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2024-02-05Check that data in geno file is validFrederick Muriuki Muriithi
Add a function to ensure the values in the geno files are all listed in the control data under the "genotypes" key.
2024-02-05Retrieve list of all files, and list of missing filesFrederick Muriuki Muriithi
Add QC a function to list all files listed in the control file, and another to list only the files missing from the bundle.
2024-02-02Ensure control file defaults are set up in code.Frederick Muriuki Muriithi
2024-01-15Process `na.strings` even for default casesFrederick Muriuki Muriithi
There was a bug where the `na.strings` were not processed correctly if the user called the `r_qtl.r_qtl2.file_data(...)` function without explicitly providing the `process_*` arguments. This commit fixes that.
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
2024-01-04Parse multiple files with same file key.Frederick 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
2024-01-03Parse 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
2024-01-03Parse the phenotype data from the R/qtl2 bundle.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