cmalign seg fault

[gjospin]

I ran into a problem where cmalign would segfault on 16s alignments for particular sequences.
I am not sure what caused the problem but I had to increase the --mxsize parameter to 10000 for it to even get there.

I was able to fix it by upgrading to INFERNAL 1.1 (we were using INFERNAL 1.0.2 ).

Doing so would require a change to the cm files provided in the marker database. This can be done by using cmconvert > <new_filename>

The -q option is no longer a recognized parameter so we would also need to change line 457 from MarkerAlign.pm

In my tests things seemed to behave properly once these changes were implemented locally.