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revision 1.6, Wed Sep 5 21:43:18 2007 UTC revision 1.7, Wed Oct 10 20:50:55 2007 UTC
# Line 53  Line 53 
53  # and rerun reformat_contigs without the split option in order  # and rerun reformat_contigs without the split option in order
54  # to recover the original contig coordinates.  # to recover the original contig coordinates.
55  #  #
56    # If keep_genecalls is enabled, we do not split the contigs.
57    #
58    
59    my $keep_genecalls = $meta->get_metadata("keep_genecalls");
60  my $unformatted = "$raw_dir/unformatted_contigs";  my $unformatted = "$raw_dir/unformatted_contigs";
61    
62  if (! -f $unformatted)  if (! -f $unformatted)
# Line 64  Line 67 
67  #  #
68  # Reformat and split.  # Reformat and split.
69  #  #
70    # Only do this if we are doing gene calling.
71    #
72    
73  my $formatted = "$raw_dir/contigs";  my $formatted = "$raw_dir/contigs";
74    my @cmd;
75    
76    if ($keep_genecalls)
77    {
78        my $reformat_log = "$errdir/reformat_contigs.stderr";
79    
80        @cmd = ("$FIG_Config::bin/reformat_contigs", "-v", "-logfile=$reformat_log", $unformatted, $formatted);
81    }
82    else
83    {
84  my $reformat_split_log = "$errdir/reformat_contigs_split.stderr";  my $reformat_split_log = "$errdir/reformat_contigs_split.stderr";
85    
86  my @cmd = ("$FIG_Config::bin/reformat_contigs", "-v", "-logfile=$reformat_split_log", "-split", $unformatted, $formatted);      @cmd = ("$FIG_Config::bin/reformat_contigs", "-v", "-logfile=$reformat_split_log", "-split", $unformatted, $formatted);
87    }
88    
89  print "Run @cmd\n";  print "Run @cmd\n";
90    
# Line 93  Line 109 
109  # Determine if we are keeping the original gene calls.  # Determine if we are keeping the original gene calls.
110  #  #
111    
 my $keep_genecalls = $meta->get_metadata("keep_genecalls");  
112  my @keep_genecalls_flag;  my @keep_genecalls_flag;
113    
114  if ($keep_genecalls)  if ($keep_genecalls)
# Line 138  Line 153 
153    
154      $meta->add_log_entry($0, ['fatal error', $msg]);      $meta->add_log_entry($0, ['fatal error', $msg]);
155      $meta->set_metadata("rp.error", $msg);      $meta->set_metadata("rp.error", $msg);
156        $meta->set_metadata("rp.running", "no");
157      $meta->set_metadata("status.rp", "error");      $meta->set_metadata("status.rp", "error");
158    
159      croak "$0: $msg";      croak "$0: $msg";

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