| Age | Commit message (Expand) | Author |
|---|
| 2024-02-28 | tests: Update unit tests: remove use of obsoleted functions. | Frederick Muriuki Muriithi |
| 2024-02-20 | Track filename in the errors...R/qtl2 bundles can contain more than one file, of the same type. When
errors are encountered in any of the files, we need to be able to
inform the user which file it is, in addition to the line and column
number.
| Frederick Muriuki Muriithi |
| 2024-02-20 | Generalise fetching of samples/cases/individuals. | Frederick Muriuki Muriithi |
| 2024-02-20 | Read samples from geno file. | Frederick Muriuki Muriithi |
| 2024-02-12 | Provide the key for each file listed in the control file. | Frederick Muriuki Muriithi |
| 2024-02-08 | Use error objects rather than plain tuple values. | Frederick Muriuki Muriithi |
| 2024-02-06 | Check that pheno values are numerical and at least 3 decimal places | Frederick Muriuki Muriithi |
| 2024-02-05 | Check that data in geno file is valid...Add a function to ensure the values in the geno files are all listed
in the control data under the "genotypes" key.
| Frederick Muriuki Muriithi |
| 2024-02-05 | Fix linting and type errors. | Frederick Muriuki Muriithi |
| 2024-02-05 | Retrieve list of all files, and list of missing files...Add QC a function to list all files listed in the control file, and
another to list only the files missing from the bundle.
| Frederick Muriuki Muriithi |
| 2024-02-02 | Ensure control file defaults are set up in code. | Frederick Muriuki Muriithi |
| 2024-01-15 | Process `na.strings` even for default cases...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.
| Frederick Muriuki Muriithi |
| 2024-01-10 | Make identifier column name explicit...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.
| Frederick Muriuki Muriithi |
| 2024-01-09 | Raise exception on reading non-existing file...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.
| 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 | Rename test module...While 'covar' files can contain cross information, they do not have
to, and therefore, we need to test for cross information separately.
| Frederick Muriuki Muriithi |
| 2024-01-04 | Parse multiple files with same file key. | Frederick Muriuki Muriithi |
| 2024-01-04 | Test parsing of multiple files for single key | Frederick Muriuki Muriithi |
| 2024-01-04 | Add tests for parsing cross information (covar) files. | Frederick Muriuki Muriithi |
| 2024-01-04 | Add tests for parsing 'phenocovar' files. | Frederick Muriuki Muriithi |
| 2024-01-04 | Rename test module. | 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....* 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
| Frederick Muriuki Muriithi |
| 2024-01-03 | Add tests for `founder_geno` parsing. | Frederick Muriuki Muriithi |
| 2024-01-03 | Parse the phenotype data from the R/qtl2 bundle. | Frederick Muriuki Muriithi |
| 2024-01-03 | Extract processing of transposed files into reusable function....The processing of transposed files is similar across files. This
commit extracts the common parts into a separate function.
| 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....Check that the parsing of non-transposed geno files.
Leave in failing test for transposed geno files.
| Frederick Muriuki Muriithi |
| 2023-12-27 | Tests: Test parsing of pmap files. Merge testing of map files. | Frederick Muriuki Muriithi |
| 2023-12-27 | Tests: Add tests for parsing gmap files. | Frederick Muriuki Muriithi |
