/usr/share/perl5/Bio/Tools/Run/BWA/Config.pm is in libbio-perl-run-perl 1.6.9-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#
# BioPerl module for Bio::Tools::Run::BWA::Config
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Mark A. Jensen <maj@fortinbras.us>
#
# Copyright Mark A. Jensen
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::BWA::Config - Configuration data for BWA commands
=head1 SYNOPSIS
Used internally by L<Bio::Tools::Run::BWA>.
=head1 DESCRIPTION
This package exports information describing BWA commands, parameters,
switches, and input and output filetypes for individual BWA commands.
See L<http://bio-bwa.sourceforge.net/bwa.shtml>.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
L<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Mark A. Jensen
Email maj@fortinbras.us
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::Run::BWA::Config;
use strict;
use warnings;
no warnings qw(qw);
use Bio::Root::Root;
use Exporter;
use base qw(Bio::Root::Root );
our (@ISA, @EXPORT, @EXPORT_OK);
push @ISA, 'Exporter';
@EXPORT = qw(
@program_commands
%command_prefixes
%composite_commands
@program_params
@program_switches
%param_translation
%command_files
);
@EXPORT_OK = qw();
our @program_commands = qw(
run
index
aln
samse
sampe
dbwtsw
);
# composite commands: pseudo-commands that run a
# sequence of commands
# composite command prefix => list of prefixes of commands this
# composite command runs
#
our %composite_commands = (
'run' => [qw( map asm c2q )]
);
# prefixes only for commands that take params/switches...
our %command_prefixes = (
'aln' => 'aln',
'dbwtsw' => 'bwt',
'index' => 'idx',
'samse' => 'sms',
'sampe' => 'smp',
'run' => 'run'
);
our @program_params = qw(
command
idx|output_prefix
idx|algorithm
aln|max_edit_dist
aln|max_gap_opens
aln|max_gap_extns
aln|deln_protect_3p
aln|deln_protect_ends
aln|subseq_seed
aln|max_edit_dist_seed
aln|n_threads
aln|mm_penalty
aln|gap_open_penalty
aln|gap_extn_penalty
aln|subopt_hit_threshold
aln|trim_parameter
sms|hit_limit
smp|max_insert_size
smp|max_read_occur
bwt|match_score
bwt|mm_penalty
bwt|gap_open_penalty
bwt|gap_extn_penalty
bwt|n_threads
bwt|band_width
bwt|rel_min_score_threshold
bwt|threshold_adj_coeff
bwt|z_best
bwt|max_sa_interval
bwt|min_seeds_to_skip
);
our @program_switches = qw(
idx|color_space_idx
aln|reverse_no_comp
aln|no_iter_search
);
our %param_translation = (
'idx|output_prefix' => 'p',
'idx|algorithm' => 'a',
'aln|max_edit_dist' => 'n',
'aln|max_gap_opens' => 'o',
'aln|max_gap_extns' => 'e',
'aln|deln_protect_3p' => 'd',
'aln|deln_protect_ends' => 'i',
'aln|subseq_seed' => 'l',
'aln|max_edit_dist_seed' => 'k',
'aln|n_threads' => 't',
'aln|mm_penalty' => 'M',
'aln|gap_open_penalty' => 'O',
'aln|gap_extn_penalty' => 'E',
'aln|subopt_hit_threshold' => 'R',
'aln|trim_parameter' => 'q',
'sms|hit_limit' => 'n',
'smp|max_insert_size' => 'a',
'smp|max_read_occur' => 'o',
'bwt|match_score' => 'a',
'bwt|mm_penalty' => 'b',
'bwt|gap_open_penalty' => 'q',
'bwt|gap_extn_penalty' => 'r',
'bwt|n_threads' => 't',
'bwt|band_width' => 'w',
'bwt|rel_min_score_threshold' => 'T',
'bwt|threshold_adj_coeff' => 'c',
'bwt|z_best' => 'z',
'bwt|max_sa_interval' => 's',
'bwt|min_seeds_to_skip' => 'N'
);
#
# the order in the arrayrefs is the order required
# on the command line
#
# the strings in the arrayrefs (less special chars)
# become the keys for named parameters to run_maq
#
# special chars:
#
# '#' implies optional
# '*' implies variable number of this type
# <|> implies stdin/stdout redirect
#
our %command_files = (
'run' => [qw( faq fas faq )],
'index' => [qw( fas )],
'aln' => [qw( fas faq >sai )],
'samse' => [qw( fas sai faq >sam )],
'sampe' => [qw( fas sai1 sai2 faq1 faq2 >sam )],
'dbwtsw' => [qw( fas faq )]
);
INIT {
# add subcommand params and switches for
# composite commands
my @sub_params;
my @sub_switches;
foreach my $cmd (keys %composite_commands) {
foreach my $subcmd ( @{$composite_commands{$cmd}} ) {
my @sub_program_params = grep /^$subcmd\|/, @program_params;
my @sub_program_switches = grep /^$subcmd\|/, @program_switches;
for (@sub_program_params) {
m/^$subcmd\|(.*)/;
push @sub_params, "$cmd\|${subcmd}_".$1;
}
for (@sub_program_switches) {
m/^$subcmd\|(.*)/;
push @sub_switches, "$cmd\|${subcmd}_".$1;
}
}
}
push @program_params, @sub_params;
push @program_switches, @sub_switches;
# translations for subcmd params/switches not necessary
}
1;
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