| Age | Commit message (Expand) | Author |
|---|
| 2024-02-12 | Provide the key for each file listed in the control file. | Frederick Muriuki Muriithi |
| 2024-02-08 | Generalise error retrieval: extract common structure...Extract the common structure into a separate function and pass in
checkers that return the errors they find.
| 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 | Do general bundle validation and show errors...* Display any and all errors on the UI
* Move `validate_bundle` to QC module and refactor to use
`missing_files`
| 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 | List file types in a single place for easier reuse | Frederick Muriuki Muriithi |
| 2024-02-02 | Ensure control file defaults are set up in code. | Frederick Muriuki Muriithi |
| 2024-01-16 | Provide defaults for various control variables...`na.strings` has a default value of "NA" as stated in
https://kbroman.org/qtl2/assets/vignettes/input_files.html#CSV_files
quote:
> Missing value codes will be specified in the control file (as
> na.strings, with default value "NA") and will apply across all
> files, so a missing value code for one file cannot be an allowed
> value in another file.
for `comment.char`
> The CSV files can include a header with a set of comment lines
> initiated by a value specified in the control file as comment.char
> (with default value "#").
for `sep`:
The default separator is expected to be the comma, as stated in
https://kbroman.org/qtl2/assets/vignettes/input_files.html#field-separator
quote:
> If the data files use a separator other than a comma ...
| 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 |
| 2024-01-15 | 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...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 |
| 2024-01-08 | 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....* 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 | 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....The processing of transposed files is similar across files. This
commit extracts the common parts into a separate function.
| Frederick Muriuki Muriithi |
| 2024-01-03 | Refactor: Extract potentially reusable functions...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.
| Frederick Muriuki Muriithi |
| 2024-01-02 | Abstract away non-transposed file processing...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.
| Frederick Muriuki Muriithi |
| 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....Check that the parsing of non-transposed geno files.
Leave in failing test for transposed geno files.
| Frederick Muriuki Muriithi |
| 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...* Set up error objects.
* Read the control data.
| Frederick Muriuki Muriithi |
