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revision 1.29, Wed Sep 14 13:06:53 2005 UTC revision 1.34, Wed Sep 14 13:43:31 2005 UTC
# Line 622  Line 622 
622          }          }
623          # Remember this specifier for the adjacent-segment test the next time through.          # Remember this specifier for the adjacent-segment test the next time through.
624          ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);          ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);
625            # Compute the initial base pair.
626            my $start = ($dir eq "+" ? $beg : $beg + $len - 1);
627          # Add the specifier to the list.          # Add the specifier to the list.
628          push @retVal, "${contigID}_$beg$dir$len";          push @retVal, "${contigID}_$start$dir$len";
629      }      }
630      # Return the list in the format indicated by the context.      # Return the list in the format indicated by the context.
631      return (wantarray ? @retVal : join(',', @retVal));      return (wantarray ? @retVal : join(',', @retVal));
# Line 765  Line 767 
767          # the start point is the ending. Note that in the latter case we must reverse the DNA string          # the start point is the ending. Note that in the latter case we must reverse the DNA string
768          # before putting it in the return value.          # before putting it in the return value.
769          my ($start, $stop);          my ($start, $stop);
770            Trace("Parse of \"$location\" is $beg$dir$len.") if T(SDNA => 4);
771          if ($dir eq "+") {          if ($dir eq "+") {
772              $start = $beg;              $start = $beg;
773              $stop = $beg + $len - 1;              $stop = $beg + $len - 1;

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