Add function to check for stop codons

[alexpiper]

While the PHMM is filtering out most non-homologous loci, some match well enough to make it through, but they have a frameshift mutation. Need to add a further function to check for this.

Potentially could use aligntranslation in decipher: seqs <- AlignTranslation(seqs) ranges <- MaskAlignment(seqs, type="ranges", threshold=0, maxFractionGaps = 0.2, showPlot = TRUE) # Mask columns with majority gaps - caused by pseudogenes seqs <- replaceAt(seqs, ranges) # remove the masked columns

[alexpiper]

This is now implemented in the function codon_filter()