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revision 1.3, Wed Nov 22 16:10:20 2006 UTC revision 1.4, Tue Nov 28 17:49:08 2006 UTC
# Line 64  Line 64 
64  my $peg_tbl  = (-s ($_ = "$org_dir/Features/peg/tbl")) ? $_ : "/dev/null";  my $peg_tbl  = (-s ($_ = "$org_dir/Features/peg/tbl")) ? $_ : "/dev/null";
65  my $orf_tbl  = (-s ($_ = "$org_dir/Features/orf/tbl")) ? $_ : "/dev/null";  my $orf_tbl  = (-s ($_ = "$org_dir/Features/orf/tbl")) ? $_ : "/dev/null";
66    
67  &FIG::run("make_overlap_report  $overlap_parms  $contigs $rna_tbl $peg_tbl $orf_tbl > $org_dir/overlap.report 2> $org_dir/overlap.summary");  if (!open(SUMMARY, ">$org_dir/overlap.summary"))
68  my @overlap_summary = `cat $org_dir/overlap.summary`;  {
69  die "make_overlap_report failed" unless @overlap_summary;      my $err = "cannot open $org_dir/overlap.summary: $!";
70        $meta->add_log_entry($0, $err) if $meta;
71        die $err;
72    }
73    
74    my $cmd = "$FIG_Config::bin/make_overlap_report  $overlap_parms  $contigs $rna_tbl $peg_tbl $orf_tbl";
75    
76    $meta->add_log_entry($0, ['start', $cmd]) if $meta;
77    if (!open(OVER, "$cmd 2>&1 1> $org_dir/overlap.report |"))
78    {
79        my $err = "Execution of $cmd  failed: $!";
80        $meta->add_log_entry($0, [$err, $cmd]) if $meta;
81        die $err;
82    }
83    
84    my @overlap_summary;
85    
86    while (<OVER>)
87    {
88        push(@overlap_summary, $_);
89        print SUMMARY $_;
90    }
91    close(SUMMARY);
92    
93    if (!close(OVER))
94    {
95        my $err = "close failed with \$!=$! \$?=$?";
96        $meta->add_log_entry($0, [$err, $cmd]) if $meta;
97        die "Execution of $cmd > $org_dir/overlap.summary failed: $err";
98    }
99    $meta->add_log_entry($0, ['end', $cmd]) if $meta;
100    $meta->add_log_entry($0, \@overlap_summary);
101    
102  my $num_features = 0;  my $num_features = 0;
103  my $bad_starts   = 0;  my $bad_starts   = 0;

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