Add an option to loqusdb to select which sample to upload / check identity in a multi sample vcf without bed

[dnil]

For BALSAMIC, ped files are missing, but we would like to select which sample to match / upload to loqusdb.

[dnil]

C f

/home/proj/stage/bin/miniconda3/envs/S_loqusdb/bin/loqusdb --config /home/proj/stage/servers/config/hasta.scilifelab.se/loqusdb-somatic-stage.yaml load --case-id grandmarmot --variant-file /home/proj/stage/housekeeper-bundles/grandmarmot/2022-12-05/SNV.somatic.grandmarmot.tnscope.vcf.gz --sv-variants /home/proj/stage/housekeeper-bundles/grandmarmot/2022-12-05/SV.somatic.grandmarmot.svdb.vcf.gz --check-profile /home/proj/stage/housekeeper-bundles/grandmarmot/2022-12-05/SNV.germline.tumor.dnascope.vcf.gz --gq-treshold 10 --hard-threshold 0.95 --soft-threshold 0.9
2022-12-06 11:42:19 [hasta.scilifelab.se](http://hasta.scilifelab.se/) loqusdb.commands.cli[74829] INFO Running loqusdb version 2.6.9
2022-12-06 11:42:19 [hasta.scilifelab.se](http://hasta.scilifelab.se/) mongo_adapter.client[74829] INFO Connecting to uri:mongodb://loqusdb-stage:******@cg-mongo-stage.scilifelab.se:27030
2022-12-06 11:42:19 [hasta.scilifelab.se](http://hasta.scilifelab.se/) mongo_adapter.client[74829] INFO Connection established
2022-12-06 11:42:19 [hasta.scilifelab.se](http://hasta.scilifelab.se/) mongo_adapter.adapter[74829] INFO Use database loqusdb-somatic-stage
2022-12-06 11:42:19 [hasta.scilifelab.se](http://hasta.scilifelab.se/) loqusdb.utils.vcf[74829] INFO Check if vcf is on correct format...
[W::hts_idx_load3] The index file is older than the data file: /home/proj/stage/housekeeper-bundles/grandmarmot/2022-12-05/SNV.somatic.grandmarmot.tnscope.vcf.gz.tbi
2022-12-06 11:42:22 [hasta.scilifelab.se](http://hasta.scilifelab.se/) loqusdb.utils.vcf[74829] INFO Vcf file /home/proj/stage/housekeeper-bundles/grandmarmot/2022-12-05/SNV.somatic.grandmarmot.tnscope.vcf.gz looks fine
2022-12-06 11:42:22 [hasta.scilifelab.se](http://hasta.scilifelab.se/) loqusdb.utils.vcf[74829] INFO Nr of variants in vcf: 223798
2022-12-06 11:42:22 [hasta.scilifelab.se](http://hasta.scilifelab.se/) loqusdb.utils.vcf[74829] INFO Type of variants in vcf: snv
2022-12-06 11:42:22 [hasta.scilifelab.se](http://hasta.scilifelab.se/) loqusdb.utils.vcf[74829] INFO Check if vcf is on correct format...
[W::vcf_parse] FILTER ‘GERMLINE’ is not defined in the header
2022-12-06 11:42:22 [hasta.scilifelab.se](http://hasta.scilifelab.se/) loqusdb.utils.vcf[74829] INFO Vcf file /home/proj/stage/housekeeper-bundles/grandmarmot/2022-12-05/SV.somatic.grandmarmot.svdb.vcf.gz looks fine
2022-12-06 11:42:22 [hasta.scilifelab.se](http://hasta.scilifelab.se/) loqusdb.utils.vcf[74829] INFO Nr of variants in vcf: 17580
2022-12-06 11:42:22 [hasta.scilifelab.se](http://hasta.scilifelab.se/) loqusdb.utils.vcf[74829] INFO Type of variants in vcf: sv
[W::hts_idx_load3] The index file is older than the data file: /home/proj/stage/housekeeper-bundles/grandmarmot/2022-12-05/SNV.somatic.grandmarmot.tnscope.vcf.gz.tbi
Traceback (most recent call last):
  File “/home/proj/stage/bin/miniconda3/envs/S_loqusdb/bin/loqusdb”, line 8, in <module>
    sys.exit(base_command())
  File “/home/proj/stage/bin/miniconda3/envs/S_loqusdb/lib/python3.7/site-packages/click/core.py”, line 829, in __call__
    return self.main(*args, **kwargs)
  File “/home/proj/stage/bin/miniconda3/envs/S_loqusdb/lib/python3.7/site-packages/click/core.py”, line 782, in main
    rv = self.invoke(ctx)
  File “/home/proj/stage/bin/miniconda3/envs/S_loqusdb/lib/python3.7/site-packages/click/core.py”, line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File “/home/proj/stage/bin/miniconda3/envs/S_loqusdb/lib/python3.7/site-packages/click/core.py”, line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File “/home/proj/stage/bin/miniconda3/envs/S_loqusdb/lib/python3.7/site-packages/click/core.py”, line 610, in invoke
    return callback(*args, **kwargs)
  File “/home/proj/stage/bin/miniconda3/envs/S_loqusdb/lib/python3.7/site-packages/click/decorators.py”, line 21, in new_func
    return f(get_current_context(), *args, **kwargs)
  File “/home/proj/stage/bin/miniconda3/envs/S_loqusdb/lib/python3.7/site-packages/loqusdb/commands/load.py”, line 144, in load
    genome_build=genome_build,
  File “/home/proj/stage/bin/miniconda3/envs/S_loqusdb/lib/python3.7/site-packages/loqusdb/utils/load.py”, line 122, in load_database
    profile_path=profile_file,
  File “/home/proj/stage/bin/miniconda3/envs/S_loqusdb/lib/python3.7/site-packages/loqusdb/build_models/case.py”, line 113, in build_case
    profile = profiles[ind_id] if profiles else None
KeyError: ‘NORMAL’