Multiple threads and initial alignment

[smirarab]

It seems that in creating the initial alignments, we don't use multiple threads, even if available. Look at this code in the mainsate:

                for unaligned_seqs in multilocus_dataset:
                    job = sate_team.aligner.create_job(unaligned_seqs,
                                                       tmp_dir_par=init_aln_dir,
                                                       context_str="initalign",
                                                       delete_temps=delete_aln_temps)
                    _RunningJobs = job
                    jobq.put(job)
                    new_alignment = job.get_results()
                    _RunningJobs = None
                    new_alignment_list.append(new_alignment)

Shouldn't we break up this for loop to two loops (one for queuing, one for reading results) so that different markers could be aligned in parallel?

[mtholder]

This has been fixed in commit 9727761
It did also require slight changes to the system for killing running jobs. Tested by hand, but we don't have a unit or integration test for this yet.