Andrew Page
and 1 contributors

NAME

Bio::VertRes::Config::Pipelines::Mapping - The base class for the mapping pipeline.

VERSION

version 1.133090

SYNOPSIS

The base class for the mapping pipeline. It wont produce useable output on its own, you need to call a sub classed mapper for that. use Bio::VertRes::Config::Pipelines::Mapping;

   my $pipeline = Bio::VertRes::Config::Pipelines::Mapping->new(
     database => 'abc',
     reference => 'Staphylococcus_aureus_subsp_aureus_ABC_v1',
     limits => {
       project => ['ABC study'],
       species => ['EFG']
     },
     slx_mapper => 'bwa',
     slx_mapper_exe => '/path/to/mapper/mapper.exe'

     );
   $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