Check for in-frame stops even if a gene is incomplete

[tomasbruna]

Currently, the mapped genes are scanned for in-frame stop codons only if they are complete. Similarly, if a gene is 5' incomplete, the 3' end is not checked.

This pull request changes the behavior to check and report the presence of start, stop, and in-frame stops independently.

This is useful because an incomplete mapping which preserves the ORF is much less concerning than an incomplete mapping with in-frame stops. There is no way to distinguish the two in the current output.

[tomasbruna]

There is also a more concerning issue with the current implementation. If the translation goes out of frame due to a frameshift in the target sequence (introducing lots of in-frame stops), Liftoff may report this as a "missing stop" even if the alignment actually ends with a stop codon (the existing stop is translated out of the frame and thus appears to be missing).

The fix also takes care of a scenario like this by adding the in-frame stop flag.