Steps for generating SA intervals for kmers

[ffranr]

0) Test latest kmer generating code i) Does it generate all kmers like the old code does? ii) Does it generate the variant overlapping kmers correctly? (unit tests pass + small-ish manual test + simulated reads that all map (on wg and toy prg))

1) For WG prg, generate all kmers with old variantKmers -n (on EBI cluster, splitting into many jobs wit independent subfiles of kmers) and generate precalc files with baseline commit. Add a commit on baseline tro use 1 thread

2) Prioritize kmer sizes 15 and 17 when generating precalc files. Run all from 2 to 20.

3) As one but for variant overlapping kemrs only. 150 kmers region size.

Parameters for cluster: 1 threads, cluster should report overall RAM usage should happen automatically.

Baseline commit: https://github.com/iqbal-lab-org/gramtools/tree/a510cbd699f37cb7c4561a1d201d549dfad97b91

[iqbal-lab]

For step 1 (and 3) - Sorina has confirmed that she used gramtools.py --quasimap to generate the precalc file

[ffranr]

I think that this work has been completed.