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revision 1.11, Mon May 18 16:54:56 2009 UTC revision 1.12, Tue Jun 23 21:18:48 2009 UTC
# Line 58  Line 58 
58  #  #
59    
60  my $keep_genecalls = $meta->get_metadata("keep_genecalls");  my $keep_genecalls = $meta->get_metadata("keep_genecalls");
61    my $call_using_glimmer = $meta->get_metadata("use_glimmer");
62  my $unformatted = "$raw_dir/unformatted_contigs";  my $unformatted = "$raw_dir/unformatted_contigs";
63    
64  if (! -f $unformatted)  if (! -f $unformatted)
# Line 154  Line 155 
155      }      }
156  }  }
157    
158    
159    #
160    # If we are to call using glimmer instead of the usual mechanism, first
161    # invoke call_genome_using_glimmer.
162    #
163    
164    if ($call_using_glimmer)
165    {
166        my @cmd = ("FIG_Config::bin/call_using_glimmer",
167                   "--glimmerV=3",
168                   "--code=$genetic_code",
169                   "--meta=$meta_file",
170                   $raw_dir);
171    
172        print "Run @cmd\n";
173        $meta->add_log_entry($0, ['running', @cmd]);
174    
175        $rc = system(@cmd);
176    
177        if ($rc != 0)
178        {
179            &fatal("call_using_glimmer command failed with rc=$rc: @cmd\n");
180        }
181    }
182    
183  for my $key (grep { /^status\.rp\./ } $meta->get_metadata_keys())  for my $key (grep { /^status\.rp\./ } $meta->get_metadata_keys())
184  {  {
185      my $old = $meta->get_metadata($key);      my $old = $meta->get_metadata($key);

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