diff --git a/HiNT/externalScripts/extract_nonHiC.pl b/HiNT/externalScripts/extract_nonHiC.pl
index a54d942..b5891bb 100644
--- a/HiNT/externalScripts/extract_nonHiC.pl
+++ b/HiNT/externalScripts/extract_nonHiC.pl
@@ -7,7 +7,7 @@
 # Input: 
 #  Pairsam file
 # Enzyme:
-#  Mbo1/Dpn2/HindIII
+#  MboI, DpnII, HindIII, AluI, NotI, NcoI, Arima, 'MboI+HinfI', 'HinfI+MboI'
 # All output options: 
 #  FASTQ file: Softclipped part of the non Hi-C chmeric reads 
 #  {OUTPUT_PREFIX}_2.txt  File contains non Hi-C chimeric reads (softclipped).\n";
@@ -22,24 +22,21 @@
 use strict;
 use POSIX;
 use Getopt::Long;
-use Data::Dumper;
 use constant { true => 1, false => 0 };
-use experimental 'smartmatch';
 use utf8;
 use open qw(:std :utf8);
 
 
 ######----------------------------------------------------------------------------------------------------------------
-###    inputs
+###    inputs, variables etc
 ######----------------------------------------------------------------------------------------------------------------
 my $psam = "";
-my $outprefix = "project";
-my $re = "MboI";
+my $re = "";
 my $sites = "";
+my $outprefix = "project";
 my $cutoff = 2;
-my $min_clip = 28;
+my $min_clip = 7;
 my $help = 0;
-
 Getopt::Long::GetOptions(
   'psam=s'          => \$psam,
   're=s'            => \$re,
@@ -51,61 +48,69 @@
   'h'               => \$help,
 ) or die "Incorrect input! Use -h for usage.\n";
 
-if ($help) {
-  print "\nUsage: perl extract_nonHiC.pl -psam psam.gz -re [STRING] -sites sites.txt -outprefix [STRING] -margin [INT,2] -min_clip [INT,28]\n\n\n";
-  print "required options:\n";
-  print "  -psam            The Input psam file\n";
-  print "  -sites           RE sites along the genome (produced using 'generate_site_positions.py' script from Juicer package)\n";
-  print "  -re              Name of the RE [MboI, DpnII, HindIII]\n";
-  print "optional options:\n";
-  print "  -outprefix       Output file PREFIX [default: project]\n";
-  print "  -margin          Upstream Margin for finding genomic RE site [default: 2]\n";
-  print "  -min_clip        Minimum length of softclipped part on the read [default : 28]\n";
-  print "  -help|-h         Display usage information.\n\n\n";
-  print "Default outputs:\n";
-  print "  {OUTPUT_PREFIX}_2.txt  File contains non Hi-C chimeric reads (softclipped).\n";
-  print "  {OUTPUT_PREFIX}_3.txt  File contains non Hi-C chimeric reads (reads with MAPQ<30, whole read sequence is reported).\n";
-  print "  {OUTPUT_PREFIX}_2dedup.txt  File contains DUPLICATE REMOVED non Hi-C chimeric reads (softclipped).\n";
-  print "  {OUTPUT_PREFIX}_3dedup.txt  File contains DUPLICATE REMOVED non Hi-C chimeric reads (reads with MAPQ<30, whole read sequence is reported).\n\n\n";
-  print "Other hardcoded parameters:\n";
-  print "  Enzyme collection: Mbo1/Dpn2/HindIII\n";
-  print "  Proximity filter for mapping two mates of the pair : 500bp \n\n\n";
-  exit 0;
+sub help{
+  my $j = shift;
+  if($j){
+    print "\nUsage: perl extract_nonHiC.pl -psam psam.gz -re [STRING] -sites sites.txt -outprefix [STRING] -margin [INT,2] -min_clip [INT,7]\n\n\n";
+    print "required options:\n";
+    print "  -psam            The Input psam file\n";
+    print "  -sites           RE sites along the genome (produced using 'generate_site_positions.py' script from Juicer package)\n";
+    print "  -re              Name of the RE [MboI, DpnII, HindIII, AluI, NotI, NcoI, Arima, 'MboI+HinfI', 'HinfI+MboI']\n";
+    print "optional options:\n";
+    print "  -outprefix       Output file PREFIX [default: project]\n";
+    print "  -margin          Margin for finding genomic RE site [default: 2]\n";
+    print "  -min_clip        Minimum length of softclipped part on the read [default : 7]\n";
+    print "  -help|-h         Display usage information.\n\n\n";
+    print "Default outputs:\n";
+    #print "  {OUTPUT_PREFIX}_2.txt  File contains non Hi-C chimeric reads (softclipped).\n";
+    #print "  {OUTPUT_PREFIX}_2dedup.txt  File contains DUPLICATE REMOVED non Hi-C chimeric reads (softclipped).\n";
+    print "  {OUTPUT_PREFIX}_3.txt  File contains non Hi-C chimeric reads (reads with MAPQ<30, whole read sequence is reported).\n";
+    print "  {OUTPUT_PREFIX}_3dedup.txt  File contains DUPLICATE REMOVED non Hi-C chimeric reads (reads with MAPQ<30, whole read sequence is reported).\n\n\n";
+    print "Other hardcoded parameters:\n";
+    print "  Enzyme collection: MboI, DpnII, HindIII, AluI, NotI, NcoI, Arima, 'MboI+HinfI', 'HinfI+MboI'\n";
+    print "  Proximity filter for mapping two mates of the pair : 500bp \n\n\n";
+    exit 1;
+  }
 }
 
 ######### Global varialbes
 my %counts;
-my $motif;
-my $len_RE = 8;
-
-if($re eq "DpnII" or $re eq "MboI"){
-  $motif = 'GATC';
-}elsif($re eq "HindIII"){
-  $motif = "AAGCTT";
-}else{
-  print " Restriction enzyme not specified. Exiting!\n";
-  exit 1;
-}
-$len_RE = 8 if($motif eq "GATC");
-$len_RE = 10 if($motif eq "AAGCTT");
-#$sites = "/n/data1/hms/dbmi/park/Dhawal/Genomes/hg19_annotations/hg19_DpnII.txt";
+my %redb;
+$redb{"AluI"}{motif} = "AGCT|TCGA";
+$redb{"AluI"}{mlen}=4;
+$redb{"NotI"}{motif} = "GCGGCCGGCCGC|CGCCGGCCGGCG";
+$redb{"NotI"}{mlen}=8;
+$redb{"MboI"}{motif} = "GATCGATC|CTAGCTAG";
+$redb{"MboI"}{mlen}=4;
+$redb{"DpnII"}{motif} = "GATCGATC|CTAGCTAG";
+$redb{"DpnII"}{mlen}=4;
+$redb{"HindIII"}{motif} = "AAGCTAGCTT|TTCGATCGAA";
+$redb{"HindIII"}{mlen}=6;
+$redb{"NcoI"}{motif} = "CCATGCATGG|GGTACGTACC";
+$redb{"NcoI"}{mlen}=6;
+$redb{"MboI+HinfI"}{motif} = "GATCGATC|CTAGCTAG|GA[ATGC]{1}TA[ATGC]{1}TC|GATCA[ATGC]{1}TC|GA[ATGC]{1}TGATC|CT[GATC]{1}AT[AGTC]{1}AG|CT[ATGC]{1}ACTAG|CTAGT[ATGC]{1}AG";
+$redb{"MboI+HinfI"}{mlen}=5;
+$redb{"HinfI+MboI"}{motif} = "GATCGATC|CTAGCTAG|GA[ATGC]{1}TA[ATGC]{1}TC|GATCA[ATGC]{1}TC|GA[ATGC]{1}TGATC|CT[GATC]{1}AT[AGTC]{1}AG|CT[ATGC]{1}ACTAG|CTAGT[ATGC]{1}AG";
+$redb{"HinfI+MboI"}{mlen}=5;
+$redb{"Arima"}{motif} = "GATCGATC|CTAGCTAG|GA[ATGC]{1}TA[ATGC]{1}TC|GATCA[ATGC]{1}TC|GA[ATGC]{1}TGATC|CT[GATC]{1}AT[AGTC]{1}AG|CT[ATGC]{1}ACTAG|CTAGT[ATGC]{1}AG";
+$redb{"Arima"}{mlen}=5;
 
 ######----------------------------------------------------------------------------------------------------------------
 ###    checks and primary readings
 ######----------------------------------------------------------------------------------------------------------------
+help($help);
+if($re eq "" or !$redb{$re}{motif} or !$redb{$re}{mlen} ){
+  print "RE not recognized\n";
+  help(1);
+}
 if($psam eq ""){
   print "ERROR: Required input psam file not provided\n";
-  exit 1;   
+  help(1);
 } 
 if($sites eq ""){
   print "ERROR: Required genomic TE location file not provided\n";
-  exit 1;   
+  help(1);
 } 
-if($motif eq ""){
-  print "ERROR: Required value for RE motif not provided\n";
-  exit 1;   
-} 
-
 
 ### Read Juicer formatted RE motif locations as a hash
 open FILE, $sites or die $!;
@@ -137,26 +142,25 @@
   s/\n//; 
   s/\r//;  
   my @psam = split(/\t+/);
+ 
   $counts{flag}{$psam[7]}++;  #flag count
-  
   $counts{pairs}{total}++;
   if($counts{pairs}{total} % 100000 == 0 ){
     print "Read-pairs: $counts{pairs}{total} \t";
-    print "non-HiC chimeric mates: $counts{mates}{nonHic_chimera} \n";
+    print "non-HiC chimeric mates: $counts{mates}{nonHic_chimera} \n" if($counts{mates}{nonHic_chimera});
+    print "non-HiC chimeric mates: 0 \n" if(!$counts{mates}{nonHic_chimera});
   }
   ## omit UU,UR,RU reads 
   next if($psam[7] eq "UU" or $psam[7] eq "UR" or $psam[7] eq "RU");
-  next if($psam[7] eq "UU" or $psam[7] eq "UR" or $psam[7] eq "RU");
-
+  
   my($a,$b,$c,$d)=parse_psam_reads($psam[8], $psam[9]);
   my @read1 = @{$a};
   my @read2 = @{$b};
   my @read3 = @{$c};
   my @read4 = @{$d};
-
-  $counts{pairs}{used_pairs}++; 
- 
   next if(!@read1 && !@read2);
+  $counts{pairs}{used_pairs}++; 
+  
   ## Get rid of all reads that have atleast 2 N bases
   if(@read1){
     my $num_N1 = $read1[9] =~ tr/N//;
@@ -171,19 +175,11 @@
   if(@read1){
     $counts{mates}{used_mates}++; 
     my $cnt = nonHiC_by_LigationSignature(\*OUT, \*OUT1, \*OUT2, \@read1, \@read3, 1);
-    if($cnt==2){
-      print "MAJOR ERROR\n";
-      exit 1; 
-    }
   }
   ############################# Read2 present
   if(@read2){ 
     $counts{mates}{used_mates}++; 
     my $cnt = nonHiC_by_LigationSignature(\*OUT, \*OUT1, \*OUT2, \@read2, \@read4, 2); 
-    if($cnt==2){
-      print "MAJOR ERROR\n";
-      exit 1; 
-    }
   }
   undef(@read1);
   undef(@read2);
@@ -191,45 +187,81 @@
   undef(@read4);
   undef(@psam);
 }
+print "Read-pairs: $counts{pairs}{total} \t";
+print "non-HiC chimeric mates: $counts{mates}{nonHic_chimera} \n" if($counts{mates}{nonHic_chimera});
+print "non-HiC chimeric mates: 0 \n" if(!$counts{mates}{nonHic_chimera});
 
 close(IN);
-close(OUT);
-close(OUT1);
+#close(OUT);
+#close(OUT1);
 close(OUT2);
 
 
 ### Remove duplicates
-my $z;
 #$z = remove_duplicates($outprefix."_2.txt",$outprefix."_2dedup.txt");
-$z = remove_duplicates($outprefix."_3.txt",$outprefix."_3dedup.txt");
-
-
-my $hic = $counts{mates}{used_mates} - $counts{mates}{nonHic_chimera};
-
+$counts{mates}{dedups} = remove_duplicates($outprefix."_3.txt",$outprefix."_3dedup.txt");
+
+##### Initializations and summary output
+$counts{mates}{nonHic_chimera}=0 if(!$counts{mates}{nonHic_chimera});
+$counts{mates}{used_mates}=0 if(!$counts{mates}{used_mates});
+$counts{pairs}{total}=0 if(!$counts{pairs}{total});
+$counts{pairs}{used_pairs}=0 if(!$counts{pairs}{used_pairs});
+$counts{mates}{count_unmapped}=0 if(!$counts{mates}{count_unmapped});
+$counts{mates}{motif_in_unmapped}=0 if(!$counts{mates}{motif_in_unmapped});
+$counts{mates}{motif_spans}=0 if(!$counts{mates}{motif_spans});
+$counts{mates}{motif_hardClip}=0 if(!$counts{mates}{motif_hardClip});
+$counts{mates}{motif_ref}=0 if(!$counts{mates}{motif_ref});
+$counts{mates}{motif_proximity}=0 if(!$counts{mates}{motif_proximity});
+$counts{mates}{double_clip}=0 if(!$counts{mates}{double_clip});
+$counts{mates}{motif_multiple}=0 if(!$counts{mates}{motif_multiple});
+$counts{mates}{nonHic_chimera}=0 if(!$counts{mates}{nonHic_chimera});
+$counts{mates}{dedups}=0 if(!$counts{mates}{dedups});
+$counts{mates}{filtered}=0 if(!$counts{mates}{filtered});
+my $perc = 0;
+print "\n\n";
 print "###---------------------------Summary------------------------------------------------------------\n";
 print "Input psam file:                                          $psam\n";
 print "RE enzyme:                                                $re\n";
-print "RE motif:                                                 $motif\n";
+print "RE motif:                                                 $redb{$re}{motif}\n";
+print "RE motif length (maximum if enzyme combination is used):  $redb{$re}{mlen}\n";
 print "Input file with genomic location of RE motifs:            $sites\n";
+print "Minimum required clipped read sequence                    $min_clip\n";
+print "Distance between clip-coordinate and RE site              $cutoff\n";
 print "Total read pairs in the file:                             $counts{pairs}{total} \n";
-print "Flag Summary\n";
+print "#Flag Summary\n";
 foreach my $cl (sort keys %{$counts{flag}}){
-  print "  $cl:  $counts{flag}{$cl}\n";
+  $counts{flag}{$cl}=0 if(!$counts{flag}{$cl});
+  $perc = round( $counts{flag}{$cl}*100/$counts{pairs}{total},2);
+  print "  >>$cl:  $counts{flag}{$cl} ($perc %)\n";
 }
 print "Total non-HiC read pairs used:                            $counts{pairs}{used_pairs}\n";
 print "Total non-HiC mates used:                                 $counts{mates}{used_mates}\n";
-print "Total Hi-C chimeric/unmapped etc. mates:                  $hic\n";
-print "Total unmapped mates                                      $counts{mates}{count_unmapped}\n";
-print "Total unmapped mates with RE motif                        $counts{mates}{motif_in_unmapped}\n";
-print "Mates with RE motif at clip junction:                     $counts{mates}{motif_spans}\n";
-print "Mates with RE motif within unmapped clip sequence:        $counts{mates}{motif_hardClip}\n";
-print "Mates with reference RE site annotation:                  $counts{mates}{motif_ref}\n";
-print "Mates with soft-clipping match at proximity <500bp:       $counts{mates}{motif_proximity}\n";
-print "Mates with both 5' and 3' clips (>$min_clip bp):          $counts{mates}{double_clip}\n";
-print "Filtered mates with both 5' and 3' clips (>$min_clip bp): $counts{mates}{motif_multiple}\n";
-print "Total non-Hi-C chimeric mates:                            $counts{mates}{nonHic_chimera}\n";
-print "Total non-Hi-C chimeric mates after duplicate removal:    $z \n";
-
+my $hic = $counts{mates}{used_mates} - $counts{mates}{nonHic_chimera};
+$perc = round( $hic*100/$counts{mates}{used_mates},2);
+print "Total Hi-C chimeric/unmapped/filtered etc. mates:         $hic ($perc % of used mates)\n";
+$perc = round( $counts{mates}{filtered}*100/$counts{mates}{used_mates},2);
+print "Total Hi-C filtered mates:                                $counts{mates}{filtered} ($perc % of used mates)\n";
+#$perc = round( $counts{mates}{count_unmapped}*100/$counts{mates}{used_mates},2);
+#print "Total unmapped mates                                      $counts{mates}{count_unmapped} ($perc % of used mates)\n";
+$perc = round( $counts{mates}{motif_in_unmapped}*100/$counts{mates}{used_mates},2);
+print "Total unmapped mates with RE motif                        $counts{mates}{motif_in_unmapped} ($perc % of used mates)\n";
+$perc = round( $counts{mates}{motif_spans}*100/$counts{mates}{used_mates},2);
+print "Mates with RE motif at clip junction:                     $counts{mates}{motif_spans} ($perc % of used mates)\n";
+$perc = round( $counts{mates}{motif_hardClip}*100/$counts{mates}{used_mates},2);
+print "Mates with RE motif within unmapped clip sequence:        $counts{mates}{motif_hardClip} ($perc % of used mates)\n";
+$perc = round( $counts{mates}{motif_ref}*100/$counts{mates}{used_mates},2);
+print "Mates with reference RE site annotation:                  $counts{mates}{motif_ref} ($perc % of used mates)\n";
+$perc = round( $counts{mates}{motif_proximity}*100/$counts{mates}{used_mates},2);
+print "Mates with soft-clipping match at proximity <500bp:       $counts{mates}{motif_proximity} ($perc % of used mates)\n";
+$perc = round( $counts{mates}{double_clip}*100/$counts{mates}{used_mates},2);
+print "Mates with both 5' and 3' clips (>$min_clip bp):          $counts{mates}{double_clip} ($perc % of used mates)\n";
+#$perc = round( $counts{mates}{motif_multiple}*100/$counts{mates}{used_mates},2);
+#print "Filtered mates with both 5' and 3' clips (>$min_clip bp): $counts{mates}{motif_multiple} ($perc % of used mates)\n";
+$perc = round( $counts{mates}{nonHic_chimera}*100/$counts{mates}{used_mates},2);
+print "Total non-Hi-C chimeric mates:                            $counts{mates}{nonHic_chimera} ($perc % of used mates)\n";
+$perc = round( $counts{mates}{dedups}*100/$counts{mates}{used_mates},2);
+print "Total non-Hi-C chimeric mates after duplicate removal:    $counts{mates}{dedups} ($perc % of used mates)\n";
+print "\n\n";
 
 ######----------------------------------------------------------------------------------------------------------------
 ###    subroutines
@@ -272,7 +304,7 @@ sub nonHiC_by_LigationSignature {
   my @read3 = @{$b};
   
   ## uses following global variables
-  # $len_RE, $min_clip, %chromosomes, $cutoff, $motif, %counts
+  # $min_clip, %chromosomes, $cutoff, %counts, $re
 
   ## Three pronged approach:
   # 1. Check if RE ligation motif spans clip junction
@@ -284,22 +316,22 @@ sub nonHiC_by_LigationSignature {
   ## Nonmapping reads do not have CIGAR, check if they have RE motif. If not, print them and move on
   ################## 
   if($read1[5] eq "*"){
-      $counts{mates}{count_unmapped}++;
-      if(re_search($read1[9],$motif,-1)==0){
-          #print $fh1 "@","$read1[0]_$readnum 1:N:0:0 $read1[-2]\n$read1[9]\n+\n$read1[10]\n";
-          #print $fh2 "$read1[0]_$readnum\t$read1[2]\t$read1[3]\t$read1[-1]\t$read1[4]\t$read1[5]\t$read1[9]\t$read1[10]\t";
-          print $fh3 "$read1[0]_$readnum\t$read1[2]\t$read1[3]\t$read1[-1]\t$read1[4]\t$read1[5]\t$read1[9]\t$read1[10]\t";
-          if(@read3){
-             #print $fh2 "$read3[2]\t$read3[3]\t$read3[-1]\t$read3[4]\t$read3[5]\t$read3[9]\t-\t-\n";
-             print $fh3 "$read3[2]\t$read3[3]\t$read3[-1]\t$read3[4]\t$read3[5]\t$read3[9]\t-\t-\n";
-          }else{
-             #print $fh2 "-\t-\t-\t-\t-\t-\t-\t-\n";
-             print $fh3 "-\t-\t-\t-\t-\t-\t-\t-\n";
-          }
+    $counts{mates}{count_unmapped}++;
+    if(re_search($read1[9],$re,-1)==0){
+      #print $fh1 "@","$read1[0]_$readnum 1:N:0:0 $read1[-2]\n$read1[9]\n+\n$read1[10]\n";
+      #print $fh2 "$read1[0]_$readnum\t$read1[2]\t$read1[3]\t$read1[-1]\t$read1[4]\t$read1[5]\t$read1[9]\t$read1[10]\t";
+      print $fh3 "$read1[0]_$readnum\t$read1[2]\t$read1[3]\t$read1[-1]\t$read1[4]\t$read1[5]\t$read1[9]\t$read1[10]\t";
+      if(@read3){
+        #print $fh2 "$read3[2]\t$read3[3]\t$read3[-1]\t$read3[4]\t$read3[5]\t$read3[9]\t-\t-\n";
+        print $fh3 "$read3[2]\t$read3[3]\t$read3[-1]\t$read3[4]\t$read3[5]\t$read3[9]\t-\t-\n";
       }else{
-          $counts{mates}{motif_in_unmapped}++; 
+        #print $fh2 "-\t-\t-\t-\t-\t-\t-\t-\n";
+        print $fh3 "-\t-\t-\t-\t-\t-\t-\t-\n";
       }
-      return(0); #success
+    }else{
+      $counts{mates}{motif_in_unmapped}++; 
+    }
+    return(0); #success
   }
 
   ################## 
@@ -308,165 +340,145 @@ sub nonHiC_by_LigationSignature {
   my @len1 = split (/\D+/,$read1[5]); # storing the length per operation
   my @ops1 = split (/\d+/,$read1[5]); # storing the operation
   shift @ops1; # remove the empty first element
-  return(1) unless (scalar @len1 == scalar @ops1);
-  return(1) if(!@ops1);
-
+  return(1) if ( !@ops1 or scalar @len1 != scalar @ops1);
+  
   ################## 
   ## Non-HiC chimera test
   ################## 
-  my $motif_len = length($motif);
-  
-  my ($seq1, $qual1) = "";
-  my $olap = "-";
   my $xalign = "-";
-  
   my %localcount;
   $localcount{motif_spans}=0;
   $localcount{motif_hardClip}=0;
   $localcount{motif_ref}=0;
   $localcount{count_prox}=0;
   $localcount{nonHic_chimera}=0;
-
-  ## 5' clip of read1
   my $is_match_a=0;
+  my $is_match_b=0;
+  my $leftoutread = 0;
+ 
+  ## 5' clip of read1
   if($ops1[0] eq "S" && $len1[0] >=  $min_clip){    
-    if(re_search($read1[9],$motif, $len1[0])>0){
-       $is_match_a++; 
-       $localcount{motif_spans}++;
+    $leftoutread=1;
+    if(re_search($read1[9],$re, $len1[0])>0){
+       $is_match_a=1; $localcount{motif_spans}=1;
     }elsif(RE_within_HardclippedSeq(\@read1,\@len1,\@ops1,\@read3)>0){
-       $is_match_a++; 
-       $localcount{motif_hardClip}++; 
-    }elsif(@read3){
+       $is_match_a=1;  $localcount{motif_hardClip}=1; 
+    }else{
       my $x1= $read1[3];
-      my $x2= $read3[3];
-      if($read3[-1] eq "+"){ $x2 = $read3[3]+length($read3[9]); }
       my $pos1 = &binarysearch( $x1, $chromosomes{$read1[2]});
-      my $pos2 = &binarysearch( $x2, $chromosomes{$read3[2]});      
-      if( (($pos1-$cutoff)<= $x1 and ($pos1+$motif_len+$cutoff)>=$x1) or (($pos2-$cutoff)<=$x2 and ($pos2+$motif_len+$cutoff)>=$x2 ) ){
-        $is_match_a++; 
-        $localcount{motif_ref}++; 
+      if( ($pos1-$cutoff)<= $x1 and ($pos1+$redb{$re}{mlen}+$cutoff)>=$x1) {
+        $is_match_a=1;  $localcount{motif_ref}=1; 
+      }
+      if($localcount{motif_ref}==0 and $is_match_a == 0 and @read3){
+        my $x2= $read3[3];
+        if($read3[-1] eq "+"){ $x2 = $read3[3]+length($read3[9]); }
+        my $pos2 = &binarysearch( $x2, $chromosomes{$read3[2]});      
+        if( ($pos2-$cutoff)<=$x2 and ($pos2+$redb{$re}{mlen}+$cutoff)>=$x2 ) {
+          $is_match_a=1;  $localcount{motif_ref}=1; 
+        }
       }
     }
-
     if($is_match_a==0){
       if(linearProximity_bw_mapped_softclip(\@read1,\@read3)==0){
-            $localcount{nonHic_chimera}++;
-            $seq1 = substr($read1[9], 0, $len1[0]);
-            $qual1 = substr($read1[10], 0, $len1[0]);
-        
-            #print $fh1 "@","$read1[0]_$readnum 1:N:0:0 $read1[-2]\n$seq1\n+\n$qual1\n";
-            #print $fh2 "$read1[0]_$readnum\t$read1[2]\t$read1[3]\t$read1[-1]\t$read1[4]\t$read1[5]\t$seq1\t$qual1\t";
-                if($read1[4]<30){
-                    print $fh3 "$read1[0]_$readnum\t$read1[2]\t$read1[3]\t$read1[-1]\t$read1[4]\t$read1[5]\t$read1[9]\t$read1[10]\t";
-                }else{
-                    print $fh3 "$read1[0]_$readnum\t$read1[2]\t$read1[3]\t$read1[-1]\t$read1[4]\t$read1[5]\t$seq1\t$qual1\t";
-                }
-                if(@read3){
-                  if($read3[-3] =~ /^XA:Z:/){
-                      $xalign = $read3[-3];
-                  }
-                  $olap = find_olap_in_chimera_mapping(\@read1,\@len1,\@ops1,\@read3);
-                  if(!$olap){$olap="-";}
-                  #print $fh2 "$read3[2]\t$read3[3]\t$read3[-1]\t$read3[4]\t$read3[5]\t$read3[9]\t$olap\t$xalign\n";
-                  print $fh3 "$read3[2]\t$read3[3]\t$read3[-1]\t$read3[4]\t$read3[5]\t$read3[9]\t$olap\t$xalign\n";
-                }else{
-                  #print $fh2 "-\t-\t-\t-\t-\t-\t-\t-\n";
-                  print $fh3 "-\t-\t-\t-\t-\t-\t-\t-\n";
-                }
+        $localcount{nonHic_chimera}=1;
+        my $seq1 = substr($read1[9], 0, $len1[0]);
+        my $qual1 = substr($read1[10], 0, $len1[0]);
+        #print $fh1 "@","$read1[0]_$readnum 1:N:0:0 $read1[-2]\n$seq1\n+\n$qual1\n";
+        #print $fh2 "$read1[0]_$readnum\t$read1[2]\t$read1[3]\t$read1[-1]\t$read1[4]\t$read1[5]\t$seq1\t$qual1\t";
+        if($read1[4]<30){
+          print $fh3 "$read1[0]_$readnum\t$read1[2]\t$read1[3]\t$read1[-1]\t$read1[4]\t$read1[5]\t$read1[9]\t$read1[10]\t";
+        }else{
+          print $fh3 "$read1[0]_$readnum\t$read1[2]\t$read1[3]\t$read1[-1]\t$read1[4]\t$read1[5]\t$seq1\t$qual1\t";
+        }
+        if(@read3){
+          $xalign = $read3[-3] if($read3[-3] =~ /^XA:Z:/);
+          my $olap = find_olap_in_chimera_mapping(\@read1,\@len1,\@ops1,\@read3);
+          if(!$olap){$olap="-";}
+            #print $fh2 "$read3[2]\t$read3[3]\t$read3[-1]\t$read3[4]\t$read3[5]\t$read3[9]\t$olap\t$xalign\n";
+            print $fh3 "$read3[2]\t$read3[3]\t$read3[-1]\t$read3[4]\t$read3[5]\t$read3[9]\t$olap\t$xalign\n";
+        }else{
+          #print $fh2 "-\t-\t-\t-\t-\t-\t-\t-\n";
+          print $fh3 "-\t-\t-\t-\t-\t-\t-\t-\n";
+        }
       }else{
-        $localcount{count_prox}++;
+        $localcount{count_prox}=1;
       }
     }
   }
-
-
+  
   ## 3' clip of read1
-  my $is_match_b=0;
   if($ops1[-1] eq "S" && $len1[-1] >=  $min_clip){
-    if(re_search($read1[9],$motif, (length($read1[9])-$len1[-1]) )>0){
-       $is_match_b++; 
-       $localcount{motif_spans}++;
+    $leftoutread=1;
+    if(re_search($read1[9],$re, (length($read1[9])-$len1[-1]) )>0){
+      $is_match_b=1;  $localcount{motif_spans}=1;
     }elsif(RE_within_HardclippedSeq(\@read1,\@len1,\@ops1,\@read3)>0){
-       $is_match_b++; 
-       $localcount{motif_hardClip}++; 
-    }elsif(@read3){
+      $is_match_b=1; $localcount{motif_hardClip}=1; 
+    }else{
       my $x1= $read1[3]+length($read1[9])-$len1[-1];
-      my $x2= $read3[3];
-      if($read3[-1] eq "-"){ $x2 = $read3[3]+length($read3[9]); }
       my $pos1 = &binarysearch( $x1, $chromosomes{$read1[2]});
-      my $pos2 = &binarysearch( $x2, $chromosomes{$read3[2]});      
-      if( (($pos1-$cutoff)<= $x1 and ($pos1+$motif_len+$cutoff)>=$x1) or (($pos2-$cutoff)<=$x2 and ($pos2+$motif_len+$cutoff)>=$x2 )){
-        $is_match_b++; 
-        $localcount{motif_ref}++; 
+      if( ($pos1-$cutoff)<= $x1 and ($pos1+$redb{$re}{mlen}+$cutoff)>=$x1) {
+        $is_match_b=1; $localcount{motif_ref}=1; 
+      }
+      if($localcount{motif_ref} == 0 and $is_match_b == 0 and @read3){
+        my $x2= $read3[3];
+        if($read3[-1] eq "-"){ $x2 = $read3[3]+length($read3[9]); }
+        my $pos2 = &binarysearch( $x2, $chromosomes{$read3[2]});      
+        if( ($pos2-$cutoff)<=$x2 and ($pos2+$redb{$re}{mlen}+$cutoff)>=$x2 ) {
+          $is_match_b=1; $localcount{motif_ref}=1; 
+        }
       }
     }
-
     if($is_match_b==0){
       if(linearProximity_bw_mapped_softclip(\@read1,\@read3)==0){
-            $localcount{nonHic_chimera}++;
-
-            $seq1 = substr($read1[9],-$len1[-1],$len1[-1]);
-            $qual1 = substr($read1[10],-$len1[-1],$len1[-1]);           
-            #print $fh1 "@","$read1[0]_$readnum 1:N:0:0 $read1[-2]\n$seq1\n+\n$qual1\n";
-            #print $fh2 "$read1[0]_$readnum\t$read1[2]\t$read1[3]\t$read1[-1]\t$read1[4]\t$read1[5]\t$seq1\t$qual1\t"; 
-                if($read1[4]<30){
-                    print $fh3 "$read1[0]_$readnum\t$read1[2]\t$read1[3]\t$read1[-1]\t$read1[4]\t$read1[5]\t$read1[9]\t$read1[10]\t";
-                }else{
-                    print $fh3 "$read1[0]_$readnum\t$read1[2]\t$read1[3]\t$read1[-1]\t$read1[4]\t$read1[5]\t$seq1\t$qual1\t";
-                }
-                if(@read3){
-                  if($read3[-3] =~ /^XA:Z:/){
-                      $xalign = $read3[-3];
-                  }
-                    $olap = find_olap_in_chimera_mapping(\@read1,\@len1,\@ops1,\@read3);
-                  if(!$olap){$olap="-";}
-                    #print $fh2 "$read3[2]\t$read3[3]\t$read3[-1]\t$read3[4]\t$read3[5]\t$read3[9]\t$olap\t$xalign\n";
-                    print $fh3 "$read3[2]\t$read3[3]\t$read3[-1]\t$read3[4]\t$read3[5]\t$read3[9]\t$olap\t$xalign\n";
-               }else{
-                    #print $fh2 "-\t-\t-\t-\t-\t-\t-\t-\n";
-                    print $fh3 "-\t-\t-\t-\t-\t-\t-\t-\n";
-                }
+        $localcount{nonHic_chimera}=1;
+        my $seq1 = substr($read1[9],-$len1[-1],$len1[-1]);
+        my $qual1 = substr($read1[10],-$len1[-1],$len1[-1]);           
+        #print $fh1 "@","$read1[0]_$readnum 1:N:0:0 $read1[-2]\n$seq1\n+\n$qual1\n";
+        #print $fh2 "$read1[0]_$readnum\t$read1[2]\t$read1[3]\t$read1[-1]\t$read1[4]\t$read1[5]\t$seq1\t$qual1\t"; 
+        if($read1[4]<30){
+          print $fh3 "$read1[0]_$readnum\t$read1[2]\t$read1[3]\t$read1[-1]\t$read1[4]\t$read1[5]\t$read1[9]\t$read1[10]\t";
+        }else{
+          print $fh3 "$read1[0]_$readnum\t$read1[2]\t$read1[3]\t$read1[-1]\t$read1[4]\t$read1[5]\t$seq1\t$qual1\t";
+        }
+        if(@read3){
+          $xalign = $read3[-3] if($read3[-3] =~ /^XA:Z:/);
+          my $olap = find_olap_in_chimera_mapping(\@read1,\@len1,\@ops1,\@read3);
+          if(!$olap){$olap="-";}
+          #print $fh2 "$read3[2]\t$read3[3]\t$read3[-1]\t$read3[4]\t$read3[5]\t$read3[9]\t$olap\t$xalign\n";
+          print $fh3 "$read3[2]\t$read3[3]\t$read3[-1]\t$read3[4]\t$read3[5]\t$read3[9]\t$olap\t$xalign\n";
+        }else{
+          #print $fh2 "-\t-\t-\t-\t-\t-\t-\t-\n";
+          print $fh3 "-\t-\t-\t-\t-\t-\t-\t-\n";
+        }
       }else{
-         $localcount{count_prox}++;
+       $localcount{count_prox}=1;
       }      
     }
   }
-
-
+  
+  ## counters
+  my $TOTAL = $localcount{motif_spans}+$localcount{motif_hardClip}+$localcount{motif_ref}+ $localcount{count_prox}+$localcount{nonHic_chimera};
   if($ops1[-1] eq "S" && $len1[-1] >=  $min_clip && $ops1[0] eq "S" && $len1[0] >=  $min_clip){
+    $leftoutread=1;
     $counts{mates}{double_clip}++;
   }
-  
-  ## counters
-  if($localcount{motif_spans}>0 && $localcount{motif_hardClip}==0 && $localcount{motif_ref}==0 && $localcount{count_prox}==0 && $localcount{nonHic_chimera}==0){
-    $counts{mates}{motif_spans}++;
-  }elsif($localcount{motif_spans}>0 && $localcount{motif_hardClip}==0 && $localcount{motif_ref}==0 && $localcount{count_prox}==0 && $localcount{nonHic_chimera}==0){
+  if($TOTAL == 1 and $localcount{motif_spans}>0){
     $counts{mates}{motif_spans}++;
-  }elsif($localcount{motif_spans}==0 && $localcount{motif_hardClip}>0 && $localcount{motif_ref}==0 && $localcount{count_prox}==0 && $localcount{nonHic_chimera}==0){
+  }elsif($TOTAL == 1 and $localcount{motif_hardClip}>0){
     $counts{mates}{motif_hardClip}++;
-  }elsif($localcount{motif_spans}==0 && $localcount{motif_hardClip}==0 && $localcount{motif_ref}>0 && $localcount{count_prox}==0 && $localcount{nonHic_chimera}==0){
+  }elsif($TOTAL == 1 and $localcount{motif_ref}>0){
     $counts{mates}{motif_ref}++;
-  }elsif($localcount{motif_spans}==0 && $localcount{motif_hardClip}==0 && $localcount{motif_ref}==0 && $localcount{count_prox}>0 && $localcount{nonHic_chimera}==0){
+  }elsif($TOTAL == 1 and $localcount{count_prox}>0){
     $counts{mates}{motif_proximity}++;
-  }elsif($localcount{motif_spans}==0 && $localcount{motif_hardClip}==0 && $localcount{motif_ref}==0 && $localcount{count_prox}==0 && $localcount{nonHic_chimera}>0){
-    $counts{mates}{nonHic_chimera}++;
-  }elsif($localcount{nonHic_chimera}>0){
+  }elsif($TOTAL == 1 and $localcount{nonHic_chimera}>0){
     $counts{mates}{nonHic_chimera}++;
-  }elsif($localcount{nonHic_chimera}==0 && ($is_match_a>0 and $is_match_b>0)){
+  }elsif($localcount{nonHic_chimera}==0 and $is_match_a>0 and $is_match_b>0){
     $counts{mates}{motif_multiple}++;
   }
-
-  
-  if($localcount{motif_spans}==0 && $localcount{motif_hardClip}==0 && $localcount{motif_ref}==0 && $localcount{count_prox}==0 && $localcount{nonHic_chimera}==0){
-    if($is_match_a>0 or $is_match_b>0){
-     return(2);
-    }else{
-      return(0);
-    }
-
-  }else{
-    return(0);
+  if($leftoutread==0){
+    $counts{mates}{filtered}++; 
   }
+  return(0);
 }
 
 sub linearProximity_bw_mapped_softclip {
@@ -487,7 +499,6 @@ sub linearProximity_bw_mapped_softclip {
     return(0);
   }
   elsif( abs($read1[3]-$read3[3]) <= 500 && $read1[2] eq $read3[2] ){  
-  ## Tetracutter cuts every 256bp on an average, hence, minimum resolution 256bp. Any two fragments within 2times the distance are likely to be non-informative
     return(1);
   }
   else{ ## for any other unforseen cases, return 0
@@ -555,50 +566,26 @@ sub find_olap_in_chimera_mapping {  #find_olap_in_chimera_mapping(\@read1,\@len1
    return($seq);
 }
 
-sub re_search{  #re_search($seq,$motif,-1)
-  my ($seq,$motif,$clip) = @_;
-  ## if CIGAR is unavailable, use clip as -1
+sub re_search{  #re_search($seq,$re,-1)
+  my ($seq,$re,$cl) = @_;
+  my $isRE = 0;
   
-  if($motif eq "" or !defined $motif){
-    print " Motif not defined in Dist2RE_fromSeq sub!! exiting! \n";
+  if($redb{$re}{motif} eq ""){
+    print " Motif not defined!! exiting! \n";
     exit 1;
-  }elsif($motif eq "GATC"){  ########## DpnII/ Mbo1
-     my $c = index($seq, "GATCGATC",0);
-     return(0) if($c == -1);
-     return(1) if($c != -1 and $clip == -1);
-     $clip -=1 if($clip !=0); 
-     if($c <= $clip and ($c+8) >= $clip ){
-        return(1);     
-     }else{
-        return(0);
-     }     
-  }elsif($motif eq "AAGCTT"){  ######## HindIII
-     my $c = index($seq, "AAGCTAGCTT",0);
-     return(0) if($c == -1);
-     return(1) if($c != -1 and $clip == -1);
-     $clip -=1 if($clip !=0); 
-     if($c <= $clip and ($c+10) >= $clip ){
-        return(1);     
-     }else{
-        return(0);
-     }     
   }
-}
-
-sub re_search_stringent {  #re_search_stringent($seq)
-  my $seq= shift;
-  my @patterns;
-
-  if($motif eq "GATC"){
-     @patterns = (qr/GATCGATC/);
-  }
-  if($motif eq "AAGCTT"){
-     @patterns = (qr/AAGCTAGCTT/);
+  if($cl == -1){
+    if($seq=~ m/$redb{$re}{motif}/g){
+      $isRE=1;
+    }
+  }else{
+    while ($seq =~ /$redb{$re}{motif}/g){
+      if(($cl-1)>= $-[0] and $cl<= $+[0] and $isRE ==0) {
+          $isRE = 1;
+      }
+    }
   }
-
-  my $is_match=0;
-  $is_match++ if( $seq ~~ @patterns );
-  return($is_match);
+  return($isRE);
 }
 
 sub RE_within_HardclippedSeq { #RE_within_HardclippedSeq(\@read1,\@len1,\@ops1,\@read3)
@@ -636,8 +623,6 @@ sub RE_within_HardclippedSeq { #RE_within_HardclippedSeq(\@read1,\@len1,\@ops1,\
       @ops3 = reverse(@ops3);
   }
 
-
-
   my $j=0;
   my $i=0;
   for($i=0;$i<scalar(@len1);$i++){
@@ -664,8 +649,8 @@ sub RE_within_HardclippedSeq { #RE_within_HardclippedSeq(\@read1,\@len1,\@ops1,\
   $seq =~ s/^[ATGC]+/-/s;
   $seq =~ s/[ATGC]+$/-/g;
   $seq =~ s/-//g;
-  if(length($seq)>= $len_RE){
-     if(re_search_stringent($seq)==0){
+  if(length($seq)>= $redb{$re}{mlen}){
+     if(re_search($seq,$re,-1)==0){
         return(0);
       }else{
         return(1);
@@ -683,7 +668,6 @@ sub binarysearch { #binarysearch($pos, \@locations)
   my $q1=0;
   my $q2=0;
 
-
   while ($l <= $u) {
     $i = int(($l + $u)/2);
     if ($a->[$i] < $x) {
@@ -693,7 +677,6 @@ sub binarysearch { #binarysearch($pos, \@locations)
       $u = $i-1;
     } 
     else {
-      # return $i+1; #original 
       $q1 = abs($a->[$i] - $x);
       $q2 = $q1;  
       if($a->[$i+1]){
@@ -704,12 +687,6 @@ sub binarysearch { #binarysearch($pos, \@locations)
       }else{
         return($a->[$i]); # found
       }
-      #if($upper==1){
-      #  return($q2);
-      #}else{
-      #  return($q1);
-      #}
-      
     }
   }
   $q2 = abs($a->[$l-1] - $x);
@@ -722,12 +699,6 @@ sub binarysearch { #binarysearch($pos, \@locations)
   }else{
     return($a->[$l-1]); # found
   }
-  #if($upper==1){
-  #  return($q1);
-  #}else{
-  #  return($q2);
-  #}
-  #return($l); #original         
 }
 
 sub flag2binary { #flag2binary($num)
@@ -828,4 +799,14 @@ sub parse_psam_reads { #parse_psam_reads($side1,$side2)
   return(\@r1,\@r2, \@r3, \@r4);
 }
 
-#####----------------------------------------- END --------------------------- 
\ No newline at end of file
+sub round {
+  my ($n, $places) = @_;
+  my $abs = abs $n;
+  my $val = substr($abs + ('0.' . '0' x $places . '5'),
+                   0,
+                   length(int($abs)) +
+                     (($places > 0) ? $places + 1 : 0)
+                  );
+  ($n < 0) ? "-" . $val : $val;
+}
+#####----------------------------------------- END ---------------------------