| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2021-07-29 | Fix imports to import both process_rqtl_mapping and process_rqtl_pairscan in ↵ | zsloan | |
| api/rqtl.py | |||
| 2021-07-26 | Added pairscan boolean kwarg and process_rqtl_pairscan function for reading ↵ | zsloan | |
| in pairscan results + renamed process_rqtl_output to process_rqtl_mapping to distinguish between that and pairscan | |||
| 2021-07-23 | Added line priting pair-scan results to CSV and changed the default ↵ | zsloan | |
| step-size to 10cM for pair-scan | |||
| 2021-07-23 | - Added scan_func function that determines whether scanone or scantwo | zsloan | |
| (pairscan) is used - For pairscan default to using step 20 (subject to change, but some step is required during calc.genoprob to make it run fast enough) - Added some new verbose prints | |||
| 2021-07-22 | Added option for running pairscan to rqtl_wrapper.R | zsloan | |
| 2021-07-10 | gn3: db: Use correct type for columns arg in fetch functions | BonfaceKilz | |
| 2021-07-10 | Fix pylint issues | BonfaceKilz | |
| 2021-07-10 | db: test_db: Test that a fetch is correct when columns are specified | BonfaceKilz | |
| 2021-07-10 | gn3: db: Add extra argument to specify column in fetch statements | BonfaceKilz | |
| 2021-07-10 | db: phenotypes: Add Probeset data structures | BonfaceKilz | |
| * gn3/db/phenotypes.py (Probeset): New dataclass. (probeset_mapping): New dict. * gn3/db/__init__.py: Add probeset_mapping and Probeset. | |||
| 2021-06-29 | Replace list with a tuple as an argument when setting success_codes | BonfaceKilz | |
| * gn3/commands.py (run_cmd): Replace type of success_codes from List to Tuple * gn3/computations/diff.py (generate_diff): Pass success_codes as a Tuple when calling "run_cmd". | |||
| 2021-06-29 | guix: Add diffutils as a propagated input | BonfaceKilz | |
| 2021-06-29 | guix: Remove commented out hunk | BonfaceKilz | |
| 2021-06-29 | gn3: diff: Set success_codes when running the diff tool | BonfaceKilz | |
| 2021-06-29 | gn3: commands: Add extra arg that sets the success codes to check | BonfaceKilz | |
| * gn3/commands.py (run_cmd): Some commands like "diff" return non-standard error codes. To make this fn more robust, add an extra optional argument that sets what successful codes to check. | |||
| 2021-06-29 | tests: test_commands: Add extra check for when an error occurs | BonfaceKilz | |
| 2021-06-29 | Add a diffing function | BonfaceKilz | |
| For now the diff function uses the Linux tool "diff" to generate the diff since it is efficient and straightforward. * gn3/computations/diff.py (generate_diff): New function. * tests/unit/computations/test_diff.py: Test cases for ☝🏾. | |||
| 2021-06-29 | tests: test_data: Add test data that contains trait data for 10007 | BonfaceKilz | |
| 2021-06-25 | Check for the correct result code | BonfaceKilz | |
| When programs terminate with an error, they usually return a -1! | |||
| 2021-06-23 | Merge pull request #21 from genenetwork/fix/biweight-errors | BonfaceKilz | |
| Fix/biweight errors | |||
| 2021-06-23 | fix pylint issues | Alexander Kabui | |
| 2021-06-23 | minor fixes for biweight script | Alexander Kabui | |
| 2021-06-22 | scripts: laminar: Add json with hooks for running a linter | BonfaceKilz | |
| 2021-06-22 | scripts: laminar: Add sh scripts for CI | BonfaceKilz | |
| 2021-06-21 | Merge pull request #20 from genenetwork/feature/biweight-correlation | BonfaceKilz | |
| add biweight r script and tests | |||
| 2021-06-20 | minor fix docstring | Alexander Kabui | |
| 2021-06-20 | merge main | Alexander Kabui | |
| 2021-06-20 | fix conflict | Alexander Kabui | |
| 2021-06-20 | make requested changes to biweight | Alexander Kabui | |
| 2021-06-18 | Merge pull request #13 from zsloan/feature/add_rqtl_endpoints | zsloan | |
| Feature/add rqtl endpoints | |||
| 2021-06-18 | Fixed another error where test_generate_rqtl_command didn't include the ↵ | zsloan | |
| filename argument (not sure why running unit tests locally doesn't detect this) | |||
| 2021-06-18 | Fixed file type from json to csv for test_generate_rqtl_command | zsloan | |
| 2021-06-18 | Fixed test_rqtl.py to include Rscript in the command | zsloan | |
| 2021-06-18 | Fixed test_compose_rqtl_command test; forgot to include Rscript in the command | zsloan | |
| 2021-06-18 | Change test_compose_rqtl_command in test_commands.py to have different ↵ | zsloan | |
| arguments to hopefully avoid github's pylint 'duplicate code' complaint Changed some parameters in test_compose_rqtl_cmd to avoid pylint complaining about duplicate code | |||
| 2021-06-18 | Fixed pylint issues | zsloan | |
| 2021-06-18 | add ignore_missing_imports for numpy in mypy.ini since it complains about ↵ | zsloan | |
| that and we seem to have done the same thing for scipy | |||
| 2021-06-18 | Resolve mypy errors in computations/rqtl.py | zsloan | |
| 2021-06-18 | Fixed spelling of coeffient to coefficient | zsloan | |
| 2021-06-18 | minor fixes | Alexander Kabui | |
| 2021-06-18 | remove ununsed variables | Alexander Kabui | |
| 2021-06-18 | refactor perf query functions | Alexander Kabui | |
| 2021-06-18 | rename perf query file | Alexander Kabui | |
| 2021-06-18 | pep8 formatting | Alexander Kabui | |
| 2021-06-18 | add tests to setup packages | Alexander Kabui | |
| 2021-06-18 | add types and dataset names | Alexander Kabui | |
| 2021-06-18 | initial commit for queries perfomance tests | Alexander Kabui | |
| 2021-06-18 | db: test_db: Add extra variable in test data for "id" | BonfaceKilz | |
| 2021-06-18 | Rename json_data column to json_diff_data | BonfaceKilz | |
| 2021-06-18 | gn3: db: Fix how columns from tables is resolved | BonfaceKilz | |
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