Hi Andreas,
I've added some more tests to kalign, but there's a slight problem.
As specified in the README file, kalign supports two ways of taking input: one is through stdin and the other through the -i flag (or even without it).
For some reason, all tests using the -i flag fail inside my testing chroot, but work perfectly outside the chroot.
However, inside the chroot and outside, stdin input works as expected.
In the run-unit-test file, all the tests take input from stdin, and all the tests pass.
It's the same as what happened with loki earlier, I guess. Please uncomment the lines with -i and try running them on your system. Maybe if they work on yours and others', it's just an issue with my chroot.
Here are the errors generated when commands using -i are run inside the chroot:
LOG : kalign -i BB11001.tfa -f msf -o out.msf
ERROR : Input alignment format could not be detected. (rwalign.c line 314)
ERROR : Function "detect_alignment_format(b, &type)" failed. (rwalign.c line 187)
ERROR : Function "tmp_msa = read_input(param->infile[i],tmp_msa)" failed. (run_kalign.c line 383)
ERROR : Function "run_kalign(param)" failed. (run_kalign.c line 353)