update agat_sp_add_start_and_stop.pl #429
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…(Use of uninitialized value)
… IUPAC code in codons. Add option to extend the sequence to find the next start/stop codon in the sequence if absent from the CDS
…create the start codon. Pass again by the omniscient parser to set proper location if extension option was activated
… if needed because the test @ was wrong because was not the number of location but the size of the location object. I took the opportunity to update that part of the code to be more concise and efficient
…o reflect last updates
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Allow to deal with stop out of the CDS (GTF case)
Add option to extend the CDS when searching a start or stop until it find one
Allow to avoid the IUPAC code used by default by bioperl. e.g. By default N is considered as A,T,G or C. So a NNN codon is seen as a start/stop codon. With the option --ni or --na codon with IUPAC code will be skipped.