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revision 1.3, Wed Jul 20 13:09:35 2011 UTC revision 1.5, Wed Jul 20 13:20:49 2011 UTC
# Line 81  Line 81 
81  } else {  } else {
82      # Get the list of directories to process.      # Get the list of directories to process.
83      my @dirs;      my @dirs;
84      if ($options->{recursive}) {      if (! $options->{recursive}) {
85          # Direct mode. Process the incoming directory.          # Direct mode. Process the incoming directory.
86            Trace("Processing $mainDirectory.") if T(2);
87          push @dirs, $mainDirectory;          push @dirs, $mainDirectory;
88      } else {      } else {
89          # Recursive mode. Process the subdirectories.          # Recursive mode. Process the subdirectories.
90            Trace("Recursive mode. Processing genomes under $mainDirectory.") if T(2);
91          if (opendir(my $dh, $mainDirectory)) {          if (opendir(my $dh, $mainDirectory)) {
92              my @genomes = grep { $_ =~ /^\d+$/ } readdir $dh;              my @genomes = grep { $_ =~ /^\d+$/ } readdir $dh;
93              push @dirs, map { "$mainDirectory/$_" } @genomes;              push @dirs, map { "$mainDirectory/$_" } @genomes;

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