| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-11-08 | Fix issue where only primary samples were used when all samples are | zsloan | |
| selected This is because base_samples was set to all_samples_ordered, which only includes primary samples + parents/f1s. Setting this to an empty list fixed the issue and caused it to use all samples again. | |||
| 2022-10-22 | fix issue;parsing sample data (#102) | Alexander Kabui | |
| 2022-10-06 | DEBUG: Collect more info for debugging | Frederick Muriuki Muriithi | |
| 2022-10-06 | DEBUG: Collect more information on possible failure. | Frederick Muriuki Muriithi | |
| 2022-10-03 | Bug: Do not process data for output too early | Frederick Muriuki Muriithi | |
| * gn3/computations/rust_correlation.py: (parse_tissue_corr_data): The function was parsing data from a file, and then converting the parsed values into a comma-separated string for output, despite the fact that the data parsed is not output in this specific function. This is a really bad idea, and leads to errors showing up down the line, far removed from the cause. | |||
| 2022-09-30 | Add escape char to avoid error notice. | Frederick Muriuki Muriithi | |
| 2022-09-29 | Use the built-in csv module for file output | Frederick Muriuki Muriithi | |
| Use the built-in csv module for file output in order to avoid subtle errors in the formats. | |||
| 2022-08-25 | revert for commit 6db3b2af8fc09999996d3acc09890a06f179c669;Bug | Alexander_Kabui | |
| 2022-08-12 | Add mandatory/expected fields to parsed data. | Frederick Muriuki Muriithi | |
| 2022-08-10 | Fix returned value for 'parse_correlation_output' | Frederick Muriuki Muriithi | |
| * Always return dict * Fix internal '__parse_line__' to always have a valid return | |||
| 2022-08-10 | code refactoring | Frederick Muriuki Muriithi | |
| 2022-08-10 | remove unnecessary parsing of floats | Alexander_Kabui | |
| 2022-08-10 | code refactoring | Frederick Muriuki Muriithi | |
| 2022-08-10 | remove unnecessary parsing of floats | Alexander_Kabui | |
| 2022-08-10 | enhancements for rust tissue | Frederick Muriuki Muriithi | |
| 2022-08-10 | pylint fixes | Alexander_Kabui | |
| 2022-08-10 | code refactoring | Alexander_Kabui | |
| 2022-08-10 | remove unnessary code | Alexander_Kabui | |
| 2022-08-10 | remove unnecessary parsing of floats | Alexander_Kabui | |
| 2022-08-10 | merge for results | Alexander_Kabui | |
| 2022-08-10 | enhancements for rust tissue | Alexander_Kabui | |
| 2022-08-03 | Refactor: Remove unnecessary whitespace and name | Frederick Muriuki Muriithi | |
| 2022-08-03 | Refactor: Remove unnecessary iterations and name | Frederick Muriuki Muriithi | |
| * remove extra iteration that is unnecessary * remove unnecessary variables | |||
| 2022-07-29 | Fix failing tests | Frederick Muriuki Muriithi | |
| * gn3/computations/correlations.py: rename function * mypy.ini: deactivate mypy error about missing imports * tests/integration/test_correlation.py: mock correct function * tests/unit/computations/test_correlation.py: test correct function | |||
| 2022-07-28 | Update sample correlations code to use multiprocessing | Frederick Muriuki Muriithi | |
| * To help speed up the processing of the correlations, convert the `compute_all_sample_correlation` function to use the multiprocessing module. | |||
| 2022-07-22 | mypy fixes | Alexander_Kabui | |
| 2022-07-22 | pep8 fixes | Alexander_Kabui | |
| 2022-07-22 | linting and tests fixes | Alexander_Kabui | |
| 2022-07-22 | compute num overlap | Alexander_Kabui | |
| 2022-07-22 | fix for bug splitting list data | Alexander_Kabui | |
| 2022-07-22 | minor fixes for parsing data | Alexander_Kabui | |
| 2022-07-22 | code to parse tissue correlation input | Alexander_Kabui | |
| 2022-07-22 | mypy pylint fixes | Alexander_Kabui | |
| 2022-07-22 | code to fetch correct sample corr data | Alexander_Kabui | |
| 2022-07-22 | delete dead_code;rename variables | Alexander_Kabui | |
| 2022-07-22 | minor fixes | Alexander_Kabui | |
| 2022-06-29 | use explicit parameters | Alexander_Kabui | |
| 2022-06-29 | fix issues | Alexander_Kabui | |
| 2022-06-29 | pylint fixes | Alexander | |
| 2022-06-29 | minor fixes | Alexander | |
| 2022-06-29 | handle tmp files generation | Alexander | |
| 2022-06-29 | parse output data | Alexander | |
| 2022-06-29 | pep8 formatting | Alexander | |
| 2022-06-29 | init rust correlation module | Alexander | |
| 2022-05-30 | Pass trait data as args to `fix_strains` and fix some bugs | Frederick Muriuki Muriithi | |
| The `fix_strains` function works on the trait data, not the basic trait info. This commit fixes the arguments passed to the function, and also some bugs in the function. | |||
| 2022-05-24 | New script to compute partial correlations | Frederick Muriuki Muriithi | |
| * Add a new script to compute the partial correlations against: - a select list of traits, or - an entire dataset depending on the specified subcommand. This new script is meant to supercede the `scripts/partial_correlations.py` script. * Fix the check for errors * Reorganise the order of arguments for the `partial_correlations_with_target_traits` function: move the `method` argument before the `target_trait_names` argument so that the common arguments in the partial correlation computation functions share the same order. | |||
| 2022-05-21 | Use multiprocessing to improve performance | Frederick Muriuki Muriithi | |
| 2022-05-21 | Process primary, target and control traits in a single iteration | Frederick Muriuki Muriithi | |
| Rework the code to process the traits in a single iteration to improve performance. | |||
| 2022-05-21 | Return generator object rather than tuples | Frederick Muriuki Muriithi | |
| Return generator objects rather than pre-computed tuples to reduce the number of iterations needed to process the data, and thus improve the performance of the system somewhat. | |||
| 2022-05-06 | Fix linting and typing errors | Frederick Muriuki Muriithi | |
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