| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-01-15 | Process `na.strings` even for default cases | Frederick 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. | |||
| 2024-01-15 | Extract common functional tools to separate package. | Frederick Muriuki Muriithi | |
| 2024-01-10 | Provide convenience functions to avoid subtle call errors | Frederick Muriuki Muriithi | |
| 2024-01-10 | Make identifier column name explicit | Frederick 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. | |||
| 2024-01-09 | Raise exception on reading non-existing file | Frederick 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. | |||
| 2024-01-08 | Upload R/qtl2 zip bundle and check for errors. | Frederick Muriuki Muriithi | |
| 2024-01-04 | Parse sex information from R/qtl bundle. | Frederick Muriuki Muriithi | |
| 2024-01-04 | Parse cross information from R/qtl2 bundle. | Frederick Muriuki Muriithi | |
| 2024-01-04 | Process sex and cross information data in "covar" files. | Frederick Muriuki Muriithi | |
| 2024-01-04 | Parse multiple files with same file key. | Frederick Muriuki Muriithi | |
| 2024-01-03 | Use generic parser. Remove obsoleted functions. | Frederick Muriuki Muriithi | |
| 2024-01-03 | Parse 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 | |||
| 2024-01-03 | Parse the phenotype data from the R/qtl2 bundle. | Frederick Muriuki Muriithi | |
| 2024-01-03 | Rename argument and add documentation to functions. | Frederick Muriuki Muriithi | |
| 2024-01-03 | Extract 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. | |||
| 2024-01-03 | Refactor: Extract potentially reusable functions | Frederick Muriuki Muriithi | |
| The processing of transposed files is probably going to be very similar, thus the need to extract some reusable code from the geno-file-specific function in preparation. | |||
| 2024-01-02 | Abstract away non-transposed file processing | Frederick Muriuki Muriithi | |
| Since the processing of non-transposed files is mostly similar, abstract away the common operations into a separate function and use the function instead of repeating the same pattern of code throughout the codebase. | |||
| 2024-01-02 | Cleanup: Fix linting and typing errors and update docs. | Frederick Muriuki Muriithi | |
| 2023-12-28 | Rework parsing of transposed geno files. | Frederick Muriuki Muriithi | |
| 2023-12-28 | Handle transposed geno files. | Frederick Muriuki Muriithi | |
| 2023-12-27 | Tests: 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. | |||
| 2023-12-27 | Tests: Add tests for parsing gmap files. | Frederick Muriuki Muriithi | |
| 2023-12-25 | Generalise to read both genetic and physical maps. | Frederick Muriuki Muriithi | |
| 2023-12-25 | Read genetic map files | Frederick Muriuki Muriithi | |
| 2023-12-20 | Read genotype files | Frederick Muriuki Muriithi | |
| 2023-12-20 | Read R/qtl2 format files | Frederick Muriuki Muriithi | |
| * Set up error objects. * Read the control data. | |||
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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