NAME

       Bio::Tools::Run::Alignment::Gmap - Wrapper for running gmap.

SYNOPSIS

         use Bio::Tools::Run::Alignment::Gmap;
         use Bio::SeqIO;

         my $sio = Bio::SeqIO->new(-file=>$filename ,-format=>'fasta');
         my @seq;
         while(my $seq = $sio->next_seq()){
           push @seq,$seq;
         }
         my $mapper =Bio::Tools::Run::Gmap->new();
         my $result = $mapper->run(\@seq);

DESCRIPTION

       Bioperl-run wrapper around gmap.  See <http://www.gene.com/share/gmap/> for information
       about gmap.

       It requires a reference to an array of bioperl SeqI objects and returns a reference to a
       filehandle from which the gmap output can be read.

       One can explicitly set the name of the genome database (defaults to NHGD_R36) using the
       'genome_db()' method.  One can also explicitly set the flags that are passed to gmap
       (defaults to '-f 9 -5 -e') using the 'flags()' method.

       The name of the gmap executable can be overridden using the program_name() method and the
       directory in which to find that executable can be overridden using the program_dir()
       method.

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

   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 - George Hartzell

       Email hartzell@alerce.com

       Describe contact details here

CONTRIBUTORS

       Additional contributors names and emails here

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

   version
        Title   : version
        Usage   : print "gmap version: " . $mapper->version() . "\n";
        Function: retrieves and returns the version of the gmap package.
        Example :
        Returns : scalar string containing the version number.  Probably looks
                  like YYYY-MM-DD.
        Args    : none.

   program_name
        Title   : program_name
        Usage   : $mapper->program_name('gmap-dev');
                  my $pname = $mapper->program_name();
        Function: sets/gets the name of the program to run.
        Returns : string representing the name of the executable.
        Args    : [optional] string representing the name of the executable
                  to set.

   program_dir
        Title   : program_dir
        Usage   : $mapper->program_dir('/usr/local/sandbox/gmap/bin');
                  my $pdir = $mapper->program_dir();
        Function: sets/gets the directory path in which
                  to find the gmap executable.
        Returns : string representing the path to the directory.
        Args    : [optional] string representing the directory path to set.

   input_file
        Title   : input_file
        Usage   : $mapper->input_file('/tmp/moose.fasta');
                  my $filename = $mapper->input_file();
        Function: sets/gets the name of a file containing sequences
                  to be mapped.
        Returns : string containing the name of the query sequence.
        Args    : [optional] string representing the directory path to set.

   genome_db
        Title   : genome_db
        Usage   : $mapper->genome_db('NHGD_R36');
                  my $genome_db = $mapper->genome_db();
        Function: sets/gets the name of the genome database, this will be
                  passed to gmap using its '-d' flag.
        Returns : name of the genome database.
        Args    : [optional] string representing the genome db to set.

   flags
        Title   : flags
        Usage   : $mapper->flags('-A -e -5');
                  my $flags = $mapper->flags();
        Function: sets/gets the flags that will be passed to gmap.
        Returns : the current value of the flags that will be passed to gmap.
        Args    : [optional] the flags to set.

   run
        Title   : run
        Usage   : $mapper->run()
        Function: runs gmap
        Example :
        Returns : a file handle, opened for reading, for gmap's output.
        Args    : An array of references query sequences (as Bio::Seq objects)

   _build_fasta_input_file
        Title   : _build_fasta_input_file
        Usage   : my $seq_file = $self->_build_fasta_input_file(@_);
        Function:
        Example :
        Returns : The name of the temporary file that contains the sequence.
        Args    : A reference to an array of Bio::Seq objects.