2);
+	my $match1=$array1[3];
+	my $match2=$array2[3];
+#	my $marker=$LongMarker.$ShortMarker;
+	my @sizes=();
+	#while($match1=~/\/(\S[^,]*\[[$marker]\])\S[^,]*:(\d*)[RF]/g)
+	while($match1=~/\/(\S[^,]*\[\w+\])\S[^,]*:(\d*)[RF]/g)
+	{
+		my $name=$1;
+		my $posa=$2;
+		#print $name,"\n";
+		
+		if($match2=~/\Q$name\E\S[^,]*:(\d*)[RF]/)
+		{
+			#print "match\n";
+			my $posb=$1;
+			push @sizes, abs($posb-$posa)+$read_size;
+			
+		}
+		
+	}
+	my %saw;
+	@saw{@sizes}=();
+	my @keya= keys %saw;
+	#print scalar(@keya),"\n";
+	if(scalar(@keya)==1)
+	{
+		print output $keya[0],"\n";
+	}
+
+}
+#close(fusefile);
+close(output);
+close(input2);
+close(input1);