Reenable writing index only

[ASLeonard]

Relatively minor change after some parameters changed. Not sure if indexing on the fly will be the preferred option going forward, but seems intuitive if you want to write the index that that is all you want to do. Also assumes if you have an index and still want to write an index, you want to overwrite it

[ekg]

I was hoping we could do this via -W[FILE], --write-index=[FILE] build and save index to FILE. Does that not work?

[ekg]

this only builds the index and saves to file

[ASLeonard]

Using --write-index will write the index file but then continue on to the mapping stage. Building the index separately would allow something like the all2all_jobs.py script or some other allocation approach to do node-level parallelisation of the mappings once the index has been built a single time.

[ekg]

Ok, then we should fix this. The behavior should be to write and exit without mapping. I would not want to map too or have an option to do that. We can load the same index.