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revision 1.25, Wed Aug 18 16:58:49 2010 UTC revision 1.26, Mon Sep 20 20:53:45 2010 UTC
# Line 591  Line 591 
591      my $genetic_code = $params->{-geneticCode};      my $genetic_code = $params->{-geneticCode};
592      my $gene_caller = lc($params->{-geneCaller});      my $gene_caller = lc($params->{-geneCaller});
593      my $non_active = $params->{-nonActive};      my $non_active = $params->{-nonActive};
594        my $determine_family = $params->{-determineFamily};
595    
596      my $work_dir = "$FIG_Config::temp/rast_submit_tmp.$$";      my $work_dir = "$FIG_Config::temp/rast_submit_tmp.$$";
597      &FIG::verify_dir($work_dir);      &FIG::verify_dir($work_dir);
# Line 700  Line 701 
701              'genome.ambig_count' => 0,              'genome.ambig_count' => 0,
702              'import.candidate' => 0,              'import.candidate' => 0,
703              'keep_genecalls' => $keep ? 1 : 0,              'keep_genecalls' => $keep ? 1 : 0,
704              'use_glimmer' => $gene_caller eq 'glimmer3' ? 1 : 0,              ('use_glimmer' => $gene_caller eq 'glimmer3' ? 1 : 0),
705              'correction.automatic' => 1,              'correction.automatic' => 1,
706              'correction.frameshifts' => 0,              'correction.frameshifts' => 0,
707              'correction.backfill_gaps' => 1,              'correction.backfill_gaps' => 1,
708              'env.debug' => 0,              'env.debug' => 0,
709              'env.verbose' => 0,              'env.verbose' => 0,
710                ('options.determine_family' => $determine_family ? 1 : 0),
711              upload_metadata => \%meta,              upload_metadata => \%meta,
712          },          },
713          non_active => ($non_active ? 1 : 0),          non_active => ($non_active ? 1 : 0),

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