[Bioperl-guts-l] bioperl-run/Bio/Tools/Run Genemark.pm,1.2,1.3

[Christopher John Fields]

Update of /home/repository/bioperl/bioperl-run/Bio/Tools/Run
In directory dev.open-bio.org:/tmp/cvs-serv10397/Bio/Tools/Run

Modified Files:
	Genemark.pm 
Log Message:
bug 2241

Index: Genemark.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Genemark.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Genemark.pm	14 Mar 2007 03:54:37 -0000	1.2
--- Genemark.pm	19 Mar 2007 20:27:09 -0000	1.3
***************
*** 21,25 ****
    my $factory =
        Bio::Tools::Run::Genemark->new('-program' => 'gmhmmp',
!                                      '-model'   => 'model.icm');
    
  
--- 21,25 ----
    my $factory =
        Bio::Tools::Run::Genemark->new('-program' => 'gmhmmp',
!                                      '-m'       => 'model.icm');
    
  
***************
*** 208,212 ****
      }
      
!     return $self->_run($file_name);
      
  }
--- 208,212 ----
      }
      
!     return $self->_run($file_name, $seq[0]->display_id());
      
  }
***************
*** 224,228 ****
  sub _run {
      
!     my ($self, $seq_file_name) = @_;
  
      my ($temp_fh, $temp_file_name) =
--- 224,228 ----
  sub _run {
      
!     my ($self, $seq_file_name, $seq_id) = @_;
  
      my ($temp_fh, $temp_file_name) =
***************
*** 266,270 ****
      $self->debug(join("\n", 'GeneMark STDERR:', $program_stderr)) if $program_stderr;
                   
!     return Bio::Tools::Genemark->new(-file => $temp_file_name);
      
  }
--- 266,271 ----
      $self->debug(join("\n", 'GeneMark STDERR:', $program_stderr)) if $program_stderr;
                   
!     return Bio::Tools::Genemark->new(-file    => $temp_file_name,
!                                      -seqname => $seq_id);
      
  }