In #636 we added a new flag bq_uses_1_based_coordinate to allow users to export variants from BQ tables that are using either 0-baed on 1-based coordinate.
Note that our default value for coordinate (both bq_uses_1_based_coordinate and use_1_based_coordinate) is set to 1-based. That's why in #633 we updated all our integration tests to test the default path and added a few for testing 0-based.
We need to do the same thing for bq_to_vcf integration tests:
we should update their use_1_based_coordinate
we should remove "bq_uses_1_based_coordinate": false, line from the json files (so we will use the default True value).
Here is the list of tests that needs to be updated:
In #636 we added a new flag
bq_uses_1_based_coordinateto allow users to export variants from BQ tables that are using either 0-baed on 1-based coordinate.Note that our default value for coordinate (both
bq_uses_1_based_coordinateanduse_1_based_coordinate) is set to 1-based. That's why in #633 we updated all our integration tests to test the default path and added a few for testing 0-based.We need to do the same thing for bq_to_vcf integration tests:
use_1_based_coordinate"bq_uses_1_based_coordinate": false,line from the json files (so we will use the defaultTruevalue).Here is the list of tests that needs to be updated:
bq_to_vcf_tests/no_options.jsonbq_to_vcf_tests/option_allow_incompatible_schema.jsonbq_to_vcf_tests/option_customized_export.jsonbq_to_vcf_tests/option_number_of_bases_per_shard.jsonbq_to_vcf_tests/option_preserve_sample_order.jsonbq_to_vcf_tests/option_representative_header_file.jsonbq_to_vcf_tests/option_use_1_based_coordinate.json