Closed jethror1 closed 1 year ago
Improves parsing of reference by using assembly field in VEP string from VCF header, which is then added to both dias and basic summary sheets.
Unit tests:
$ python3 -m pytest resources/home/dnanexus/generate_workbook/tests/test_vcf.py -k TestHeader --disable-warnings =================================================== test session starts =================================================== platform linux -- Python 3.8.10, pytest-7.0.1, pluggy-1.0.0 rootdir: /home/jethro/Projects/eggd_generate_variant_workbook/resources/home/dnanexus/generate_workbook/tests, configfile: pytest.ini plugins: Faker-14.0.0, mock-3.9.0, cov-4.0.0 collected 17 items / 13 deselected / 4 selected resources/home/dnanexus/generate_workbook/tests/test_vcf.py .... [100%] ============================================ 4 passed, 13 deselected in 0.32s =============================================
Example WES vcf with dias summary:
Example TSO500 vcf with basic summary:
This change is
Improves parsing of reference by using assembly field in VEP string from VCF header, which is then added to both dias and basic summary sheets.
Unit tests:
Example WES vcf with dias summary:
Example TSO500 vcf with basic summary:
This change is