CHANGELOG, 7/31/00:
   - Weak scores are now only invoked with the -w option.  Any weak-score
     gene is rejected automatically by an overlap with a regular gene.
   - Weak-scores genes and "voted" genes are now annotated by [Weak] and
     [Vote] in the final listing.  Voted genes are those which have a
     significant number of relatively high-scoring subregions.  Voted
     genes also are rejected automatically by overlaps with regular genes.
   - Weak scores are computed to be more independent of architecture-dependent
     floating-point features.  (Previously, 64-bit machines would sometimes
     generate different results from 32-bit machines.)
   - Fixed bug in RNABin function that occurred when the gene
     started on the very last base of the genome.  This function is
     now not called at all if the Choose_First_Start_Codon option is
     selected (which is the default).
   - Fixed problem that occurred on short pieces of genome when one
     frame (or more) had no stop codons.  
   - An ignore option (-i) to specify a list of regions in which no predictions
     will be made, such as ribosomal RNAs.  This feature has not yet been
     thoroughly tested.


CHANGELOG, 9 December 2002
   - Raw scores are now printed in the main listing and in []'s in
     the final list of putatative genes
   - Add +S option to us a "stricter" independent (intergenic) model
     that discounts stop codons.  Since only orfs (which have no stop
     codons) are ever scored, the independent model is at a disadvantage
     unless it also assumes that it is only scoring orfs.  Thus, with the
     +S option, the independent score is done codon by codon.
     The probabilities of codons are intially set to what the
     previous independent model would be:
     The probability of a codon "atg", for example is:
         Pr[a] * Pr[t] * Pr[g]
     Then each of these is divide by the sum of the probabilities of the
     non-stop codons.
   - Add -L option to specify the name of a file containing a list
     of coordinates.  The genes in these lists are scored separately by
     the ICM, output, and then the program stops (i.e., no
     overlapping/voting rules).

CHANGELOG, 5 February 2003
   - The strict independent (intergenic) model is now the only mode.
     The +S option is tolerated but has no effect.

CHANGELOG, 18 April 2003 
   - Compute the optimal length for minimum "long" orfs, so that the 
     program will return the largest number of orfs possible.  The -g 
     switch still works if specified, but I don't know why anyone would 
     want to use that for a training set.  
   - Change minimum overlap by default to be 0.  This means that genes
     that overlap even by 1 base will be considered in conflict by Glimmer,
     and the program will try to adjust their start codons to remove the
     conflict or else delete one of the genes.

CHANGELOG, 7 October 2003
   - Fix bug on long-orfs.cc to avoid occasional array out-of-bounds
     error (detected on Mac OS X).
CHANGELOG, 12 October 2003
    add -X option to glimmer2, to allow orfs extending off ends of 
    sequence to be scored.  Also fix bug affecting -p and -o options
    when user chose zero overlap.