Concat of interleaved nexus files produces erroneous alignments, but without error

[jphruska]

Hi Marek --

Thanks so much for writing AMAS. It's been a useful and easy program to use. I've been using the concat function a lot, and in particular to concatenate hundreds of UCE nexus alignments. I recognize that users can, and should, properly specify the alignment input type, but I noticed that AMAS still ran (returned no error) when the input alignment type has been misspecified. In this case I was able to concat interleaved nexus files despite incorrectly using the -i nexus, and not the -i nexus-int, flag. It ran without error, but it did produce concatenated alignments of odd length (e.g., shorter than the input alignments combined). It was only after checking the size of the resulting concatenated files that I noticed something was off. Anyway, might not be something to be concerned about, but I figured you might want to know, in case it was of interest.