diff --git a/MYMETA.json b/MYMETA.json
deleted file mode 100644
index e410705..0000000
--- a/MYMETA.json
+++ /dev/null
@@ -1,57 +0,0 @@
-{
-   "abstract" : "unknown",
-   "author" : [
-      "unknown"
-   ],
-   "dynamic_config" : 0,
-   "generated_by" : "ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.131560",
-   "license" : [
-      "agpl_3"
-   ],
-   "meta-spec" : {
-      "url" : "http://search.cpan.org/perldoc?CPAN::Meta::Spec",
-      "version" : "2"
-   },
-   "name" : "Vagrent",
-   "no_index" : {
-      "directory" : [
-         "t",
-         "inc"
-      ]
-   },
-   "prereqs" : {
-      "build" : {
-         "requires" : {
-            "ExtUtils::MakeMaker" : "0"
-         }
-      },
-      "configure" : {
-         "requires" : {
-            "ExtUtils::MakeMaker" : "0"
-         }
-      },
-      "runtime" : {
-         "requires" : {
-            "Attribute::Abstract" : "1.02",
-            "Bio::DB::Sam" : "1.39",
-            "Bio::Root::Version" : "1.006924",
-            "Capture::Tiny" : "0.24",
-            "Config::IniFiles" : "2.83",
-            "Const::Fast" : "0.014",
-            "File::ShareDir" : "1.102",
-            "File::Temp" : "0.2304",
-            "File::Type" : "0.22",
-            "IPC::System::Simple" : "1.25",
-            "LWP::Simple" : "6.00",
-            "List::Util" : "1.41",
-            "Log::Log4perl" : "1.44",
-            "Pod::Usage" : "1.64",
-            "Sort::Key" : "1.33",
-            "TAP::Harness" : "3.33",
-            "Try::Tiny" : "0.22"
-         }
-      }
-   },
-   "release_status" : "stable",
-   "version" : "v2.1.2"
-}
diff --git a/MYMETA.yml b/MYMETA.yml
deleted file mode 100644
index 00320a4..0000000
--- a/MYMETA.yml
+++ /dev/null
@@ -1,38 +0,0 @@
----
-abstract: unknown
-author:
-  - unknown
-build_requires:
-  ExtUtils::MakeMaker: 0
-configure_requires:
-  ExtUtils::MakeMaker: 0
-dynamic_config: 0
-generated_by: 'ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.131560'
-license: open_source
-meta-spec:
-  url: http://module-build.sourceforge.net/META-spec-v1.4.html
-  version: 1.4
-name: Vagrent
-no_index:
-  directory:
-    - t
-    - inc
-requires:
-  Attribute::Abstract: 1.02
-  Bio::DB::Sam: 1.39
-  Bio::Root::Version: 1.006924
-  Capture::Tiny: 0.24
-  Config::IniFiles: 2.83
-  Const::Fast: 0.014
-  File::ShareDir: 1.102
-  File::Temp: 0.2304
-  File::Type: 0.22
-  IPC::System::Simple: 1.25
-  LWP::Simple: 6.00
-  List::Util: 1.41
-  Log::Log4perl: 1.44
-  Pod::Usage: 1.64
-  Sort::Key: 1.33
-  TAP::Harness: 3.33
-  Try::Tiny: 0.22
-version: v2.1.2
diff --git a/docs.tar.gz b/docs.tar.gz
index 605040d..c11c306 100644
Binary files a/docs.tar.gz and b/docs.tar.gz differ
diff --git a/lib/Sanger/CGP/Vagrent.pm b/lib/Sanger/CGP/Vagrent.pm
index 2cc762d..f7f421c 100644
--- a/lib/Sanger/CGP/Vagrent.pm
+++ b/lib/Sanger/CGP/Vagrent.pm
@@ -2,21 +2,21 @@ package Sanger::CGP::Vagrent;
 
 ##########LICENCE##########
 # Copyright (c) 2014 Genome Research Ltd.
-# 
+#
 # Author: Cancer Genome Project cgpit@sanger.ac.uk
-# 
+#
 # This file is part of VAGrENT.
-# 
+#
 # VAGrENT is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free
 # Software Foundation; either version 3 of the License, or (at your option) any
 # later version.
-# 
+#
 # This program is distributed in the hope that it will be useful, but WITHOUT
 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 # FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
 # details.
-# 
+#
 # You should have received a copy of the GNU Affero General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 ##########LICENCE##########
@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 
 use base 'Exporter';
-our $VERSION = '2.1.2';
+our $VERSION = '2.1.3';
 our @EXPORT = qw($VERSION);
 
 1;
diff --git a/lib/Sanger/CGP/Vagrent/Annotators/AbstractAnnotator.pm b/lib/Sanger/CGP/Vagrent/Annotators/AbstractAnnotator.pm
index b039a6a..7fae898 100644
--- a/lib/Sanger/CGP/Vagrent/Annotators/AbstractAnnotator.pm
+++ b/lib/Sanger/CGP/Vagrent/Annotators/AbstractAnnotator.pm
@@ -2,21 +2,21 @@ package Sanger::CGP::Vagrent::Annotators::AbstractAnnotator;
 
 ##########LICENCE##########
 # Copyright (c) 2014 Genome Research Ltd.
-# 
+#
 # Author: Cancer Genome Project cgpit@sanger.ac.uk
-# 
+#
 # This file is part of VAGrENT.
-# 
+#
 # VAGrENT is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free
 # Software Foundation; either version 3 of the License, or (at your option) any
 # later version.
-# 
+#
 # This program is distributed in the hope that it will be useful, but WITHOUT
 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 # FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
 # details.
-# 
+#
 # You should have received a copy of the GNU Affero General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 ##########LICENCE##########
@@ -28,6 +28,7 @@ use Log::Log4perl;
 use POSIX qw(ceil);
 use Data::Dumper;
 use Attribute::Abstract;
+use Const::Fast qw(const);
 
 use Sanger::CGP::Vagrent qw($VERSION);
 
@@ -38,20 +39,19 @@ use base qw(Sanger::CGP::Vagrent::Ontology::SequenceOntologyClassifier);
 
 my $log = Log::Log4perl->get_logger(__PACKAGE__);
 
-
-1;
-
 # constant reference values for consensus splice site values.
-use constant CONSENSUS_SPLICE_OFFSETS => (-2, -1, 1, 2, 5);
-use constant CONSENSUS_SPLICE_BEFORE_BOUNDRY => -2;
-use constant CONSENSUS_SPLICE_AFTER_BOUNDRY => 5;
+const my @CONSENSUS_SPLICE_OFFSETS => (-2, -1, 1, 2, 5);
+const my $CONSENSUS_SPLICE_BEFORE_BOUNDRY => -2;
+const my $CONSENSUS_SPLICE_AFTER_BOUNDRY => 5;
 
 # constant value representing the cutoff for intronic calls
-use constant INTRONIC_OFFSET_CUTOFF => 11;
+const my $INTRONIC_OFFSET_CUTOFF => 11;
 
-use constant UPDOWNSTREAM_5KB_CUTOFF => 5000;
-use constant UPSTREAM_2KB_CUTOFF => -2000;
-use constant DOWNSTREAM_500BP_CUTOFF => 500;
+const my $UPDOWNSTREAM_5KB_CUTOFF => 5000;
+const my $UPSTREAM_2KB_CUTOFF => -2000;
+const my $DOWNSTREAM_500BP_CUTOFF => 500;
+
+1;
 
 sub new {
   my $proto = shift;
@@ -63,6 +63,10 @@ sub new {
 	return $self;
 }
 
+sub getConsensusSpliceOffsets {
+  return @CONSENSUS_SPLICE_OFFSETS;
+}
+
 sub getAnnotation {
 	my ($self,$var) = @_;
 	my @ann = $self->_getAnnotation($var);
@@ -462,7 +466,7 @@ sub _buildProteinAnnotation {
  		# something has gone wrong
  		return undef;
  	}
-  
+
 	my $mtDna = $self->_getMutatedCdsSequence($wtDna,$cdsMinPos,$cdsMaxPos,$cAnnot->getMt());
 	my $mtProt = Bio::Seq->new(-seq => $prePad . $mtDna . $postPad)->translate->seq(); # mutant protein sequence
 	my $maxMtProt = Bio::Seq->new(-seq => $prePad . $mtDna . substr($tran->getcDNASeq,$tran->getCdsMaxPos()))->translate->seq(); # maximised protein sequence, overruns the natural stop and translates to the end of the transcript
@@ -513,7 +517,7 @@ sub _buildProteinAnnotation {
 			substr($wt,-1,1,'');
 			substr($mt,-1,1,'');
 		}
-    
+
 		#warn "|$wt| to |$mt|\n";
 		if($wt ne ''){
 			# wild type residue has been changed
@@ -843,7 +847,7 @@ sub _buildUnknownMRNAAnnotation {
 
 sub _isOffsetAConsensusSpliceDistance {
 	my ($self,$offset) = @_;
-  foreach my $cf($self->CONSENSUS_SPLICE_OFFSETS){
+  foreach my $cf(@CONSENSUS_SPLICE_OFFSETS){
   	if($offset == $cf){
   		return 1;
   	}
@@ -852,16 +856,16 @@ sub _isOffsetAConsensusSpliceDistance {
 }
 
 sub _getConsesnsusSpliceBeforeBoundry {
-	return CONSENSUS_SPLICE_BEFORE_BOUNDRY;
+	return $CONSENSUS_SPLICE_BEFORE_BOUNDRY;
 }
 
 sub _getConsesnsusSpliceAfterBoundry {
-	return CONSENSUS_SPLICE_AFTER_BOUNDRY;
+	return $CONSENSUS_SPLICE_AFTER_BOUNDRY;
 }
 
 sub _isIntronicOffsetDistance {
 	my ($self,$offset) = @_;
-	if(abs($offset) >= $self->INTRONIC_OFFSET_CUTOFF){
+	if(abs($offset) >= $INTRONIC_OFFSET_CUTOFF){
 		return 1;
 	}
 	return 0;
@@ -869,7 +873,7 @@ sub _isIntronicOffsetDistance {
 
 sub _isWithin5KBOffsetDistance {
 	my ($self,$offset) = @_;
-	if(abs($offset) <= $self->UPDOWNSTREAM_5KB_CUTOFF){
+	if(abs($offset) <= $UPDOWNSTREAM_5KB_CUTOFF){
 		return 1;
 	}
 	return 0;
@@ -877,7 +881,7 @@ sub _isWithin5KBOffsetDistance {
 
 sub _isWithin2KBUpstreamOffsetDistance {
 	my ($self,$offset) = @_;
-	if($offset < 0 && $offset >= $self->UPSTREAM_2KB_CUTOFF){
+	if($offset < 0 && $offset >= $UPSTREAM_2KB_CUTOFF){
 		return 1;
 	}
 	return 0;
@@ -885,7 +889,7 @@ sub _isWithin2KBUpstreamOffsetDistance {
 
 sub _isWithin500BPDownstreamOffsetDistance {
 	my ($self,$offset) = @_;
-	if($offset > 0 && $offset <= $self->DOWNSTREAM_500BP_CUTOFF){
+	if($offset > 0 && $offset <= $DOWNSTREAM_500BP_CUTOFF){
 		return 1;
 	}
 	return 0;
@@ -897,7 +901,7 @@ sub _coversStartCodon {
 		# if the transcript isn't protein coding it can't have a start codon
 		return 0;
 	}
-  
+
   my ($startMin,$startMax);
   if($anno->getContext eq Sanger::CGP::Vagrent::Data::Annotation::getmRNAAnnotationContext()){
     $startMin = $tran->getCdsMinPos;
@@ -909,7 +913,7 @@ sub _coversStartCodon {
     # don't know, assume no
 		return 0;
   }
-  
+
   if($anno->hasClassification($self->getInsertionClass)){
     # insertions are a special case, coordinates are outside the variant
     if($anno->getMinPos < $startMax && $anno->getMaxPos > $startMin){
@@ -944,7 +948,7 @@ sub _coversStopCodon {
     # don't know, assume no
 		return 0;
   }
-  
+
   if($anno->hasClassification($self->getInsertionClass)){
     # insertions are a special case, coordinates are outside the variant
     if($anno->getMinPos < $stopMax && $anno->getMaxPos > $stopMin){
@@ -1010,10 +1014,10 @@ sub _canAnnotateToCDS {
 		if($anno->hasClassification($self->getInsertionClass)){
 			# insertions are a special case.
 			# Coordinates are the last WT positions, and not the first variant ones like everything else
-      
+
       print 'ANNO POS: '.$anno->getMinPos.' , '.$anno->getMinOffset.' - '.$anno->getMaxPos.' , '.$anno->getMaxOffset."\n" if $self->_debug();
       print 'CDS POS: '.$tran->getCdsMinPos.' , '.$tran->getCdsMaxPos."\n" if $self->_debug();
-      
+
       if($anno->getMaxPos < $tran->getCdsMinPos || $anno->getMinPos > $tran->getCdsMaxPos){
         # ends before CDS or starts afterwards
         return 0;
@@ -1051,7 +1055,7 @@ sub _canAnnotateToCDS {
 		} elsif($anno->hasClassification($self->getUnknownVariantClass)){
 			return 0;
     } elsif($anno->hasClassification($self->getInsertionClass) && $anno->hasClassification($self->get5PrimeUtrVariantClass)){
-      # odd case, insertions close to the start codons can be described on the CDS even though they don't change it. 
+      # odd case, insertions close to the start codons can be described on the CDS even though they don't change it.
       return 1;
 		} else {
 			my $msg = "Unable to calculate CDS relevance - UNKNOWN CLASSIFICATION: ".join(' ',$anno->getClassifications);
diff --git a/lib/Sanger/CGP/Vagrent/Bookmarkers/MostDeleteriousBookmarker.pm b/lib/Sanger/CGP/Vagrent/Bookmarkers/MostDeleteriousBookmarker.pm
index f764ddf..40a78bf 100644
--- a/lib/Sanger/CGP/Vagrent/Bookmarkers/MostDeleteriousBookmarker.pm
+++ b/lib/Sanger/CGP/Vagrent/Bookmarkers/MostDeleteriousBookmarker.pm
@@ -2,21 +2,21 @@ package Sanger::CGP::Vagrent::Bookmarkers::MostDeleteriousBookmarker;
 
 ##########LICENCE##########
 # Copyright (c) 2014 Genome Research Ltd.
-# 
+#
 # Author: Cancer Genome Project cgpit@sanger.ac.uk
-# 
+#
 # This file is part of VAGrENT.
-# 
+#
 # VAGrENT is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free
 # Software Foundation; either version 3 of the License, or (at your option) any
 # later version.
-# 
+#
 # This program is distributed in the hope that it will be useful, but WITHOUT
 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 # FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
 # details.
-# 
+#
 # You should have received a copy of the GNU Affero General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 ##########LICENCE##########
@@ -27,39 +27,41 @@ use strict;
 use Log::Log4perl qw(:easy);
 use Data::Dumper;
 use Carp qw(croak);
+use Const::Fast qw(const);
 
 use Sanger::CGP::Vagrent qw($VERSION);
 use base qw(Sanger::CGP::Vagrent::Bookmarkers::RepresentativeTranscriptBookmarker);
 
+const my $DOWNSTREAM_SCORE => 4;
+const my $UPSTREAM_SCORE => 7;
+const my $INTRONIC_SCORE => 10;
+const my $NONCODING_GENE_SCORE => 15;
+const my $COMPLEX_IN_MRNA_SCORE => 50;
+const my $NONCODING_GENE_SPLICE_REGION_SCORE => 95;
+const my $THREEPRIME_UTR_SPLICE_REGION_SCORE => 100;
+const my $FIVEPRIME_UTR_SPLICE_REGION_SCORE => 105;
+const my $CODING_SPLICE_REGION_SCORE => 200;
+const my $FIVEPRIME_UTR_SCORE => 300;
+const my $THREEPRIME_UTR_SCORE => 305;
+const my $NONCODING_GENE_ESS_SPLICE_SCORE => 395;
+const my $THREEPRIME_UTR_ESS_SPLICE_SCORE => 400;
+const my $FIVEPRIME_UTR_ESS_SPLICE_SCORE => 405;
+const my $START_GAINED_SCORE => 450;
+const my $SYNONYMOUS_SCORE => 500;
+const my $COMPLETE_NONCODING_TRANSCRIPT_LOSS_SCORE => 525;
+const my $COMPLEX_IN_CDS_SCORE => 550;
+const my $NON_SYNONYMOUS_SCORE => 600;
+const my $STOP_LOST_SCORE => 700;
+const my $INITIATOR_CHANGE_SCORE => 800;
+const my $INFRAME_CODON_GAIN_SCORE => 825;
+const my $INFRAME_CODON_LOSS_AND_GAIN_SCORE => 840;
+const my $INFRAME_CODON_LOSS_SCORE => 850;
+const my $CODING_ESS_SPLICE_SCORE => 900;
+const my $STOP_GAINED_SCORE => 1000;
+const my $FRAMESHIFT_SCORE => 1100;
+const my $COMPLETE_PROTEIN_LOSS_SCORE => 1200;
+
 1;
-use constant DOWNSTREAM_SCORE => 4;
-use constant UPSTREAM_SCORE => 7;
-use constant INTRONIC_SCORE => 10;
-use constant NONCODING_GENE_SCORE => 15;
-use constant COMPLEX_IN_MRNA_SCORE => 50;
-use constant NONCODING_GENE_SPLICE_REGION_SCORE => 95;
-use constant THREEPRIME_UTR_SPLICE_REGION_SCORE => 100;
-use constant FIVEPRIME_UTR_SPLICE_REGION_SCORE => 105;
-use constant CODING_SPLICE_REGION_SCORE => 200;
-use constant FIVEPRIME_UTR_SCORE => 300;
-use constant THREEPRIME_UTR_SCORE => 305;
-use constant NONCODING_GENE_ESS_SPLICE_SCORE => 395;
-use constant THREEPRIME_UTR_ESS_SPLICE_SCORE => 400;
-use constant FIVEPRIME_UTR_ESS_SPLICE_SCORE => 405;
-use constant START_GAINED_SCORE => 450;
-use constant SYNONYMOUS_SCORE => 500;
-use constant COMPLETE_NONCODING_TRANSCRIPT_LOSS_SCORE => 525;
-use constant COMPLEX_IN_CDS_SCORE => 550;
-use constant NON_SYNONYMOUS_SCORE => 600;
-use constant STOP_LOST_SCORE => 700;
-use constant INITIATOR_CHANGE_SCORE => 800;
-use constant INFRAME_CODON_GAIN_SCORE => 825;
-use constant INFRAME_CODON_LOSS_AND_GAIN_SCORE => 840;
-use constant INFRAME_CODON_LOSS_SCORE => 850;
-use constant CODING_ESS_SPLICE_SCORE => 900;
-use constant STOP_GAINED_SCORE => 1000;
-use constant FRAMESHIFT_SCORE => 1100;
-use constant COMPLETE_PROTEIN_LOSS_SCORE => 1200;
 
 sub _getAnnotation {
 	my $self = shift;
@@ -75,271 +77,271 @@ sub _getMostDeleterious {
 	my $mostGroup = undef;
 	foreach my $g(@groups){
 		my $score = 1;
-		my $mrna = $g->getAnnotationByContext(Sanger::CGP::Vagrent::Data::Annotation::getmRNAAnnotationContext);
-		my $cds = $g->getAnnotationByContext(Sanger::CGP::Vagrent::Data::Annotation::getCDSAnnotationContext);
-		my $prot = $g->getAnnotationByContext(Sanger::CGP::Vagrent::Data::Annotation::getProteinAnnotationContext);
+		my $mrna = $g->getAnnotationByContext(Sanger::CGP::Vagrent::Data::Annotation->getmRNAAnnotationContext);
+		my $cds = $g->getAnnotationByContext(Sanger::CGP::Vagrent::Data::Annotation->getCDSAnnotationContext);
+		my $prot = $g->getAnnotationByContext(Sanger::CGP::Vagrent::Data::Annotation->getProteinAnnotationContext);
 		if($g->hasClassification($self->getProteinCodingClass)){
 			# protein coding transcript
 			if(defined($prot) && $prot->getType() ne $mrna->getUnknownAnnotationType){
 				# Protein annotation
-				if($self->COMPLETE_PROTEIN_LOSS_SCORE > $score &&
+				if($COMPLETE_PROTEIN_LOSS_SCORE > $score &&
 					$prot->hasClassification($self->getDeletionClass) &&
 					$prot->getMinPos() == 1 && $prot->getMaxPos() == $prot->getSequenceLength()){
 					# if marked as a deletion, start = 1 and end = protein length the protein is gone.
-						$score = $self->COMPLETE_PROTEIN_LOSS_SCORE;
+						$score = $COMPLETE_PROTEIN_LOSS_SCORE;
 				}
-				if($self->FRAMESHIFT_SCORE > $score &&
+				if($FRAMESHIFT_SCORE > $score &&
 					$g->hasClassification($self->getExonClass) && $g->hasClassification($self->getCDSClass) &&
 					$prot->hasClassification($self->getFrameShiftVariantClass)){
 					# Frameshift
-						$score = $self->FRAMESHIFT_SCORE;
+						$score = $FRAMESHIFT_SCORE;
 				}
-				if($self->STOP_GAINED_SCORE > $score &&
+				if($STOP_GAINED_SCORE > $score &&
 					$g->hasClassification($self->getExonClass) && $g->hasClassification($self->getCDSClass) &&
 					$prot->hasClassification($self->getStopGainedVariantClass)){
 					# non-sense / stop gained
-						$score = $self->STOP_GAINED_SCORE;
+						$score = $STOP_GAINED_SCORE;
 				}
-				if($self->INFRAME_CODON_LOSS_SCORE > $score &&
+				if($INFRAME_CODON_LOSS_SCORE > $score &&
 					$g->hasClassification($self->getExonClass) && $g->hasClassification($self->getCDSClass) &&
 					$prot->hasClassification($self->getInFrameCodonLossVariantClass)){
 					# in frame deletion
-						$score = $self->INFRAME_CODON_LOSS_SCORE;
+						$score = $INFRAME_CODON_LOSS_SCORE;
 				}
-				if($self->INFRAME_CODON_LOSS_AND_GAIN_SCORE > $score &&
+				if($INFRAME_CODON_LOSS_AND_GAIN_SCORE > $score &&
 					$g->hasClassification($self->getExonClass) && $g->hasClassification($self->getCDSClass) &&
 					$prot->hasClassification($self->getComplexIndelClass)){
 					# in frame complex sub
-						$score = $self->INFRAME_CODON_LOSS_AND_GAIN_SCORE;
+						$score = $INFRAME_CODON_LOSS_AND_GAIN_SCORE;
 				}
-				if($self->INFRAME_CODON_GAIN_SCORE > $score &&
+				if($INFRAME_CODON_GAIN_SCORE > $score &&
 					$g->hasClassification($self->getExonClass) && $g->hasClassification($self->getCDSClass) &&
 					$prot->hasClassification($self->getInFrameCodonGainVariantClass)){
 					# in frame insertion
-						$score = $self->INFRAME_CODON_GAIN_SCORE;
+						$score = $INFRAME_CODON_GAIN_SCORE;
 				}
-				if($self->INITIATOR_CHANGE_SCORE > $score &&
+				if($INITIATOR_CHANGE_SCORE > $score &&
 					$g->hasClassification($self->getExonClass) && $g->hasClassification($self->getCDSClass) &&
 					$prot->hasClassification($self->getStartLostVariantClass)){
 					# start lost
-						$score = $self->INITIATOR_CHANGE_SCORE;
+						$score = $INITIATOR_CHANGE_SCORE;
 				}
-				if($self->STOP_LOST_SCORE > $score &&
+				if($STOP_LOST_SCORE > $score &&
 					$g->hasClassification($self->getExonClass) && $g->hasClassification($self->getCDSClass) &&
 					$prot->hasClassification($self->getStopLostVariantClass)){
 					# stop lost
-						$score = $self->STOP_LOST_SCORE;
+						$score = $STOP_LOST_SCORE;
 				}
-				if($self->NON_SYNONYMOUS_SCORE > $score &&
+				if($NON_SYNONYMOUS_SCORE > $score &&
 					$g->hasClassification($self->getExonClass) && $g->hasClassification($self->getCDSClass) &&
 					$prot->hasClassification($self->getNonSynonymousVariantClass)){
 					# mis sense
-						$score = $self->NON_SYNONYMOUS_SCORE;
+						$score = $NON_SYNONYMOUS_SCORE;
 				}
-				if($self->SYNONYMOUS_SCORE > $score &&
+				if($SYNONYMOUS_SCORE > $score &&
 					$g->hasClassification($self->getExonClass) && $g->hasClassification($self->getCDSClass) &&
 					($prot->hasClassification($self->getSynonymousVariantClass) || $prot->hasClassification($self->getStopRetainedVariantClass))){
 					# silent including terminator silent
-						$score = $self->SYNONYMOUS_SCORE;
+						$score = $SYNONYMOUS_SCORE;
 				}
 			} elsif(defined($cds) && $cds->getType() ne $mrna->getUnknownAnnotationType){
 				# CDS annotation
-				if($self->FRAMESHIFT_SCORE > $score &&
+				if($FRAMESHIFT_SCORE > $score &&
 					$g->hasClassification($self->getExonClass) && $g->hasClassification($self->getCDSClass) &&
 					$cds->hasClassification($self->getFrameShiftVariantClass)){
 					# frame shift again, incase protein translation was too complex
-						$score = $self->FRAMESHIFT_SCORE;
+						$score = $FRAMESHIFT_SCORE;
 				}
-				if($self->CODING_ESS_SPLICE_SCORE > $score &&
+				if($CODING_ESS_SPLICE_SCORE > $score &&
 					$g->hasClassification($self->getEssentialSpliceSiteClass) && $g->hasClassification($self->getCDSClass) &&
 					$cds->hasClassification($self->getEssentialSpliceSiteVariantClass)){
 					# essential splice change in CDS
-						$score = $self->CODING_ESS_SPLICE_SCORE;
+						$score = $CODING_ESS_SPLICE_SCORE;
 				}
 
-				if($self->COMPLEX_IN_CDS_SCORE > $score &&
+				if($COMPLEX_IN_CDS_SCORE > $score &&
 					$g->hasClassification($self->getCDSClass) &&
 					$cds->hasClassification($self->getComplexChangeVariantClass)){
 					# complex transcript consequence involving CDS
 						if($cds->getMinPos() == 1 && $cds->getMaxPos() == $cds->getSequenceLength()){
 							# position 1 to CDS length effected, transcript lost
-							$score = $self->COMPLETE_PROTEIN_LOSS_SCORE;
+							$score = $COMPLETE_PROTEIN_LOSS_SCORE;
 						} elsif($g->hasClassification($self->getEssentialSpliceSiteClass) && $g->hasClassification($self->getExonClass) && $g->hasClassification($self->getCDSClass)){
 							# essential splice change
-							$score = $self->CODING_ESS_SPLICE_SCORE;
+							$score = $CODING_ESS_SPLICE_SCORE;
 						} elsif($g->hasClassification($self->getExonClass) && $g->hasClassification($self->getCDSClass) &&
 									($g->hasClassification($self->get5PrimeUtrClass) || $mrna->hasClassification($self->get2KBUpStreamVariantClass)) &&
 									$cds->getMinPos() == 1){
 							# start codon lost
-							$score = $self->INITIATOR_CHANGE_SCORE;
+							$score = $INITIATOR_CHANGE_SCORE;
 						} elsif($g->hasClassification($self->getExonClass) && $g->hasClassification($self->getCDSClass) &&
 									($g->hasClassification($self->get3PrimeUtrClass) || $mrna->hasClassification($self->get500BPDownStreamVariantClass)) &&
 									$cds->getMaxPos() == $cds->getSequenceLength()){
 							# stop codon lost
-							$score = $self->STOP_LOST_SCORE;
+							$score = $STOP_LOST_SCORE;
 						} else {
 							# if its none of the above, its just complex in CDS
-							$score = $self->COMPLEX_IN_CDS_SCORE;
+							$score = $COMPLEX_IN_CDS_SCORE;
 						}
 				}
-				if($self->CODING_SPLICE_REGION_SCORE > $score &&
+				if($CODING_SPLICE_REGION_SCORE > $score &&
 					$g->hasClassification($self->getSpliceRegionClass) && $g->hasClassification($self->getCDSClass) &&
 					$cds->hasClassification($self->getSpliceRegionVariantClass)){
 					# splice region change in CDS
-						$score = $self->CODING_SPLICE_REGION_SCORE;
+						$score = $CODING_SPLICE_REGION_SCORE;
 				}
-        if($self->FIVEPRIME_UTR_ESS_SPLICE_SCORE > $score &&
+        if($FIVEPRIME_UTR_ESS_SPLICE_SCORE > $score &&
 					$g->hasClassification($self->getEssentialSpliceSiteClass) && $g->hasClassification($self->get5PrimeUtrClass) &&
 					$mrna->hasClassification($self->getEssentialSpliceSiteVariantClass) && $mrna->hasClassification($self->get5PrimeUtrVariantClass)){
             # essential splice change in 5' UTR, the splice site is probably directly before to the start codon
-            $score = $self->FIVEPRIME_UTR_ESS_SPLICE_SCORE;
+            $score = $FIVEPRIME_UTR_ESS_SPLICE_SCORE;
         }
-        if($self->THREEPRIME_UTR_ESS_SPLICE_SCORE > $score &&
+        if($THREEPRIME_UTR_ESS_SPLICE_SCORE > $score &&
 					$g->hasClassification($self->getEssentialSpliceSiteClass) && $g->hasClassification($self->get3PrimeUtrClass) &&
 					$mrna->hasClassification($self->getEssentialSpliceSiteVariantClass) && $mrna->hasClassification($self->get3PrimeUtrVariantClass)){
 						# essential splice change in 3' UTR, the splice site is probably directly after to the stop codon
-						$score = $self->THREEPRIME_UTR_ESS_SPLICE_SCORE;
+						$score = $THREEPRIME_UTR_ESS_SPLICE_SCORE;
 				}
-        if($self->FIVEPRIME_UTR_SPLICE_REGION_SCORE > $score &&
+        if($FIVEPRIME_UTR_SPLICE_REGION_SCORE > $score &&
 					$g->hasClassification($self->getSpliceRegionClass) && $g->hasClassification($self->get5PrimeUtrClass) &&
 					$mrna->hasClassification($self->getSpliceRegionVariantClass) && $mrna->hasClassification($self->get5PrimeUtrVariantClass)){
 						# splice region change in 5' UTR, the splice site is probably directly before to the start codon
-						$score = $self->FIVEPRIME_UTR_SPLICE_REGION_SCORE;
+						$score = $FIVEPRIME_UTR_SPLICE_REGION_SCORE;
 				}
-				if($self->THREEPRIME_UTR_SPLICE_REGION_SCORE > $score &&
+				if($THREEPRIME_UTR_SPLICE_REGION_SCORE > $score &&
 					$g->hasClassification($self->getSpliceRegionClass) && $g->hasClassification($self->get3PrimeUtrClass) &&
 					$mrna->hasClassification($self->getSpliceRegionVariantClass) && $mrna->hasClassification($self->get3PrimeUtrVariantClass)){
 						# splice region change in 3' UTR, the splice site is probably directly after to the stop codon
-						$score = $self->THREEPRIME_UTR_SPLICE_REGION_SCORE;
+						$score = $THREEPRIME_UTR_SPLICE_REGION_SCORE;
 				}
 			} elsif(defined($mrna)) {
 				# cDNA annotation
-				if($self->START_GAINED_SCORE > $score &&
+				if($START_GAINED_SCORE > $score &&
 					$g->hasClassification($self->getExonClass) && $g->hasClassification($self->get5PrimeUtrClass) &&
 					$mrna->hasClassification($self->getPrematureStartGainedVariantClass)){
 						# new start codon created in the 5' UTR
-						$score = $self->START_GAINED_SCORE;
+						$score = $START_GAINED_SCORE;
 				}
-				if($self->FIVEPRIME_UTR_ESS_SPLICE_SCORE > $score &&
+				if($FIVEPRIME_UTR_ESS_SPLICE_SCORE > $score &&
 					$g->hasClassification($self->getEssentialSpliceSiteClass) && $g->hasClassification($self->get5PrimeUtrClass) &&
 					$mrna->hasClassification($self->getEssentialSpliceSiteVariantClass) && $mrna->hasClassification($self->get5PrimeUtrVariantClass)){
 						# essential splice change in 5' UTR
-						$score = $self->FIVEPRIME_UTR_ESS_SPLICE_SCORE;
+						$score = $FIVEPRIME_UTR_ESS_SPLICE_SCORE;
 				}
-				if($self->THREEPRIME_UTR_ESS_SPLICE_SCORE > $score &&
+				if($THREEPRIME_UTR_ESS_SPLICE_SCORE > $score &&
 					$g->hasClassification($self->getEssentialSpliceSiteClass) && $g->hasClassification($self->get3PrimeUtrClass) &&
 					$mrna->hasClassification($self->getEssentialSpliceSiteVariantClass) && $mrna->hasClassification($self->get3PrimeUtrVariantClass)){
 						# essential splice change in 3' UTR
-						$score = $self->THREEPRIME_UTR_ESS_SPLICE_SCORE;
+						$score = $THREEPRIME_UTR_ESS_SPLICE_SCORE;
 				}
-				if($self->THREEPRIME_UTR_SCORE > $score &&
+				if($THREEPRIME_UTR_SCORE > $score &&
 					$g->hasClassification($self->getExonClass) && $g->hasClassification($self->get3PrimeUtrClass) &&
 					$mrna->hasClassification($self->get3PrimeUtrVariantClass)){
 						# change in 3' UTR exon
-						$score = $self->THREEPRIME_UTR_SCORE;
+						$score = $THREEPRIME_UTR_SCORE;
 				}
-				if($self->FIVEPRIME_UTR_SCORE > $score &&
+				if($FIVEPRIME_UTR_SCORE > $score &&
 					$g->hasClassification($self->getExonClass) && $g->hasClassification($self->get5PrimeUtrClass) &&
 					$mrna->hasClassification($self->get5PrimeUtrVariantClass)){
 						# change in 5' UTR exon
-						$score = $self->FIVEPRIME_UTR_SCORE;
+						$score = $FIVEPRIME_UTR_SCORE;
 				}
-				if($self->FIVEPRIME_UTR_SPLICE_REGION_SCORE > $score &&
+				if($FIVEPRIME_UTR_SPLICE_REGION_SCORE > $score &&
 					$g->hasClassification($self->getSpliceRegionClass) && $g->hasClassification($self->get5PrimeUtrClass) &&
 					$mrna->hasClassification($self->getSpliceRegionVariantClass) && $mrna->hasClassification($self->get5PrimeUtrVariantClass)){
 						# splice region change in 5' UTR
-						$score = $self->FIVEPRIME_UTR_SPLICE_REGION_SCORE;
+						$score = $FIVEPRIME_UTR_SPLICE_REGION_SCORE;
 				}
-				if($self->THREEPRIME_UTR_SPLICE_REGION_SCORE > $score &&
+				if($THREEPRIME_UTR_SPLICE_REGION_SCORE > $score &&
 					$g->hasClassification($self->getSpliceRegionClass) && $g->hasClassification($self->get3PrimeUtrClass) &&
 					$mrna->hasClassification($self->getSpliceRegionVariantClass) && $mrna->hasClassification($self->get3PrimeUtrVariantClass)){
 						# splice region change in 3' UTR
-						$score = $self->THREEPRIME_UTR_SPLICE_REGION_SCORE;
+						$score = $THREEPRIME_UTR_SPLICE_REGION_SCORE;
 				}
-				if($self->COMPLEX_IN_MRNA_SCORE > $score &&
+				if($COMPLEX_IN_MRNA_SCORE > $score &&
 					$g->hasClassification($self->getCDSClass) &&
 					$mrna->hasClassification($self->getComplexChangeVariantClass)){
 					# complex transcript consequence involving only UTR (no CDS)
 						if($g->hasClassification($self->getEssentialSpliceSiteClass) && $g->hasClassification($self->getExonClass) && $g->hasClassification($self->get5PrimeUtrClass)){
 							# essential splice change in 5' UTR
-							$score = $self->FIVEPRIME_UTR_ESS_SPLICE_SCORE;
+							$score = $FIVEPRIME_UTR_ESS_SPLICE_SCORE;
 						} elsif($g->hasClassification($self->getEssentialSpliceSiteClass) && $g->hasClassification($self->getExonClass) && $g->hasClassification($self->get3PrimeUtrClass)){
 							# essential splice change in 3' UTR
-							$score = $self->THREEPRIME_UTR_ESS_SPLICE_SCORE;
+							$score = $THREEPRIME_UTR_ESS_SPLICE_SCORE;
 						} else {
 							# if its none of the above, its just complex in mrna
-							$score = $self->COMPLEX_IN_MRNA_SCORE;
+							$score = $COMPLEX_IN_MRNA_SCORE;
 						}
 				}
-				if($self->INTRONIC_SCORE > $score &&
+				if($INTRONIC_SCORE > $score &&
 					$g->hasClassification($self->getIntronClass) &&
 					$mrna->hasClassification($self->getIntronVariantClass)){
 						# intronic change
-						$score = $self->INTRONIC_SCORE;
+						$score = $INTRONIC_SCORE;
 				}
-				if($self->UPSTREAM_SCORE > $score &&
+				if($UPSTREAM_SCORE > $score &&
 					($mrna->hasClassification($self->get2KBUpStreamVariantClass) || $mrna->hasClassification($self->get5KBUpStreamVariantClass))){
 						# upstream of transcript
-						$score = $self->UPSTREAM_SCORE;
+						$score = $UPSTREAM_SCORE;
 				}
-				if($self->DOWNSTREAM_SCORE > $score &&
+				if($DOWNSTREAM_SCORE > $score &&
 					($mrna->hasClassification($self->get500BPDownStreamVariantClass) || $mrna->hasClassification($self->get5KBDownStreamVariantClass))){
 						# downstream of transcript
-						$score = $self->DOWNSTREAM_SCORE;
+						$score = $DOWNSTREAM_SCORE;
 				}
 			}
 
 		} else {
 			# non-coding transcript
-			if($self->COMPLETE_NONCODING_TRANSCRIPT_LOSS_SCORE > $score &&
+			if($COMPLETE_NONCODING_TRANSCRIPT_LOSS_SCORE > $score &&
 				$mrna->getMinPos() == 1 && $mrna->getMaxPos() == $mrna->getSequenceLength()){
 				# if marked as a variant, start = 1 and end = sequence length the transcript is gone.
-				$score = $self->COMPLETE_NONCODING_TRANSCRIPT_LOSS_SCORE;
+				$score = $COMPLETE_NONCODING_TRANSCRIPT_LOSS_SCORE;
 			}
-			if($self->NONCODING_GENE_ESS_SPLICE_SCORE > $score &&
+			if($NONCODING_GENE_ESS_SPLICE_SCORE > $score &&
 				$g->hasClassification($self->getEssentialSpliceSiteClass) &&
 				$mrna->hasClassification($self->getEssentialSpliceSiteVariantClass)){
 					# essential splice change
-					$score = $self->NONCODING_GENE_ESS_SPLICE_SCORE;
+					$score = $NONCODING_GENE_ESS_SPLICE_SCORE;
 			}
-			if($self->NONCODING_GENE_SPLICE_REGION_SCORE > $score &&
+			if($NONCODING_GENE_SPLICE_REGION_SCORE > $score &&
 				$g->hasClassification($self->getSpliceRegionClass) &&
 				$mrna->hasClassification($self->getSpliceRegionVariantClass)){
 					# splice region change
-					$score = $self->NONCODING_GENE_SPLICE_REGION_SCORE;
+					$score = $NONCODING_GENE_SPLICE_REGION_SCORE;
 			}
 
-			if($self->COMPLEX_IN_MRNA_SCORE > $score && $mrna->hasClassification($self->getComplexChangeVariantClass)){
+			if($COMPLEX_IN_MRNA_SCORE > $score && $mrna->hasClassification($self->getComplexChangeVariantClass)){
 				# complex transcript consequence
 				if($g->hasClassification($self->getEssentialSpliceSiteClass) && $g->hasClassification($self->getExonClass)){
 					# essential splice change
-					$score = $self->NONCODING_GENE_ESS_SPLICE_SCORE;
+					$score = $NONCODING_GENE_ESS_SPLICE_SCORE;
 				} else {
 					# if its not ess splice, its just complex (probably straddles transcript boundary)
-					$score = $self->COMPLEX_IN_MRNA_SCORE;
+					$score = $COMPLEX_IN_MRNA_SCORE;
 				}
 			}
-			if($self->NONCODING_GENE_SCORE > $score &&
+			if($NONCODING_GENE_SCORE > $score &&
 				$g->hasClassification($self->getExonClass) &&
 				$mrna->hasClassification($self->getNonCodingTranscriptVariantClass)){
 					# exonic change
-					$score = $self->NONCODING_GENE_SCORE;
+					$score = $NONCODING_GENE_SCORE;
 			}
-			if($self->INTRONIC_SCORE > $score &&
+			if($INTRONIC_SCORE > $score &&
 				$g->hasClassification($self->getIntronClass) &&
 				$mrna->hasClassification($self->getIntronVariantClass)){
 					# intronic change
-					$score = $self->INTRONIC_SCORE;
+					$score = $INTRONIC_SCORE;
 			}
-			if($self->UPSTREAM_SCORE > $score &&
+			if($UPSTREAM_SCORE > $score &&
 				($mrna->hasClassification($self->get2KBUpStreamVariantClass) || $mrna->hasClassification($self->get5KBUpStreamVariantClass))){
 					# upstream of transcript
-					$score = $self->UPSTREAM_SCORE;
+					$score = $UPSTREAM_SCORE;
 			}
-			if($self->DOWNSTREAM_SCORE > $score &&
+			if($DOWNSTREAM_SCORE > $score &&
 				($mrna->hasClassification($self->get500BPDownStreamVariantClass) || $mrna->hasClassification($self->get5KBDownStreamVariantClass))){
 					# downstream of transcript
-					$score = $self->DOWNSTREAM_SCORE;
+					$score = $DOWNSTREAM_SCORE;
 			}
 		}
 
diff --git a/lib/Sanger/CGP/Vagrent/Data/Annotation.pm b/lib/Sanger/CGP/Vagrent/Data/Annotation.pm
index c02371c..ef7a008 100644
--- a/lib/Sanger/CGP/Vagrent/Data/Annotation.pm
+++ b/lib/Sanger/CGP/Vagrent/Data/Annotation.pm
@@ -2,21 +2,21 @@ package Sanger::CGP::Vagrent::Data::Annotation;
 
 ##########LICENCE##########
 # Copyright (c) 2014 Genome Research Ltd.
-# 
+#
 # Author: Cancer Genome Project cgpit@sanger.ac.uk
-# 
+#
 # This file is part of VAGrENT.
-# 
+#
 # VAGrENT is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free
 # Software Foundation; either version 3 of the License, or (at your option) any
 # later version.
-# 
+#
 # This program is distributed in the hope that it will be useful, but WITHOUT
 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 # FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
 # details.
-# 
+#
 # You should have received a copy of the GNU Affero General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 ##########LICENCE##########
@@ -26,38 +26,39 @@ use strict;
 use Data::Dumper;
 use List::Util qw(first);
 use Carp;
+use Const::Fast qw(const);
 
 use Sanger::CGP::Vagrent qw($VERSION);
 use base qw(Sanger::CGP::Vagrent);
 
-1;
-
 # sequence context constant values
 
-use constant CDS_ANNOTATION_CONTEXT => 'CDS';
-use constant MRNA_ANNOTATION_CONTEXT => 'mRNA';
-use constant PROTEIN_ANNOTATION_CONTEXT => 'Protein';
+const my $CDS_ANNOTATION_CONTEXT => 'CDS';
+const my $MRNA_ANNOTATION_CONTEXT => 'mRNA';
+const my $PROTEIN_ANNOTATION_CONTEXT => 'Protein';
 
-use constant ALL_ANNOTATION_CONTEXT => (CDS_ANNOTATION_CONTEXT,MRNA_ANNOTATION_CONTEXT,PROTEIN_ANNOTATION_CONTEXT);
+const my @ALL_ANNOTATION_CONTEXT => ($CDS_ANNOTATION_CONTEXT,$MRNA_ANNOTATION_CONTEXT,$PROTEIN_ANNOTATION_CONTEXT);
 
 # variation type constant values
 
-use constant SUBSTITUTION_ANNOTATION_TYPE => 'Substitution';
-use constant DELETION_ANNOTATION_TYPE => 'Deletion';
-use constant INSERTION_ANNOTATION_TYPE => 'Insertion';
-use constant COMPLEX_ANNOTATION_TYPE => 'Complex';
-use constant FRAMESHIFT_ANNOTATION_TYPE => 'FrameShift';
-use constant UNKNOWN_ANNOTATION_TYPE => 'Unknown';
+const my $SUBSTITUTION_ANNOTATION_TYPE => 'Substitution';
+const my $DELETION_ANNOTATION_TYPE => 'Deletion';
+const my $INSERTION_ANNOTATION_TYPE => 'Insertion';
+const my $COMPLEX_ANNOTATION_TYPE => 'Complex';
+const my $FRAMESHIFT_ANNOTATION_TYPE => 'FrameShift';
+const my $UNKNOWN_ANNOTATION_TYPE => 'Unknown';
 
-use constant ALL_ANNOTATION_TYPES => (COMPLEX_ANNOTATION_TYPE,FRAMESHIFT_ANNOTATION_TYPE,INSERTION_ANNOTATION_TYPE,DELETION_ANNOTATION_TYPE,SUBSTITUTION_ANNOTATION_TYPE,UNKNOWN_ANNOTATION_TYPE);
+const my @ALL_ANNOTATION_TYPES => ($COMPLEX_ANNOTATION_TYPE,$FRAMESHIFT_ANNOTATION_TYPE,$INSERTION_ANNOTATION_TYPE,$DELETION_ANNOTATION_TYPE,$SUBSTITUTION_ANNOTATION_TYPE,$UNKNOWN_ANNOTATION_TYPE);
 
 # variation subtype constant values for location data description
 
-use constant POSITION_KNOWN_SUBTYPE => 'POS-KNOWN';
-use constant POSITION_OFFSET_SUBTYPE => 'POS-OFFSET';
-use constant POSITION_OFF_SEQUENCE_SUBTYPE => 'POS-OFFSEQ';
+const my $POSITION_KNOWN_SUBTYPE => 'POS-KNOWN';
+const my $POSITION_OFFSET_SUBTYPE => 'POS-OFFSET';
+const my $POSITION_OFF_SEQUENCE_SUBTYPE => 'POS-OFFSEQ';
 
-use constant ALL_ANNOTATION_SUBTYPES => (POSITION_OFF_SEQUENCE_SUBTYPE,POSITION_OFFSET_SUBTYPE,POSITION_KNOWN_SUBTYPE);
+const my @ALL_ANNOTATION_SUBTYPES => ($POSITION_OFF_SEQUENCE_SUBTYPE,$POSITION_OFFSET_SUBTYPE,$POSITION_KNOWN_SUBTYPE);
+
+1;
 
 sub new {
   my $proto = shift;
@@ -98,7 +99,7 @@ sub _init {
 			$self->{_description} = $vars{description};
 		} elsif($k eq 'context'){
 			my $good = undef;
-			foreach my $context(Sanger::CGP::Vagrent::Data::Annotation::ALL_ANNOTATION_CONTEXT){
+			foreach my $context(@ALL_ANNOTATION_CONTEXT){
 				if($vars{context} eq $context){
 					$good = $vars{context};
 					last;
@@ -111,7 +112,7 @@ sub _init {
 			}
 		} elsif($k eq 'type'){
 			my $good = undef;
-			foreach my $type(Sanger::CGP::Vagrent::Data::Annotation::ALL_ANNOTATION_TYPES){
+			foreach my $type(@ALL_ANNOTATION_TYPES){
 				if($vars{type} eq $type){
 					$good = $vars{type};
 					last;
@@ -124,7 +125,7 @@ sub _init {
 			}
 		} elsif($k eq 'subtype'){
 			my $good = undef;
-			foreach my $subtype(Sanger::CGP::Vagrent::Data::Annotation::ALL_ANNOTATION_SUBTYPES){
+			foreach my $subtype(@ALL_ANNOTATION_SUBTYPES){
 				if($vars{subtype} eq $subtype){
 					$good = $vars{subtype};
 					last;
@@ -141,51 +142,51 @@ sub _init {
 }
 
 sub getCDSAnnotationContext {
-	return CDS_ANNOTATION_CONTEXT;
+	return $CDS_ANNOTATION_CONTEXT;
 }
 
 sub getmRNAAnnotationContext {
-	return MRNA_ANNOTATION_CONTEXT;
+	return $MRNA_ANNOTATION_CONTEXT;
 }
 
 sub getProteinAnnotationContext {
-	return PROTEIN_ANNOTATION_CONTEXT;
+	return $PROTEIN_ANNOTATION_CONTEXT;
 }
 
 sub getSubstitutionAnnotationType {
-	return SUBSTITUTION_ANNOTATION_TYPE;
+	return $SUBSTITUTION_ANNOTATION_TYPE;
 }
 
 sub getDeletionAnnotationType {
-	return DELETION_ANNOTATION_TYPE;
+	return $DELETION_ANNOTATION_TYPE;
 }
 
 sub getComplexAnnotationType {
-	return COMPLEX_ANNOTATION_TYPE;
+	return $COMPLEX_ANNOTATION_TYPE;
 }
 
 sub getInsertionAnnotationType {
-	return INSERTION_ANNOTATION_TYPE;
+	return $INSERTION_ANNOTATION_TYPE;
 }
 
 sub getFrameShiftAnnotationType {
-	return FRAMESHIFT_ANNOTATION_TYPE;
+	return $FRAMESHIFT_ANNOTATION_TYPE;
 }
 
 sub getUnknownAnnotationType {
-	return UNKNOWN_ANNOTATION_TYPE;
+	return $UNKNOWN_ANNOTATION_TYPE;
 }
 
 sub getPositionKnownSubtype {
-	return POSITION_KNOWN_SUBTYPE;
+	return $POSITION_KNOWN_SUBTYPE;
 }
 
 sub getPositionOffsetSubtype {
-	return POSITION_OFFSET_SUBTYPE;
+	return $POSITION_OFFSET_SUBTYPE;
 }
 
 sub getPositionOffSequenceSubtype {
-	return POSITION_OFF_SEQUENCE_SUBTYPE;
+	return $POSITION_OFF_SEQUENCE_SUBTYPE;
 }
 
 sub getMinPos {
diff --git a/lib/Sanger/CGP/Vagrent/Data/AnnotationGroup.pm b/lib/Sanger/CGP/Vagrent/Data/AnnotationGroup.pm
index c081f6e..30bda82 100644
--- a/lib/Sanger/CGP/Vagrent/Data/AnnotationGroup.pm
+++ b/lib/Sanger/CGP/Vagrent/Data/AnnotationGroup.pm
@@ -2,21 +2,21 @@ package Sanger::CGP::Vagrent::Data::AnnotationGroup;
 
 ##########LICENCE##########
 # Copyright (c) 2014 Genome Research Ltd.
-# 
+#
 # Author: Cancer Genome Project cgpit@sanger.ac.uk
-# 
+#
 # This file is part of VAGrENT.
-# 
+#
 # VAGrENT is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free
 # Software Foundation; either version 3 of the License, or (at your option) any
 # later version.
-# 
+#
 # This program is distributed in the hope that it will be useful, but WITHOUT
 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 # FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
 # details.
-# 
+#
 # You should have received a copy of the GNU Affero General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 ##########LICENCE##########
@@ -55,7 +55,7 @@ sub _init {
 			$self->{_accession} = $vars{accession};
 		} elsif($k eq 'type'){
 			my $good = undef;
-			foreach my $type(Sanger::CGP::Vagrent::Data::Transcript::ALL_GENE_TYPES){
+			foreach my $type(Sanger::CGP::Vagrent::Data::Transcript->getAllGeneTypes){
 				if($vars{type} eq $type){
 					$good = $vars{type};
 					last;
diff --git a/lib/Sanger/CGP/Vagrent/Data/Transcript.pm b/lib/Sanger/CGP/Vagrent/Data/Transcript.pm
index e06b737..fc7dd62 100644
--- a/lib/Sanger/CGP/Vagrent/Data/Transcript.pm
+++ b/lib/Sanger/CGP/Vagrent/Data/Transcript.pm
@@ -2,21 +2,21 @@ package Sanger::CGP::Vagrent::Data::Transcript;
 
 ##########LICENCE##########
 # Copyright (c) 2014 Genome Research Ltd.
-# 
+#
 # Author: Cancer Genome Project cgpit@sanger.ac.uk
-# 
+#
 # This file is part of VAGrENT.
-# 
+#
 # VAGrENT is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free
 # Software Foundation; either version 3 of the License, or (at your option) any
 # later version.
-# 
+#
 # This program is distributed in the hope that it will be useful, but WITHOUT
 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 # FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
 # details.
-# 
+#
 # You should have received a copy of the GNU Affero General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 ##########LICENCE##########
@@ -27,19 +27,20 @@ use Carp;
 use Data::Dumper;
 use Sanger::CGP::Vagrent qw($VERSION);
 use Sort::Key qw(nkeysort);
+use Const::Fast qw(const);
 
 use base qw(Sanger::CGP::Vagrent);
 
-1;
+const my $PROTEIN_CODING_TYPE => 'ProteinCoding';
+const my $MIRCO_RNA_TYPE => 'miRNA';
+const my $LINC_RNA_TYPE => 'lincRNA';
+const my $SNO_RNA_TYPE => 'snoRNA';
+const my $SN_RNA_TYPE => 'snRNA';
+const my $R_RNA_TYPE => 'rRNA';
 
-use constant PROTEIN_CODING_TYPE => 'ProteinCoding';
-use constant MIRCO_RNA_TYPE => 'miRNA';
-use constant LINC_RNA_TYPE => 'lincRNA';
-use constant SNO_RNA_TYPE => 'snoRNA';
-use constant SN_RNA_TYPE => 'snRNA';
-use constant R_RNA_TYPE => 'rRNA';
+const my @ALL_GENE_TYPES => ($PROTEIN_CODING_TYPE,$MIRCO_RNA_TYPE,$LINC_RNA_TYPE,$SNO_RNA_TYPE,$SN_RNA_TYPE,$R_RNA_TYPE);
 
-use constant ALL_GENE_TYPES => (PROTEIN_CODING_TYPE,MIRCO_RNA_TYPE,LINC_RNA_TYPE,SNO_RNA_TYPE,SN_RNA_TYPE,R_RNA_TYPE);
+1;
 
 sub new {
   my $proto = shift;
@@ -89,7 +90,7 @@ sub _init {
 		} elsif($k eq 'genetype'){
 			$self->{_genetype} = $vars{genetype};
 			my $good = undef;
-			foreach my $type(Sanger::CGP::Vagrent::Data::Transcript::ALL_GENE_TYPES){
+			foreach my $type(@ALL_GENE_TYPES){
 				if($vars{genetype} eq $type){
 					$good = $vars{genetype};
 					last;
@@ -104,6 +105,10 @@ sub _init {
 	}
 }
 
+sub getAllGeneTypes {
+  return @ALL_GENE_TYPES;
+}
+
 sub getGeneType {
 	return shift->{_genetype};
 }
@@ -205,7 +210,7 @@ sub getGenomicMaxPos {
 }
 
 sub isProteinCoding {
-	if(shift->getGeneType eq PROTEIN_CODING_TYPE){
+	if(shift->getGeneType eq $PROTEIN_CODING_TYPE){
 		return 1;
 	} else {
 		return 0;
@@ -213,27 +218,27 @@ sub isProteinCoding {
 }
 
 sub getProteinCodingType {
-	return PROTEIN_CODING_TYPE;
+	return $PROTEIN_CODING_TYPE;
 }
 
 sub getMicroRnaType {
-	return MIRCO_RNA_TYPE;
+	return $MIRCO_RNA_TYPE;
 }
 
 sub getLincRnaType {
-	return LINC_RNA_TYPE;
+	return $LINC_RNA_TYPE;
 }
 
 sub getSnoRnaType {
-	return SNO_RNA_TYPE;
+	return $SNO_RNA_TYPE;
 }
 
 sub getSnRnaType {
-	return SN_RNA_TYPE;
+	return $SN_RNA_TYPE;
 }
 
 sub getRRnaType {
-	return R_RNA_TYPE;
+	return $R_RNA_TYPE;
 }
 
 __END__
diff --git a/lib/Sanger/CGP/Vagrent/GenomicRegionDumper/AbstractGenomicRegionDumper.pm b/lib/Sanger/CGP/Vagrent/GenomicRegionDumper/AbstractGenomicRegionDumper.pm
index efca1df..7ce3456 100644
--- a/lib/Sanger/CGP/Vagrent/GenomicRegionDumper/AbstractGenomicRegionDumper.pm
+++ b/lib/Sanger/CGP/Vagrent/GenomicRegionDumper/AbstractGenomicRegionDumper.pm
@@ -2,21 +2,21 @@ package Sanger::CGP::Vagrent::GenomicRegionDumper::AbstractGenomicRegionDumper;
 
 ##########LICENCE##########
 # Copyright (c) 2014 Genome Research Ltd.
-# 
+#
 # Author: Cancer Genome Project cgpit@sanger.ac.uk
-# 
+#
 # This file is part of VAGrENT.
-# 
+#
 # VAGrENT is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free
 # Software Foundation; either version 3 of the License, or (at your option) any
 # later version.
-# 
+#
 # This program is distributed in the hope that it will be useful, but WITHOUT
 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 # FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
 # details.
-# 
+#
 # You should have received a copy of the GNU Affero General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 ##########LICENCE##########
@@ -35,8 +35,6 @@ my $log = Log::Log4perl->get_logger(__PACKAGE__);
 
 1;
 
-use constant REGION_DUMP_SUB_WINDOW => 99999;
-
 sub _init {
 	my $self = shift;
 	my %vars = @_;
diff --git a/lib/Sanger/CGP/Vagrent/GenomicRegionDumper/SubstitutionGenomicRegionDumper.pm b/lib/Sanger/CGP/Vagrent/GenomicRegionDumper/SubstitutionGenomicRegionDumper.pm
index ab6ffeb..5d788aa 100644
--- a/lib/Sanger/CGP/Vagrent/GenomicRegionDumper/SubstitutionGenomicRegionDumper.pm
+++ b/lib/Sanger/CGP/Vagrent/GenomicRegionDumper/SubstitutionGenomicRegionDumper.pm
@@ -2,21 +2,21 @@ package Sanger::CGP::Vagrent::GenomicRegionDumper::SubstitutionGenomicRegionDump
 
 ##########LICENCE##########
 # Copyright (c) 2014 Genome Research Ltd.
-# 
+#
 # Author: Cancer Genome Project cgpit@sanger.ac.uk
-# 
+#
 # This file is part of VAGrENT.
-# 
+#
 # VAGrENT is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free
 # Software Foundation; either version 3 of the License, or (at your option) any
 # later version.
-# 
+#
 # This program is distributed in the hope that it will be useful, but WITHOUT
 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 # FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
 # details.
-# 
+#
 # You should have received a copy of the GNU Affero General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 ##########LICENCE##########
@@ -182,7 +182,7 @@ sub _convertExonToAnnotatableCodingExonicRegions {
 }
 
 sub _getLowestContinuousAcceptorEssentialSpliceSiteOffset {
-	my @offsets = sort {$b <=> $a} Sanger::CGP::Vagrent::Annotators::AbstractAnnotator::CONSENSUS_SPLICE_OFFSETS;
+	my @offsets = sort {$b <=> $a} Sanger::CGP::Vagrent::Annotators::AbstractAnnotator->getConsensusSpliceOffsets;
 	my $out = 0;
 	foreach my $o(@offsets){
 		next if $o > 0;
@@ -196,7 +196,7 @@ sub _getLowestContinuousAcceptorEssentialSpliceSiteOffset {
 }
 
 sub _getHighestContinuousDonorEssentialSpliceSiteOffset {
-	my @offsets = sort {$a <=> $b} Sanger::CGP::Vagrent::Annotators::AbstractAnnotator::CONSENSUS_SPLICE_OFFSETS;
+	my @offsets = sort {$a <=> $b} Sanger::CGP::Vagrent::Annotators::AbstractAnnotator->getConsensusSpliceOffsets;
 	my $out = 0;
 	foreach my $o(@offsets){
 		next if $o < 0;
@@ -210,7 +210,7 @@ sub _getHighestContinuousDonorEssentialSpliceSiteOffset {
 }
 
 sub _getIsolatedDonorEssentialSpliceSiteOffset {
-	my ($out) = sort {$b <=> $a} Sanger::CGP::Vagrent::Annotators::AbstractAnnotator::CONSENSUS_SPLICE_OFFSETS;
+	my ($out) = sort {$b <=> $a} Sanger::CGP::Vagrent::Annotators::AbstractAnnotator->getConsensusSpliceOffsets;
 	return $out;
 }
 
diff --git a/lib/Sanger/CGP/Vagrent/IO/Writer/SingleLineCsvFileWriter.pm b/lib/Sanger/CGP/Vagrent/IO/Writer/SingleLineCsvFileWriter.pm
index c53bc6e..7bf1c92 100644
--- a/lib/Sanger/CGP/Vagrent/IO/Writer/SingleLineCsvFileWriter.pm
+++ b/lib/Sanger/CGP/Vagrent/IO/Writer/SingleLineCsvFileWriter.pm
@@ -2,21 +2,21 @@ package Sanger::CGP::Vagrent::IO::Writer::SingleLineCsvFileWriter;
 
 ##########LICENCE##########
 # Copyright (c) 2014 Genome Research Ltd.
-# 
+#
 # Author: Cancer Genome Project cgpit@sanger.ac.uk
-# 
+#
 # This file is part of VAGrENT.
-# 
+#
 # VAGrENT is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free
 # Software Foundation; either version 3 of the License, or (at your option) any
 # later version.
-# 
+#
 # This program is distributed in the hope that it will be useful, but WITHOUT
 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 # FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
 # details.
-# 
+#
 # You should have received a copy of the GNU Affero General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 ##########LICENCE##########
diff --git a/lib/Sanger/CGP/Vagrent/Ontology/SequenceOntologyClassifier.pm b/lib/Sanger/CGP/Vagrent/Ontology/SequenceOntologyClassifier.pm
index 9562655..16dc49b 100644
--- a/lib/Sanger/CGP/Vagrent/Ontology/SequenceOntologyClassifier.pm
+++ b/lib/Sanger/CGP/Vagrent/Ontology/SequenceOntologyClassifier.pm
@@ -14,21 +14,21 @@ package Sanger::CGP::Vagrent::Ontology::SequenceOntologyClassifier;
 
 ##########LICENCE##########
 # Copyright (c) 2014 Genome Research Ltd.
-# 
+#
 # Author: Cancer Genome Project cgpit@sanger.ac.uk
-# 
+#
 # This file is part of VAGrENT.
-# 
+#
 # VAGrENT is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free
 # Software Foundation; either version 3 of the License, or (at your option) any
 # later version.
-# 
+#
 # This program is distributed in the hope that it will be useful, but WITHOUT
 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 # FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
 # details.
-# 
+#
 # You should have received a copy of the GNU Affero General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 ##########LICENCE##########
@@ -129,9 +129,9 @@ sub _loadOntologySummaryIni {
 
 sub getOntologySummary {
   my ($self,$anno) = @_;
-  my $mrna = $anno->getAnnotationByContext(Sanger::CGP::Vagrent::Data::Annotation::getmRNAAnnotationContext);
-	my $cds = $anno->getAnnotationByContext(Sanger::CGP::Vagrent::Data::Annotation::getCDSAnnotationContext);
-	my $prot = $anno->getAnnotationByContext(Sanger::CGP::Vagrent::Data::Annotation::getProteinAnnotationContext);
+  my $mrna = $anno->getAnnotationByContext(Sanger::CGP::Vagrent::Data::Annotation::getmRNAAnnotationContext());
+	my $cds = $anno->getAnnotationByContext(Sanger::CGP::Vagrent::Data::Annotation::getCDSAnnotationContext());
+	my $prot = $anno->getAnnotationByContext(Sanger::CGP::Vagrent::Data::Annotation::getProteinAnnotationContext());
   my @class = $anno->getClassifications;
   my @terms;
   foreach my $a($anno,$mrna,$cds,$prot){
diff --git a/prerelease.sh b/prerelease.sh
index 80dca4c..e18b993 100755
--- a/prerelease.sh
+++ b/prerelease.sh
@@ -2,21 +2,21 @@
 
 ##########LICENCE##########
 # Copyright (c) 2014 Genome Research Ltd.
-# 
+#
 # Author: Cancer Genome Project cgpit@sanger.ac.uk
-# 
+#
 # This file is part of VAGrENT.
-# 
+#
 # VAGrENT is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free
 # Software Foundation; either version 3 of the License, or (at your option) any
 # later version.
-# 
+#
 # This program is distributed in the hope that it will be useful, but WITHOUT
 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 # FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
 # details.
-# 
+#
 # You should have received a copy of the GNU Affero General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 ##########LICENCE##########
@@ -46,12 +46,11 @@ echo '########## Running perl tests ##########'
 export HARNESS_PERL_SWITCHES=-MDevel::Cover=-db,reports,-ignore,'t/.*\.t,/Bio',
 rm -rf docs
 mkdir -p docs/reports_text
-set -o pipefail;
-prove -w --nocolor -I ./lib | sed 's/^/  /' # indent output of prove
+prove -w -I lib t
 
 echo '### Generating test/pod coverage reports ###'
 # removed 'condition' from coverage as '||' 'or' doesn't work properly
-cover -coverage branch,subroutine,pod -report_c0 50 -report_c1 85 -report_c2 100 -report html_basic reports -silent > /dev/null
+cover -coverage branch,subroutine,pod -report_c0 50 -report_c1 85 -report_c2 100 -report html_basic reports -silent
 cover -coverage branch,subroutine,pod -report text reports -silent > docs/reports_text/coverage.txt
 rm -rf reports/structure reports/digests reports/cover.13 reports/runs
 cp reports/coverage.html reports/index.html
diff --git a/setup.sh b/setup.sh
index e72dc81..72b92dc 100755
--- a/setup.sh
+++ b/setup.sh
@@ -82,10 +82,8 @@ cd $INIT_DIR
 
 # make sure that build is self contained
 unset PERL5LIB
-ARCHNAME=`perl -e 'use Config; print $Config{archname};'`
 PERLROOT=$INST_PATH/lib/perl5
-PERLARCH=$PERLROOT/$ARCHNAME
-export PERL5LIB="$PERLROOT:$PERLARCH"
+export PERL5LIB="$PERLROOT"
 
 # log information about this system
 (
@@ -127,18 +125,18 @@ if [ -e $SETUP_DIR/$CURR_TOOL.success ]; then
   echo -n " previously installed ..."
 else
   (
-    set -ex
+    set -x
     get_distro $CURR_TOOL $CURR_SOURCE
-    cd $SETUP_DIR/$CURR_TOOL
-    make -j$CPU
-    cp tabix $INST_PATH/bin/.
-    cp bgzip $INST_PATH/bin/.
-    cd perl
-    patch Makefile.PL < $INIT_DIR/patches/tabixPerlLinker.diff
-    perl Makefile.PL INSTALL_BASE=$INST_PATH
-    make
-    make test
-    make install
+    cd $SETUP_DIR/$CURR_TOOL && \
+    make -j$CPU && \
+    cp tabix $INST_PATH/bin/. && \
+    cp bgzip $INST_PATH/bin/. && \
+    cd perl && \
+    patch Makefile.PL < $INIT_DIR/patches/tabixPerlLinker.diff && \
+    perl Makefile.PL INSTALL_BASE=$INST_PATH && \
+    make && \
+    make test && \
+    make install && \
     touch $SETUP_DIR/$CURR_TOOL.success
   ) >>$INIT_DIR/setup.log 2>&1
 fi
@@ -153,12 +151,12 @@ if [ -e $SETUP_DIR/$CURR_TOOL.success ]; then
   echo -n " previously installed ..."
 else
   (
-    set -ex
+    set -x
     get_distro $CURR_TOOL $CURR_SOURCE
-    cd $SETUP_DIR/$CURR_TOOL
-    patch Makefile < $INIT_DIR/patches/vcfToolsInstLocs.diff
-    patch perl/Vcf.pm < $INIT_DIR/patches/vcfToolsProcessLog.diff
-    make -j$CPU PREFIX=$INST_PATH
+    cd $SETUP_DIR/$CURR_TOOL && \
+    patch Makefile < $INIT_DIR/patches/vcfToolsInstLocs.diff && \
+    patch perl/Vcf.pm < $INIT_DIR/patches/vcfToolsProcessLog.diff && \
+    make -j$CPU PREFIX=$INST_PATH && \
     touch $SETUP_DIR/$CURR_TOOL.success
   ) >>$INIT_DIR/setup.log 2>&1
 fi
@@ -177,7 +175,7 @@ else
     get_distro "samtools" $SOURCE_SAMTOOLS
     perl -i -pe 's/^CFLAGS=\s*/CFLAGS=-fPIC / unless /\b-fPIC\b/' samtools/Makefile
   fi
-  make -C samtools -j$CPU
+  make -C samtools -j$CPU && \
   touch $SETUP_DIR/samtools.success
   )>>$INIT_DIR/setup.log 2>&1
 fi
@@ -204,11 +202,10 @@ done_message "" "Failed during installation of core dependencies."
 
 echo -n "Installing vagrent ..."
 (
-  set -e
-  cd $INIT_DIR
-  perl Makefile.PL INSTALL_BASE=$INST_PATH
-  make
-  make test
+  cd $INIT_DIR && \
+  perl Makefile.PL INSTALL_BASE=$INST_PATH && \
+  make && \
+  make test && \
   make install
 ) >>$INIT_DIR/setup.log 2>&1
 done_message "" "vagrent install failed."
@@ -216,13 +213,10 @@ done_message "" "vagrent install failed."
 # cleanup all junk
 rm -rf $SETUP_DIR
 
-
-
 echo
 echo
 echo "Please add the following to beginning of path:"
 echo "  $INST_PATH/bin"
 echo "Please add the following to beginning of PERL5LIB:"
 echo "  $PERLROOT"
-echo "  $PERLARCH"
 echo
diff --git a/t/1_pm_compile.t b/t/1_pm_compile.t
index a726ea0..3adef27 100644
--- a/t/1_pm_compile.t
+++ b/t/1_pm_compile.t
@@ -1,20 +1,20 @@
 ##########LICENCE##########
 # Copyright (c) 2014 Genome Research Ltd.
-# 
+#
 # Author: Cancer Genome Project cgpit@sanger.ac.uk
-# 
+#
 # This file is part of VAGrENT.
-# 
+#
 # VAGrENT is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free
 # Software Foundation; either version 3 of the License, or (at your option) any
 # later version.
-# 
+#
 # This program is distributed in the hope that it will be useful, but WITHOUT
 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 # FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
 # details.
-# 
+#
 # You should have received a copy of the GNU Affero General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 ##########LICENCE##########
@@ -28,6 +28,7 @@ use List::Util qw(first);
 use File::Find;
 use Cwd;
 use Try::Tiny qw(try finally);
+use Capture::Tiny qw(capture);
 use File::Spec;
 use Const::Fast qw(const);
 
@@ -46,28 +47,25 @@ const my @NEW_SKIP => qw( Sanger::CGP::Vagrent::Data::AbstractGenomicPosition
                           Sanger::CGP::Vagrent::Data::Substitution
                           Sanger::CGP::Vagrent::TranscriptSource::AbstractTranscriptSource );
 
-#warn "\n###################### WARNING #######################\n# 1_pm_compile.pl DISABLED until vagrent core update #\n###################### WARNING #######################\n\n";
-#ok(1,'Here to show willing');
-#done_testing();
-#exit;
-
 my $init_cwd = getcwd;
 
+my $bail_count;
+
 my @modules;
 try {
   chdir($lib_path);
-  find({ wanted => \&build_module_set, no_chdir => 1 }, './');
+  find({ wanted => \&compile_modules, no_chdir => 1 }, './');
 } finally {
   chdir $init_cwd;
   die "The try block died with: @_\n" if(@_);
 };
 
-for my $mod(@modules) {
-  next if( first {$mod eq $_} @USE_SKIP );
-  use_ok($mod) or BAIL_OUT("Unable to 'use' module $mod");
+if($bail_count) {
+  BAIL_OUT("Modules failed to compile, see above errors");
 }
 
 for my $mod(@modules) {
+  use_ok($mod);
   ok($mod->VERSION, "Check version inheritance exists ($mod)");
   if($mod->can('new')) { # only try new on things that have new defined
     new_ok($mod) unless( first {$mod eq $_} (@USE_SKIP, @NEW_SKIP) );
@@ -76,9 +74,19 @@ for my $mod(@modules) {
 
 done_testing();
 
-sub build_module_set {
+sub compile_modules {
+#return unless($_ =~ m/SequenceOntologyClassifier.pm/);
   if($_ =~ m/\.pm$/) {
+    my ($stdout, $stderr, $exit) = capture { system("$^X -c $_"); };
+    warn "\n$stderr" if($exit);
+    is($exit, 0, "Module fails to compile cleanly: $_");
 
+    $bail_count += $exit;
+  }
+}
+
+sub build_module_set {
+  if($_ =~ m/\.pm$/) {
     my ($dir_str,$file) = (File::Spec->splitpath( $_ ))[1,2];
     $file =~ s/\.pm$//;
     my @dirs = File::Spec->splitdir( $dir_str );