NAME

       Bio::Tools::Run::BWA - Run wrapper for the BWA short-read assembler *BETA*

SYNOPSIS

        # create an assembly

        # run BWA commands separately

DESCRIPTION

       This module provides a wrapper interface for Heng Li's reference-directed short read
       assembly suite "bwa" (see <http://bio-bwa.sourceforge.net/bwa.shtml> for manuals and
       downloads).

       Manipulating the alignments requires "samtools"
       (<http://sourceforge.net/projects/samtools/>) and Lincoln Stein's package "Bio-SamTools"
       (<http://search.cpan.org/perldoc?Bio::DB::Sam>).

       There are two modes of action.

       •   Easy assembly

           The first is a simple pipeline through the "maq" commands, taking your read data in
           and squirting out an assembly object of type Bio::Assembly::IO::maq. The pipeline is
           based on the one performed by "maq.pl easyrun":

            Action                  maq commands
            ------                  ------------
            data conversion to      fasta2bfa, fastq2bfq
            maq binary formats

            map sequence reads      map
            to reference seq

            assemble, creating      assemble
            consensus

            convert map & cns       mapview, cns2fq
            files to plaintext
            (for B:A:IO:maq)

           Command-line options can be directed to the "map", "assemble", and "cns2fq" steps. See
           "OPTIONS" below.

       •   BWA command mode

           The second mode is direct access to "bwa" commands. To run a "bwa" command, construct
           a run factory, specifying the desired command using the "-command" argument in the
           factory constructor, along with options specific to that command (see "OPTIONS"):

            $bwafac = Bio::Tools::Run::BWA->new( -command => 'fasta2bfa' );

           To execute, use the "run_bwa" methods. Input and output files are specified in the
           arguments of "run_bwa" (see "FILES"):

            $bwafac->run_bwa( -fas => "myref.fas", -bfa => "myref.bfa" );

OPTIONS

       "bwa" is complex, with many subprograms (commands) and command-line options and file specs
       for each. This module attempts to provide commands and options comprehensively. You can
       browse the choices like so:

        $bwafac = Bio::Tools::Run::BWA->new( -command => 'aln' );
        # all maq commands
        @all_commands = $bwafac->available_parameters('commands');
        @all_commands = $bwafac->available_commands; # alias
        # just for aln
        @aln_params = $bwafac->available_parameters('params');
        @aln_switches = $bwafac->available_parameters('switches');
        @aln_all_options = $bwafac->available_parameters();

       Reasonably mnemonic names have been assigned to the single-letter command line options.
       These are the names returned by "available_parameters", and can be used in the factory
       constructor like typical BioPerl named parameters.

       See <http://bio-bwa.sourceforge.net/bwa.shtml> for the gory details.

FILES

       When a command requires filenames, these are provided to the "run_bwa" method, not the
       constructor ("new()"). To see the set of files required by a command, use
       "available_parameters('filespec')" or the alias "filespec()":

         $bwafac = Bio::Tools::Run::BWA->new( -command => 'aln' );
         @filespec = $bwafac->filespec;

       This example returns the following array:

        fas
        faq
        >sai

       This indicates that the FASTA database (faq) and the FASTQ reads (faq) MUST be specified,
       and the STDOUT of this program (SA coordinates) MAY be slurped into a file specified in
       the "run_bwa" argument list:

        $bwafac->run_bwa( -fas => 'my.db.fas', -faq => 'reads.faq',
                          -sai => 'out.sai' );

       If files are not specified per the filespec, text sent to STDOUT and STDERR is saved and
       is accessible with "$bwafac-"stdout()> and "$bwafac-"stderr()>.

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 _

   new()
        Title   : new
        Usage   : my $obj = new Bio::Tools::Run::BWA();
        Function: Builds a new Bio::Tools::Run::BWA object
        Returns : an instance of Bio::Tools::Run::BWA
        Args    :

   run
        Title   : run
        Usage   : $assembly = $bwafac->run( @args );
        Function: Run the bwa assembly pipeline.
        Returns : Assembly results (file, IO object or Assembly object)
        Args    : - fastq file containing single-end reads
                  - fasta file containing the reference sequence
                  - [optional] fastq file containing paired-end reads

   run_bwa()
        Title   : run_bwa
        Usage   : $obj->run_bwa( @file_args )
        Function: Run a bwa command as specified during object contruction
        Returns :
        Args    : a specification of the files to operate on:

   stdout()
        Title   : stdout
        Usage   : $fac->stdout()
        Function: store the output from STDOUT for the run,
                  if no file specified in run_maq()
        Example :
        Returns : scalar string
        Args    : on set, new value (a scalar or undef, optional)

   stderr()
        Title   : stderr
        Usage   : $fac->stderr()
        Function: store the output from STDERR for the run,
                  if no file is specified in run_maq()
        Example :
        Returns : scalar string
        Args    : on set, new value (a scalar or undef, optional)

Bio::Tools::Run::AssemblerBase overrides

   _check_sequence_input()
        No-op.

   _check_optional_quality_input()
        No-op.

   _prepare_input_sequences
        Convert input fastq and fasta to maq format.

   _collate_subcmd_args()
        Title   : _collate_subcmd_args
        Usage   : $args_hash = $self->_collate_subcmd_args
        Function: collate parameters and switches into command-specific
                  arg lists for passing to new()
        Returns : hash of named argument lists
        Args    : [optional] composite cmd prefix (scalar string)
                  [default is 'run']

   _run()
        Title   :   _run
        Usage   :   $factory->_run()
        Function:   Run a bwa assembly pipeline
        Returns :   a text-formatted sam alignment
        Args    :   - single end read file in maq bfq format
                    - reference seq file in maq bfa format
                    - [optional] paired end read file in maq bfq format

   available_parameters()
        Title   : available_parameters
        Usage   : @cmds = $fac->available_commands('commands');
        Function: Use to browse available commands, params, or switches
        Returns : array of scalar strings
        Args    : 'commands' : all bwa commands
                  'params'   : parameters for this object's command
                  'switches' : boolean switches for this object's command
                  'filespec' : the filename spec for this object's command
        4Geeks  : Overrides Bio::ParameterBaseI via
                  Bio::Tools::Run::AssemblerBase