v2.1.0 - Fix filtering

[jethror1]

Changes

• Fix for issue where variants were not correctly excluded if they already had strings in the FILTER column
  • Fixes #104
• Fix typo in test causing columns.test_parsed_correct_gnomAD_AF_values() to fail
• Fix reference to gnomad_base_url

$ python3 -m pytest -v resources/home/dnanexus/generate_workbook/tests/
======================================================== test session starts =========================================================
platform linux -- Python 3.8.10, pytest-7.0.1, pluggy-1.0.0 -- /usr/bin/python3
cachedir: .pytest_cache
rootdir: /home/jethro/Projects/eggd_vcf2xls_nirvana/resources/home/dnanexus/generate_workbook/tests, configfile: pytest.ini
collected 27 items                                                                                                                   

resources/home/dnanexus/generate_workbook/tests/test_columns.py::test PASSED                                                   [  3%]
resources/home/dnanexus/generate_workbook/tests/test_columns.py::TestMainColumns::test_chrom PASSED                            [  7%]
resources/home/dnanexus/generate_workbook/tests/test_columns.py::TestMainColumns::test_pos PASSED                              [ 11%]
resources/home/dnanexus/generate_workbook/tests/test_columns.py::TestMainColumns::test_id PASSED                               [ 14%]
resources/home/dnanexus/generate_workbook/tests/test_columns.py::TestMainColumns::test_ref PASSED                              [ 18%]
resources/home/dnanexus/generate_workbook/tests/test_columns.py::TestMainColumns::test_alt PASSED                              [ 22%]
resources/home/dnanexus/generate_workbook/tests/test_columns.py::TestMainColumns::test_qual PASSED                             [ 25%]
resources/home/dnanexus/generate_workbook/tests/test_columns.py::TestMainColumns::test_filter PASSED                           [ 29%]
resources/home/dnanexus/generate_workbook/tests/test_columns.py::TestInfoColumn::test_parsed_correct_columns_from_info_records PASSED [ 33%]
resources/home/dnanexus/generate_workbook/tests/test_columns.py::TestInfoColumn::test_parsed_correct_gnomAD_AF_values PASSED   [ 37%]
resources/home/dnanexus/generate_workbook/tests/test_columns.py::TestFormatSample::test_format_sample_values_are_correct PASSED [ 40%]
resources/home/dnanexus/generate_workbook/tests/test_filters.py::TestModifyingFieldTypes::test_type_correctly_modified PASSED  [ 44%]
resources/home/dnanexus/generate_workbook/tests/test_filters.py::TestModifyingFieldTypes::test_header_overwritten_correctly PASSED [ 48%]
resources/home/dnanexus/generate_workbook/tests/test_filters.py::TestFilters::test_filter_with_include_eq PASSED               [ 51%]
resources/home/dnanexus/generate_workbook/tests/test_filters.py::TestFilters::test_filter_with_exclude_eq PASSED               [ 55%]
resources/home/dnanexus/generate_workbook/tests/test_filters.py::TestFilters::test_filter_with_exclude_gt PASSED               [ 59%]
resources/home/dnanexus/generate_workbook/tests/test_filters.py::TestFilters::test_combined_exclude_float_and_string PASSED    [ 62%]
resources/home/dnanexus/generate_workbook/tests/test_filters.py::TestFilters::test_combined_filter_and_recover PASSED          [ 66%]
resources/home/dnanexus/generate_workbook/tests/test_vcf.py::TestHeader::test_column_names PASSED                              [ 70%]
resources/home/dnanexus/generate_workbook/tests/test_vcf.py::TestHeader::test_parse_reference PASSED                           [ 74%]
resources/home/dnanexus/generate_workbook/tests/test_vcf.py::TestHeader::test_only_header_parsed PASSED                        [ 77%]
resources/home/dnanexus/generate_workbook/tests/test_vcf.py::TestDataFrameActions::test_drop_columns_exclude PASSED            [ 81%]
resources/home/dnanexus/generate_workbook/tests/test_vcf.py::TestDataFrameActions::test_drop_columns_include PASSED            [ 85%]
resources/home/dnanexus/generate_workbook/tests/test_vcf.py::TestDataFrameActions::test_reorder_columns_correct_order PASSED   [ 88%]
resources/home/dnanexus/generate_workbook/tests/test_vcf.py::TestDataFrameActions::test_reorder_columns_no_dropped_columns PASSED [ 92%]
resources/home/dnanexus/generate_workbook/tests/test_vcf.py::TestDataFrameActions::test_non_rename_columns_unaffacted PASSED   [ 96%]
resources/home/dnanexus/generate_workbook/tests/test_vcf.py::TestDataFrameActions::test_renamed_correctly PASSED               [100%]

======================================================== 27 passed in 31.03s =========================================================

---

This change is 

[pep8speaks]

Hello @jethror1! Thanks for opening 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 178:5: E303 too many blank lines (2) Line 187:34: W605 invalid escape sequence '.' Line 187:37: W605 invalid escape sequence '-' Line 198:80: E501 line too long (80 > 79 characters)