| line |
stmt |
bran |
cond |
sub |
pod |
time |
code |
|
1
|
|
|
|
|
|
|
package Bio::VertRes::Config::Pipelines::BwaMapping; |
|
2
|
|
|
|
|
|
|
|
|
3
|
|
|
|
|
|
|
# ABSTRACT: Base class for the BWA mapper |
|
4
|
|
|
|
|
|
|
|
|
5
|
|
|
|
|
|
|
|
|
6
|
3
|
|
|
3
|
|
238574
|
use Moose; |
|
|
0
|
|
|
|
|
|
|
|
|
0
|
|
|
|
|
|
|
|
7
|
|
|
|
|
|
|
extends 'Bio::VertRes::Config::Pipelines::Mapping'; |
|
8
|
|
|
|
|
|
|
|
|
9
|
|
|
|
|
|
|
has 'slx_mapper' => ( is => 'ro', isa => 'Str', default => 'bwa' ); |
|
10
|
|
|
|
|
|
|
has 'slx_mapper_exe' => ( is => 'ro', isa => 'Str', default => '/software/pathogen/external/apps/usr/local/bwa-0.7.5a/bwa' ); |
|
11
|
|
|
|
|
|
|
|
|
12
|
|
|
|
|
|
|
__PACKAGE__->meta->make_immutable; |
|
13
|
|
|
|
|
|
|
no Moose; |
|
14
|
|
|
|
|
|
|
1; |
|
15
|
|
|
|
|
|
|
|
|
16
|
|
|
|
|
|
|
__END__ |
|
17
|
|
|
|
|
|
|
|
|
18
|
|
|
|
|
|
|
=pod |
|
19
|
|
|
|
|
|
|
|
|
20
|
|
|
|
|
|
|
=head1 NAME |
|
21
|
|
|
|
|
|
|
|
|
22
|
|
|
|
|
|
|
Bio::VertRes::Config::Pipelines::BwaMapping - Base class for the BWA mapper |
|
23
|
|
|
|
|
|
|
|
|
24
|
|
|
|
|
|
|
=head1 VERSION |
|
25
|
|
|
|
|
|
|
|
|
26
|
|
|
|
|
|
|
version 1.133090 |
|
27
|
|
|
|
|
|
|
|
|
28
|
|
|
|
|
|
|
=head1 SYNOPSIS |
|
29
|
|
|
|
|
|
|
|
|
30
|
|
|
|
|
|
|
Base class for the BWA mapper |
|
31
|
|
|
|
|
|
|
use Bio::VertRes::Config::Pipelines::BwaMapping; |
|
32
|
|
|
|
|
|
|
|
|
33
|
|
|
|
|
|
|
my $pipeline = Bio::VertRes::Config::Pipelines::BwaMapping->new( |
|
34
|
|
|
|
|
|
|
database => 'abc', |
|
35
|
|
|
|
|
|
|
reference => 'Staphylococcus_aureus_subsp_aureus_ABC_v1', |
|
36
|
|
|
|
|
|
|
limits => { |
|
37
|
|
|
|
|
|
|
project => ['ABC study'], |
|
38
|
|
|
|
|
|
|
species => ['EFG'] |
|
39
|
|
|
|
|
|
|
}, |
|
40
|
|
|
|
|
|
|
|
|
41
|
|
|
|
|
|
|
); |
|
42
|
|
|
|
|
|
|
$pipeline->to_hash(); |
|
43
|
|
|
|
|
|
|
|
|
44
|
|
|
|
|
|
|
=head1 AUTHOR |
|
45
|
|
|
|
|
|
|
|
|
46
|
|
|
|
|
|
|
Andrew J. Page <ap13@sanger.ac.uk> |
|
47
|
|
|
|
|
|
|
|
|
48
|
|
|
|
|
|
|
=head1 COPYRIGHT AND LICENSE |
|
49
|
|
|
|
|
|
|
|
|
50
|
|
|
|
|
|
|
This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. |
|
51
|
|
|
|
|
|
|
|
|
52
|
|
|
|
|
|
|
This is free software, licensed under: |
|
53
|
|
|
|
|
|
|
|
|
54
|
|
|
|
|
|
|
The GNU General Public License, Version 3, June 2007 |
|
55
|
|
|
|
|
|
|
|
|
56
|
|
|
|
|
|
|
=cut |