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