Feature/breakends

[MalinAhlberg]

Describe the pull request:

• Bug fix
• New feature

Pull request long description:

Add parser for MANTA-vcf files and adds breakends variants to the database model.

./scripts/manage.sh import --add_raw_data \
                   --dataset beacon_test \
                   --version 2030-01-01 \
                  --assembly_id "GRCh38" \
                   --add_mates \
                   --variant_file MANTA.vcf

Changes made:

Related changes:

1. Add table data.mate and view beacon.beacon_mate_table.
2. Add flag --add_mates to the importer, which will add all BNDs from the given vcf-file (instead of runnig _insert_variants()!)

Less related changes:

1. Use PRIVATE instead of None as access type for beacon.available_datasets
2. Small adjustments in code for reading files and logging
3. Remove duplicated if

Open questions:

• keep the sql mate table under data or beacon schema?
• merge parsing of "normal" vcf files and MANTA or keep them separated?
• should the imported variants be part of another dataset (eg SweGen)?
• if so, how to calculate the counts for the whole dataset? Eg callCount and variantCount to store in beacon_dataset_counts_table. Are they the same as when reading the standard vcf, or do they change?
• how to get the counts for each variants (variant- and callcount)? They are not included in the MANTA, as far as I can tell.
• naming confusion: mate, fusion, breakend... What do we call what?