NAME

       Bio::Tools::Run::Samtools - a run wrapper for the samtools suite *BETA*

SYNOPSIS

        # convert a sam to a bam
        $samt = Bio::Tools::Run::Samtools( -command => 'view',
                                           -sam_input => 1,
                                           -bam_output => 1 );
        $samt->run( -bam => "mysam.sam", -out => "mysam.bam" );
        # sort it
        $samt = Bio::Tools::Run::Samtools( -command => 'sort' );
        $samt->run( -bam => "mysam.bam", -pfx => "mysam.srt" );
        # now create an assembly
        $assy = Bio::IO::Assembly->new( -file => "mysam.srt.bam",
                                        -refdb => "myref.fas" );

DESCRIPTION

       This is a wrapper for running samtools, a suite of large-alignment reading and
       manipulation programs available at <http://samtools.sourceforge.net/>.

RUNNING COMMANDS

       To run a "samtools" 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"):

        $samt = Bio::Tools::Run::Samtools->new( -command => 'view',
                                                -sam_input => 1,
                                                -bam_output => 1);

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

        $samt->run( -bam => "mysam.sam", -out => "mysam.bam" );

OPTIONS

       "samtools" 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:

        $samt = Bio::Tools::Run::Samtools->new( -command => 'pileup' );
        # all samtools commands
        @all_commands = $samt->available_parameters('commands');
        @all_commands = $samt->available_commands; # alias
        # just for pileup
        @pup_params = $samt->available_parameters('params');
        @pup_switches = $samt->available_parameters('switches');
        @pup_all_options = $samt->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://samtools.sourceforge.net/samtools.shtml> for the gory details.

FILES

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

         $samt = Bio::Tools::Run::Samtools->new( -command => 'view' );
         @filespec = $samt->filespec;

       This example returns the following array:

        bam
        >out

       This indicates that the bam/sam file (bam) and the output file (out) MUST be specified in
       the "run()" argument list:

        $samt->run( -bam => 'mysam.sam', -out => 'mysam.cvt' );

       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::Samtools();
        Function: Builds a new Bio::Tools::Run::Samtools object
        Returns : an instance of Bio::Tools::Run::Samtools
        Args    :