diff --git a/src/perllib/CiceroUtil.pm b/src/perllib/CiceroUtil.pm
index de0a84a..3ba1e68 100755
--- a/src/perllib/CiceroUtil.pm
+++ b/src/perllib/CiceroUtil.pm
@@ -823,6 +823,18 @@ sub normalizeChromosomeName {
 	return $query; 
 }
 
+sub exist_multiplename_checking {
+	my %genelist = %{(shift)};
+    	my $targetgene = shift;#e.g. targetgene UBTF,MIR6782
+	my @genes = split(/,|\|/, $targetgene);
+
+	foreach my $g1 (@genes) {
+                return 1 if(exists($genelist{$g1}));
+	}
+
+	return 0;
+}
+
 1;
 
 =head1 LICENCE AND COPYRIGHT
diff --git a/src/scripts/annotate.pl b/src/scripts/annotate.pl
index 11af969..4bf6b1b 100755
--- a/src/scripts/annotate.pl
+++ b/src/scripts/annotate.pl
@@ -17,7 +17,7 @@
 
 use CiceroSCValidator qw($lowqual_cutoff LEFT_CLIP RIGHT_CLIP);
 use CiceroUtil qw(prepare_reads_file parse_range rev_comp
-	is_PCR_dup read_fa_file get_discordant_reads get_sclip_reads normalizeChromosomeName);
+	is_PCR_dup read_fa_file get_discordant_reads get_sclip_reads normalizeChromosomeName exist_multiplename_checking);
 
 require CiceroExtTools;
 
@@ -27,6 +27,8 @@
 use Gene;
 use GeneModel;
 
+use constant BADFUSION_DISTANCE_CUTOFF => 200;
+
 my $debug = 0;
 
 my $out_header = join("\t", "sample", "geneA", "chrA", "posA", "ortA", "featureA", "geneB", "chrB", "posB", "ortB", "featureB", 
@@ -257,20 +259,16 @@
 }
 
 sub is_bad_fusion{
-	my $badfusion_distance_cutoff = 200;
 	my ($chrA, $posA, $chrB, $posB) = @_;
 	$chrA = "chr".$chrA unless($chrA =~ /chr/);
 	$chrB = "chr".$chrB unless($chrB =~ /chr/);
-	#print STDERR " test |".$chrA.":".$posA.":".$chrB.":".$posB."\n";
-	my $size = keys %bad_fusions;
-	#print STDERR " size |".$size."\n";
 	foreach my $xx (keys %bad_fusions) {
 		my ($chr1, $pos1, $chr2, $pos2) = split(":",$xx);
 		#print STDERR " badfusionlist |".$chr1.":".$pos1.":".$chr2.":".$pos2."\n";
 		return 1 if($chrA eq $chr1 && $chrB eq $chr2 &&
-			    abs($pos1 - $posA) <$badfusion_distance_cutoff && abs($pos2 - $posB) <$badfusion_distance_cutoff);# cutoff is based on the cutoff of merging GTEx false positive fusions from CICERO running
+			    abs($pos1 - $posA) < BADFUSION_DISTANCE_CUTOFF && abs($pos2 - $posB) < BADFUSION_DISTANCE_CUTOFF);# cutoff is based on the cutoff of merging GTEx false positive fusions from CICERO running
 		return 1 if($chrA eq $chr2 && $chrB eq $chr1 &&
-			    abs($pos2 - $posA) <$badfusion_distance_cutoff && abs($pos1 - $posB) <$badfusion_distance_cutoff);
+			    abs($pos2 - $posA) < BADFUSION_DISTANCE_CUTOFF && abs($pos1 - $posB) < BADFUSION_DISTANCE_CUTOFF);
 	}
 	return 0;
 }
@@ -414,7 +412,7 @@ sub is_bad_fusion{
 	$second_bp->{tname} = normalizeChromosomeName($seq_ids[0], $second_bp->{tname});
 
 	# Ensure that the breakpoint chromosome names match
-	if(!$internal)	{next if(is_bad_fusion($first_bp->{tname}, $first_bp->{tpos}, $second_bp->{tname}, $second_bp->{tpos}));}
+	next if(!$internal && is_bad_fusion($first_bp->{tname}, $first_bp->{tpos}, $second_bp->{tname}, $second_bp->{tpos}));
 
 	# Determine the variant type: CTX, Internal_inv, Interal_splicing, Internal_dup, ITX, read_through, DEL, INS
 	my $type = get_type($first_bp, $second_bp, $same_gene);
@@ -811,34 +809,6 @@ sub exist_multiplename_pair_checking {
 	return 0;
 }
 
-sub is_knownfusiongenepair{
-        my @genes1_tmp = %{(shift)};
-        my @genes2_tmp = %{(shift)};
-
-        foreach my $g1 (@genes1_tmp) {
-                foreach my $g2 (@genes2_tmp) {
-                        return 1 if (exists($known_fusion_partners{$g1}{$g2}));
-                }
-        }
-
-        return 0;
-}
-
-
-
-sub exist_multiplename_checking {
-	my %genelist = %{(shift)};
-    	my $targetgene = shift;#e.g. targetgene UBTF,MIR6782
-	my @genes = split(/,|\|/, $targetgene);
-
-	foreach my $g1 (@genes) {
-                return 1 if(exists($genelist{$g1}));
-	}
-
-	return 0;
-}
-
-
 sub is_good_ITD {
 	my($bp1, $bp2) = @_;
 	my @genes = split(/,|\|/, $bp1->{gene});
diff --git a/src/scripts/get_geneInfo.pl b/src/scripts/get_geneInfo.pl
index 340cb82..3c9d977 100755
--- a/src/scripts/get_geneInfo.pl
+++ b/src/scripts/get_geneInfo.pl
@@ -18,7 +18,7 @@
 use lib dirname($0);
 my $script_dir = dirname($0);
 #custom packages
-use CiceroUtil qw(parse_range is_PCR_dup);
+use CiceroUtil qw(parse_range is_PCR_dup exist_multiplename_checking);
 use TdtConfig; 
 
 use constant FQ_BASE_NUMBER => 33;
@@ -172,19 +172,6 @@ sub is_bad_chrom{
 	return 0;
 }
 
-sub exist_multiplename_checking {
-        my %genelist = %{(shift)};
-        my $targetgene = shift;#e.g. targetgene UBTF,MIR6782
-        my @genes = split(/,|\|/, $targetgene);
-
-        foreach my $g1 (@genes) {
-                return 1 if(exists($genelist{$g1}));
-        }
-
-        return 0;
-}
-
-
 =head1 LICENCE AND COPYRIGHT
 Copyright 2019 St. Jude Children's Research Hospital 
 
diff --git a/src/scripts/rank_SVs.pl b/src/scripts/rank_SVs.pl
index 626d8a7..d5072e8 100755
--- a/src/scripts/rank_SVs.pl
+++ b/src/scripts/rank_SVs.pl
@@ -11,6 +11,8 @@
 use List::Util qw[min max];
 use TdtConfig; 
 
+use CiceroUtil qw(exist_multiplename_checking)
+
 use DelimitedFile;
 use File::Temp qw/ tempdir /;
 
@@ -299,15 +301,15 @@ sub scoring {
 	my $rating = 'LQ';
 
 	$medal = 1 if(exist_multiplename_checking(\%known_fusion_partners,$fg1));
-        $medal = 1 if(exist_multiplename_checking(\%known_fusion_partners,$fg2) && $sv->{ort} eq "?");
-        $medal = 2 if(exist_multiplename_checking(\%known_fusion_partners,$fg2) && $sv->{ort} eq ">");
-        $medal = 3 if(exist_multiplename_checking(\%known_fusion_partners,$fg1) && exist_multiplename_checking(\%known_fusion_partners,$fg2) && $sv->{type} !~ /Internal/);
-        $medal = 4 if(exists_knownfusionlist_checking(\%known_fusions,$fg1,$fg2));
+	$medal = 1 if(exist_multiplename_checking(\%known_fusion_partners,$fg2) && $sv->{ort} eq "?");
+	$medal = 2 if(exist_multiplename_checking(\%known_fusion_partners,$fg2) && $sv->{ort} eq ">");
+	$medal = 3 if(exist_multiplename_checking(\%known_fusion_partners,$fg1) && exist_multiplename_checking(\%known_fusion_partners,$fg2) && $sv->{type} !~ /Internal/);
+	$medal = 4 if(exists_knownfusionlist_checking(\%known_fusions,$fg1,$fg2));
 
-	my ($Is_known_ITD, $ITD_left_coor, $ITD_rightt_coor)=match_known_ITD(\%known_ITDs,$fg1);	
+	my ($Is_known_ITD, $ITD_left_coor, $ITD_right_coor)=match_known_ITD(\%known_ITDs,$fg1);
 	if($Is_known_ITD && $type eq 'Internal_dup' &&
-	   ($bp1->{tpos} >= $ITD_left_coor) && ($bp1->{tpos} <= $ITD_rightt_coor) &&
-	   ($bp2->{tpos} >= $ITD_left_coor) && ($bp2->{tpos} <= $ITD_rightt_coor)){
+	   ($bp1->{tpos} >= $ITD_left_coor) && ($bp1->{tpos} <= $ITD_right_coor) &&
+	   ($bp2->{tpos} >= $ITD_left_coor) && ($bp2->{tpos} <= $ITD_right_coor)){
 			$rating = 'HQ'; $medal = 4;
 	}
 
@@ -366,7 +368,6 @@ sub is_dup_SV {
 }
 
 sub exists_knownfusionlist_checking {
-        my %genelist = %{(shift)};
         my $targetgene1 = shift;#e.g. targetgene UBTF,MIR6782
         my $targetgene2 = shift;#e.g. targetgene UBTF,MIR6782
         my @genes1 = split(/,|\|/, $targetgene1);
@@ -382,18 +383,6 @@ sub exists_knownfusionlist_checking {
         return 0;
 }
 
-sub exist_multiplename_checking {
-        my %genelist = %{(shift)};
-        my $targetgene = shift;#e.g. targetgene UBTF,MIR6782
-        my @genes = split(/,|\|/, $targetgene);
-
-        foreach my $g1 (@genes) {
-                return 1 if(exists($known_fusion_partners{$g1}));
-        }
-
-        return 0;
-}
-
 sub match_known_ITD {
 	my %knownITDlist = %{(shift)};
 	my $targetgene = shift;#e.g. targetgene UBTF,MIR6782