NAME

Bio::VertRes::Config::Pipelines::SmaltMapping - Base class for the smalt mapper

VERSION

version 1.133090

SYNOPSIS

Base class for the smalt mapper. Can be used on its own as is, or more probably subclassed to provide a standard mapping method for a particular group. use Bio::VertRes::Config::Pipelines::SmaltMapping;

   my $pipeline = Bio::VertRes::Config::Pipelines::SmaltMapping->new(
     database => 'abc',
     reference => 'Staphylococcus_aureus_subsp_aureus_ABC_v1',
     limits => {
       project => ['ABC study'],
       species => ['EFG']
     },
     additional_mapper_params => '-x',
     mapper_index_params => '-s 5'
     );
   $pipeline->to_hash();

AUTHOR

Andrew J. Page <ap13@sanger.ac.uk>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007