Issues with setup

[DRL]

It is currently possible to parse more variants than can be placed in intervals.

Requires

• gimble._set_intervals() to be called before gimble._set_variants()
• filtering of variant position array by interval position array (based on all samples)

Possibly related to Noora's issue:

[+] Running 'gimble blocks'
[+] Parameters = [-l 64 -m 128 -u 3 -i 3]
[#] Preflight...
[#] Making blocks...
[%] Building blocks :   0%|                                              | 0.00/330 [00:02<?, ?it/s]
Traceback (most recent call last):
  File "gIMble/./gIMble", line 8, in <module>
    main(os.path.dirname(os.path.realpath(file)))
  File "/data/lohse/drosophila/analyses/18_gimble/combined_ref/gIMble/cli/interface.py", line 69, in main
    blocks.main(params)
  File "/data/lohse/drosophila/analyses/18_gimble/combined_ref/gIMble/cli/blocks.py", line 61, in main
    gimbleStore.blocks(parameterObj)
  File "/data/lohse/drosophila/analyses/18_gimble/combined_ref/gIMble/lib/gimble.py", line 1039, in blocks
    self._make_blocks(parameterObj)
  File "/data/lohse/drosophila/analyses/18_gimble/combined_ref/gIMble/lib/gimble.py", line 2659, in _make_blocks
    block_sites = genotype_to_mutype_array(sa_sample_set_genotype_array, idx_block_sites_in_pos, block_sites, debug)
  File "/data/lohse/drosophila/analyses/18_gimble/combined_ref/gIMble/lib/gimble.py", line 462, in genotype_to_mutype_array
    block_sites[idx_block_sites_in_pos] = szudzik_pairing(folded_minor_allele_counts) + 2               # add 2 so that not negative for bincount
ValueError: NumPy boolean array indexing assignment cannot assign 616352 input values to the 621913 output values where the mask is true```

[DRL]

Refactored gimble.Store._set_variants()to now

• first parse BED intervals and then
• parse VCF while using
• *_get_interval_coordinates_for_sample_set() to fetch BED intervals which
• are used to decide which variant records get save/counted

[DRL]

fixed in https://github.com/DRL/gIMble/commit/65ef9e5ac52bbdfe4fedc4511957f64c179a4d56