IN-406 - handle pre-split VCFs

[jethror1]

• update to handle VCFs alreasy split with bcftools +split-vep, as well as non-VEP annotated VCFs
  • this is primarialy done through the vcfs.check_vep_vcf() function, if the VCF is not to be split it patches in a temporary VCF to continue downstream processing
  • fixes #138
• fix lots of tests broken by prior changes
  • includes adding test control VCF to test_data dir
• added GitHub action to run unit tests to make sure any failing tests don't get missed in future
• fix lots of minor typos
• fixes #156

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This change is 

[pep8speaks]

Hello @jethror1! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file resources/home/dnanexus/generate_workbook/tests/test_columns.py:

Line 317:41: W605 invalid escape sequence '.' Line 329:80: E501 line too long (83 > 79 characters)

• In the file resources/home/dnanexus/generate_workbook/tests/test_vcf.py:

Line 119:5: E303 too many blank lines (2) Line 130:5: E303 too many blank lines (2) Line 142:5: E303 too many blank lines (2) Line 153:5: E303 too many blank lines (2) Line 405:9: E303 too many blank lines (2) Line 415:80: E501 line too long (82 > 79 characters)

• In the file resources/home/dnanexus/generate_workbook/utils/vcf.py:

Line 231:80: E501 line too long (82 > 79 characters) Line 280:5: E303 too many blank lines (2)

Comment last updated at 2024-01-31 16:45:53 UTC