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package Sanger::CGP::Vcf::Contig; |
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##########LICENCE########## |
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# Copyright (c) 2014,2015 Genome Research Ltd. |
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# |
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# Author: Jon Hinton <cgpit@sanger.ac.uk> |
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# |
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# This file is part of cgpVcf. |
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# |
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# cgpVcf is free software: you can redistribute it and/or modify it under |
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# the terms of the GNU Affero General Public License as published by the Free |
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# Software Foundation; either version 3 of the License, or (at your option) any |
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# later version. |
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# |
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# This program is distributed in the hope that it will be useful, but WITHOUT |
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# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS |
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# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more |
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# details. |
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# |
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# You should have received a copy of the GNU Affero General Public License |
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# along with this program. If not, see <http://www.gnu.org/licenses/>. |
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# |
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# 1. The usage of a range of years within a copyright statement contained within |
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# this distribution should be interpreted as being equivalent to a list of years |
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# including the first and last year specified and all consecutive years between |
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# them. For example, a copyright statement that reads âCopyright (c) 2005, 2007- |
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# 2009, 2011-2012â should be interpreted as being identical to a statement that |
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# reads âCopyright (c) 2005, 2007, 2008, 2009, 2011, 2012â and a copyright |
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# statement that reads âCopyright (c) 2005-2012â should be interpreted as being |
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# identical to a statement that reads âCopyright (c) 2005, 2006, 2007, 2008, |
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# 2009, 2010, 2011, 2012â." |
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########## LICENCE ########## |
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use Sanger::CGP::Vcf; |
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our $VERSION = Sanger::CGP::Vcf->VERSION; |
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use strict; |
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use Carp qw(croak); |
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use warnings FATAL => 'all'; |
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1; |
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sub new{ |
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my $proto = shift; |
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my (%args) = @_; |
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my $class = ref($proto) || $proto; |
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my $self = { |
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_name => $args{'-name'}, |
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_length => $args{'-length'}, |
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_species => $args{'-species'}, |
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_assembly => $args{'-assembly'}, |
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_checksum => $args{'-checksum'}, |
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}; |
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bless $self, $class; |
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return $self; |
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} |
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sub name{ |
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my($self,$value) = @_; |
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$self->{_name} = $value if defined $value; |
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return $self->{_name}; |
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} |
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sub length{ |
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my($self,$value) = @_; |
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$self->{_length} = $value if defined $value; |
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return $self->{_length}; |
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} |
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sub species{ |
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my($self,$value) = @_; |
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$self->{_species} = $value if defined $value; |
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return $self->{_species}; |
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} |
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sub assembly{ |
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my($self,$value) = @_; |
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$self->{_assembly} = $value if defined $value; |
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return $self->{_assembly}; |
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} |
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sub checksum{ |
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my($self,$value) = @_; |
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$self->{_checksum} = $value if defined $value; |
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return $self->{_checksum}; |
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} |
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sub compare{ |
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my($self,$contig) = @_; |
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croak 'Incorrect input' unless ref $contig eq 'Sanger::CGP::Vcf::Contig'; |
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# check for defined mismatch |
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return 0 if((defined $contig->name ? 1 : 0) != (defined $self->{_name} ? 1 : 0)); |
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return 0 if((defined $contig->length ? 1 : 0) != (defined $self->{_length} ? 1 : 0)); |
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return 0 if((defined $contig->assembly ? 1 : 0) != (defined $self->{_assembly} ? 1 : 0)); |
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return 0 if((defined $contig->species ? 1 : 0) != (defined $self->{_species} ? 1 : 0)); |
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return 0 if((defined $contig->checksum ? 1 : 0) != (defined $self->{_checksum} ? 1 : 0)); |
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return 0 if defined $self->{_name} && $contig->name ne $self->{_name}; |
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return 0 if defined $self->{_length} && $contig->length != $self->{_length}; |
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return 0 if defined $self->{_assembly} && $contig->assembly ne $self->{_assembly}; |
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return 0 if defined $self->{_species} && $contig->species ne $self->{_species}; |
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return 0 if defined $self->{_checksum} && $contig->checksum ne $self->{_checksum}; |
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return 1; |
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# $same = 0 unless $contig->name eq $self->{_name}; |
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# $same = 0 unless $contig->length eq $self->{_length}; |
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# $same = 0 unless $contig->assembly eq $self->{_assembly}; |
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# $same = 0 unless $contig->species eq $self->{_species}; |
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# if(defined ($contig->checksum) && defined ($self->{_checksum})){ |
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# $same = 0 unless $contig->checksum eq $self->{_checksum}; |
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# } |
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# return $same; |
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} |