Bio::Tools::Run::Samtools::Config - configurator for Bio::Tools::Run::Samtools
Index
Code Index:
NAME
Bio::Tools::Run::Samtools::Config - configurator for Bio::Tools::Run::Samtools
SYNOPSIS
DESCRIPTION
Exports global configuration variables (as required by
Bio::Tools::Run::WrapperBase::CommandExts) to Samtools.pm.
FEEDBACK
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
Support
Please direct usage questions or support issues to the mailing list:
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.
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
AUTHOR - Mark A. Jensen
Email maj -at- fortinbras -dot- us
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
# $Id$
#
# BioPerl module for Bio::Tools::Run::Samtools::Config
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Mark A. Jensen <maj -at- fortinbras -dot- 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::Samtools::Config;
use strict;
use warnings;
no warnings qw(qw);
use Exporter;
our (@ISA, @EXPORT, @EXPORT_OK);
push @ISA, 'Exporter';
@EXPORT = qw(
$program_dir
@program_commands
%command_prefixes
@program_params
@program_switches
%param_translation
%command_files
);
@EXPORT_OK = qw();
our $program_dir;
our @program_commands = qw(
view
sort
index
merge
faidx
pileup
fixmate
rmdup
fillmd
);
# composite commands: pseudo-commands that run a
# sequence of commands
# composite command prefix => list of prefixes of commands this
# composite command runs
#
# prefixes only for commands that take params/switches...
our %command_prefixes = (
'view' => 'view',
'sort' => 'srt',
'index' => 'idx',
'merge' => 'mrg',
'faidx' => 'fai',
'pileup' => 'pup',
'fillmd' => 'fmd'
);
our @program_params = qw(
command
view|tab_delim
view|out_file
view|pass_flags
view|filt_flags
view|refseq
view|qual_threshold
view|library
view|read_group
srt|mem_hint
mrg|headers_in
pup|refseq
pup|map_qcap
pup|ref_list
pup|site_list
pup|theta
pup|n_haplos
pup|exp_hap_diff
pup|indel_prob
);
our @program_switches = qw(
view|bam_output
view|uncompressed
view|add_header
view|only_header
view|sam_input
srt|sort_by_names
mrg|sort_by_names
pup|qual_last_col
pup|sam_input
pup|indels_only
pup|call_cons
pup|genot_L
fmd|match_with_eq
);
our %param_translation = (
'view|tab_delim' => 't',
'view|out_file' => 'o',
'view|pass_flags' => 'f',
'view|refseq' => 'T',
'view|filt_flags' => 'F',
'view|qual_threshold' => 'q',
'view|library' => 'l',
'view|read_group' => 'r',
'view|bam_output' => 'b',
'view|uncompressed' => 'u',
'view|add_header' => 'h',
'view|only_header' => 'H',
'view|sam_input' => 'S',
'srt|mem_hint' => 'm',
'srt|sort_by_names' => 'n',
'mrg|headers_in' => 'h',
'mrg|sort_by_names' => 'n',
'pup|refseq' => 'f',
'pup|map_qcap' => 'M',
'pup|ref_list' => 't',
'pup|site_list' => 'l',
'pup|theta' => 'T',
'pup|n_haplos' => 'N',
'pup|exp_hap_diff' => 'f',
'pup|indel_prob' => 'I',
'pup|qual_last_col' => 's',
'pup|sam_input' => 'S',
'pup|indels_only' => 'i',
'pup|call_cons' => 'c',
'pup|genot_L' => 'g',
'fmd|match_with_eq' => 'e'
);
#
# 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 = (
'view' => [qw( bam #*rgn >out )],
'sort' => [qw( bam pfx )],
'index' => [qw( bam )],
'merge' => [qw( obm *ibm )],
'faidx' => [qw( fas #*rgn )],
'pileup' => [qw( bam >out )],
'fixmate' => [qw( ibm obm )],
'rmdup' => [qw( ibm obm )],
'fillmd' => [qw( bam fas )]
);
1;