Split VCF line in builder and storage object#18
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tcezard merged 2 commits intoEBIvariation:mainfrom Dec 2, 2025
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khetherin
reviewed
Dec 1, 2025
| pragmas_to_add.append(generate_vcf_header_unstructured_line(vcf_header_key, pragma_value)) | ||
| for vcf_obj in list_of_vcf_objects: | ||
| pragmas_to_add.append(generate_vcf_header_unstructured_line("source", vcf_obj.source)) | ||
| # FIXME: Why are we adding header from the VCF lines |
Collaborator
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Adding the source (displayed in VCF header as: ##source=DGVa). This comes from the GVF feature line. Alsopragmas_to_add is probably a misleading name, these were GVF pragmas that have been converted to VCF header.
khetherin
reviewed
Dec 1, 2025
| unique_info_lines_to_add = list(dict.fromkeys(info_line for info_line in standard_lines_dictionary["INFO"] if info_line not in unique_info_lines_to_add)) | ||
| unique_filter_lines_to_add = list(dict.fromkeys(filter_line for filter_line in standard_lines_dictionary["FILTER"] if filter_line not in unique_filter_lines_to_add)) | ||
| unique_format_lines_to_add = list(dict.fromkeys(format_line for format_line in standard_lines_dictionary["FORMAT"] if format_line not in unique_format_lines_to_add)) | ||
| # TODO: The addition of headers from the VCF lines should be done in the VCF builder |
Collaborator
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I agree with the TODO. I also think the function generate_vcf_header_metainfo could be simplified.
khetherin
reviewed
Dec 1, 2025
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| # This is the main conversion logic | ||
| def convert_gvf_features_to_vcf_objects(gvf_lines_obj_list, reference_lookup): | ||
| def convert_gvf_features_to_vcf_objects(gvf_lines_obj_list, reference_lookup, ordered_list_of_samples): |
Collaborator
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Having an ordered_list_of_Samples is a good idea and will be useful in this function. Getting this ordered list will need to come from the GVF pragmas and should be done early on.
khetherin
reviewed
Dec 1, 2025
| self.info_dict = merged_info_dict | ||
| other_vcf_line.info_dict = merged_info_dict | ||
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| def merge_vcf_values_for_format(self, other_vcf_line): |
khetherin
approved these changes
Dec 1, 2025
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