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revision 1.8, Thu Dec 20 07:53:36 2007 UTC revision 1.9, Fri May 15 23:52:36 2009 UTC
# Line 107  Line 107 
107  #       $gap_len = $gap_end - $gap_beg + 1;  #       $gap_len = $gap_end - $gap_beg + 1;
108          $gap_loc = "$contig\_$gap_beg\_$gap_end";          $gap_loc = "$contig\_$gap_beg\_$gap_end";
109    
110          if (($gap_beg < 1) || ($gap_end > $len_of->{$contig})) {          if (($gap_beg < 1) || ($gap_end > $len_of->{$contig}) || ($gap_beg > $gap_end)) {
111              print STDERR "Skipping out-of-bounds location: $gap_loc\n";              print STDERR "Skipping out-of-bounds location: $gap_loc\n" if $ENV{VERBOSE};
112              next;              next;
113          }          }
114    
115          print "fig|$org_id.gap.".(++$gap_num) . "\t$gap_loc\n";          print STDOUT (qq(fig|$org_id.gap.), (++$gap_num), qq(\t$gap_loc\n));
116      }      }
117  }  }
118  print STDERR "\n$this_tool done\n\n" if $ENV{VERBOSE};  print STDERR "\n$this_tool done\n\n" if $ENV{VERBOSE};

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