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package Bio::VertRes::Config::Pipelines::Ssaha2Mapping; |
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# ABSTRACT: Base class for the Ssaha2 mapper |
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use Moose; |
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extends 'Bio::VertRes::Config::Pipelines::Mapping'; |
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has 'slx_mapper' => ( is => 'ro', isa => 'Str', default => 'ssaha' ); |
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has 'slx_mapper_exe' => ( is => 'ro', isa => 'Str', default => '/software/pathogen/external/apps/usr/local/ssaha2/ssaha2' ); |
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override 'to_hash' => sub { |
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my ($self) = @_; |
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my $output_hash = super(); |
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$output_hash->{data}{'454_mapper'} = $self->slx_mapper; |
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$output_hash->{data}{'454_mapper_exe'} = $self->slx_mapper_exe; |
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return $output_hash; |
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}; |
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__PACKAGE__->meta->make_immutable; |
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no Moose; |
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1; |
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__END__ |
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=pod |
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=head1 NAME |
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Bio::VertRes::Config::Pipelines::Ssaha2Mapping - Base class for the Ssaha2 mapper |
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=head1 VERSION |
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version 1.133090 |
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=head1 SYNOPSIS |
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Base class for the Ssaha2 mapper |
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use Bio::VertRes::Config::Pipelines::Ssaha2Mapping; |
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my $pipeline = Bio::VertRes::Config::Pipelines::Ssaha2Mapping->new( |
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database => 'abc', |
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reference => 'Staphylococcus_aureus_subsp_aureus_ABC_v1', |
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limits => { |
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project => ['ABC study'], |
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species => ['EFG'] |
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}, |
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); |
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$pipeline->to_hash(); |
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=head1 AUTHOR |
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Andrew J. Page <ap13@sanger.ac.uk> |
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=head1 COPYRIGHT AND LICENSE |
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This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. |
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This is free software, licensed under: |
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The GNU General Public License, Version 3, June 2007 |
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=cut |