———package
BioX::Wrapper;
use
Moose;
use
File::Find::Rule;
use
File::Basename;
use
File::Find::Rule;
use
Cwd;
our
$VERSION
=
'1.1'
;
=head2 Wrapper Options
=cut
=head3 indir
A path to your vcf files can be given, and using File::Find::Rule it will recursively search for vcf or vcf.gz
=cut
has
'indir'
=> (
is
=>
'rw'
,
isa
=>
'Str|Undef'
,
required
=> 0,
);
=head3 outdir
Path to write out annotation files. It creates the structure
outdir
--annovar_interim
--annovar_final
--vcf-annotate_interim #If you choose to reannotate VCF file
--vcf-annotate_final #If you choose to reannotate VCF file
A lot of interim files are created by annovar, and the only one that really matters unless you debugging a new database is the multianno file found in annovar_final
If not given the outdirectory is assumed to be the current working directory.
=cut
has
'outdir'
=> (
is
=>
'rw'
,
isa
=>
'Str'
,
required
=> 1,
default
=>
sub
{
return
getcwd() },
);
1;
__END__
=encoding utf-8
=head1 NAME
BioX::Wrapper - Base class for BioX::Wrappers
=head1 SYNOPSIS
use BioX::Wrapper;
=head1 DESCRIPTION
BioX::Wrapper is
=head1 AUTHOR
Jillian Rowe E<lt>jillian.e.rowe@gmail.comE<gt>
=head1 COPYRIGHT
Copyright 2015- Jillian Rowe
=head1 LICENSE
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
=head1 SEE ALSO
=cut