Trailing "//" from stockholm files causes crashes (sometimes)

[defleury]

The trailing "//" appended to sto alignment files seems to cause two types of problems:

• when passing sto files, missing the terminal "//" leads to the last sequence being dropped (at least that was the behaviour when I last checked)
• when converting sto to fasta and forgetting to remove the "//", the program will crash. While this it "correct" behaviour (fasta files shouldn't have an appended "//" line), could you maybe throw a warning instead?