[maker-devel] <MAKER Trac Server> #5: Negative values in quality index (fraction of ..., length of 3' UTR)

[MAKER]

#5: Negative values in quality index (fraction of ..., length of 3' UTR)
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  Reporter:  sspao at ucdavis.edu  |       Owner:        
      Type:  defect             |      Status:  closed
  Priority:  minor              |   Milestone:        
 Component:  Documentation      |     Version:  0.001 
Resolution:  fixed              |    Keywords:        
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Changes (by carson.holt at genetics.utah.edu):

  * status:  new => closed
  * type:  enhancement => defect
  * resolution:  => fixed

Comment:

 negative UTR length is caused by a bug in which maker always assumes there
 is  stop codon when determining the length of the UTR (stop codons are
 part of the CDS and not the UTR in accordance with gff3 and SO
 specifications).  Correcting UTR lengths for non existent stop codons
 results in a negative value.  Changes I have made seem to have fixed this
 bug.  Also the -1 in the fraction splice sites confirmed means that their
 are no splice sites to even be confirmed (this is more informative than 0
 since 0 can be ambiguous to no splice sites confirmed or no splice sites
 exist).

-- 
Ticket URL: <http://malachite.genetics.utah.edu/projects/maker/ticket/5#comment:1>
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