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2024-01-10Make identifier column name explicitFrederick Muriuki Muriithi
Since the R/qtl2 bundle generator could name the identifier column anything, this commit converts the incoming identifier column name into something explicit that we know and can use.
2024-01-09Raise exception on reading non-existing fileFrederick Muriuki Muriithi
The validation checks ensure that whatever files are listed in the control file exist in the zip file bundle. It is still possible, however, that the code tries to read a file that does not exist in the file and is not listed in the control file. In those cases, raise the appropriate exception.
2024-01-04Parse sex information from R/qtl bundle.Frederick Muriuki Muriithi
2024-01-04Parse cross information from R/qtl2 bundle.Frederick Muriuki Muriithi
2024-01-04Process sex and cross information data in "covar" files.Frederick Muriuki Muriithi
2024-01-04Rename test moduleFrederick Muriuki Muriithi
While 'covar' files can contain cross information, they do not have to, and therefore, we need to test for cross information separately.
2024-01-04Parse multiple files with same file key.Frederick Muriuki Muriithi
2024-01-04Test parsing of multiple files for single keyFrederick Muriuki Muriithi
2024-01-04Add tests for parsing cross information (covar) files.Frederick Muriuki Muriithi
2024-01-04Add tests for parsing 'phenocovar' files.Frederick Muriuki Muriithi
2024-01-04Rename test module.Frederick Muriuki Muriithi
2024-01-03Use generic parser. Remove obsoleted functions.Frederick Muriuki Muriithi
2024-01-03Parse founder_geno files. Generalise parsing files.Frederick Muriuki Muriithi
* Add tests for parsing "founder_geno" files * Extract common file parsing structure out to more general function * Use generic function to parse "founder_geno" file in test
2024-01-03Add tests for `founder_geno` parsing.Frederick Muriuki Muriithi
2024-01-03Parse the phenotype data from the R/qtl2 bundle.Frederick Muriuki Muriithi
2024-01-03Extract processing of transposed files into reusable function.Frederick Muriuki Muriithi
The processing of transposed files is similar across files. This commit extracts the common parts into a separate function.
2023-12-28Rework parsing of transposed geno files.Frederick Muriuki Muriithi
2023-12-28Handle transposed geno files.Frederick Muriuki Muriithi
2023-12-27Tests: Test parsing of non-transposed geno files.Frederick Muriuki Muriithi
Check that the parsing of non-transposed geno files. Leave in failing test for transposed geno files.
2023-12-27Tests: Test parsing of pmap files. Merge testing of map files.Frederick Muriuki Muriithi
2023-12-27Tests: Add tests for parsing gmap files.Frederick Muriuki Muriithi