| Age | Commit message (Expand) | Author |
|---|
| 2022-11-08 | Fix issue where only primary samples were used when all samples are...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.
| zsloan |
| 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...* 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.
| Frederick Muriuki Muriithi |
| 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...Use the built-in csv module for file output in order to avoid subtle errors in
the formats.
| Frederick Muriuki Muriithi |
| 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'...* Always return dict
* Fix internal '__parse_line__' to always have a valid return
| Frederick Muriuki Muriithi |
| 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...* remove extra iteration that is unnecessary
* remove unnecessary variables
| Frederick Muriuki Muriithi |
| 2022-07-29 | Fix failing tests...* 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
| Frederick Muriuki Muriithi |
| 2022-07-28 | Update sample correlations code to use multiprocessing...* To help speed up the processing of the correlations, convert the
`compute_all_sample_correlation` function to use the multiprocessing module.
| Frederick Muriuki Muriithi |
| 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...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.
| Frederick Muriuki Muriithi |
| 2022-05-24 | New script to compute partial correlations...* 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.
| Frederick Muriuki Muriithi |
| 2022-05-21 | Use multiprocessing to improve performance | Frederick Muriuki Muriithi |
| 2022-05-21 | Process primary, target and control traits in a single iteration...Rework the code to process the traits in a single iteration to improve
performance.
| Frederick Muriuki Muriithi |
| 2022-05-21 | Return generator object rather than tuples...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.
| Frederick Muriuki Muriithi |
| 2022-05-06 | Fix linting and typing errors | Frederick Muriuki Muriithi |
