Bio::Tools::Run::BWA::Config - Configuration data for BWA commands

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# $Id$
#
# 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

# 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;