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    :