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2024-11-26feat: Implement reading from file functionalityAlexander_Kabui
Implement read from the last position for a file.
2024-11-22feat: return pointer position from where the file was last read.Alexander_Kabui
2024-11-22feat: Add new endpoint to read stdout given a file identifier.Alexander_Kabui
2024-11-22feat: register rqtl2 blueprint to app.Alexander_Kabui
2024-11-22feat: implement ednpoint for computing qtl using rqtl2.Alexander_Kabui
Capture stdout results to a file.
2024-11-20Merge pull request #201 from genenetwork/feature/rqtl2-implementationAlexander Kabui
feat: Implementation for qtl using r-qtl2
2024-11-15Fix bug where case attribute editing didn't work if a case attribute waszsloan
called 'Strain' This is because the code was also using 'Strain' for the strain name. At least for the time being, I addressed this by changing those instances to 'Sample' instead (which I don't believe is ever a case attribute name).
2024-11-14Fix auth endpoint for case attribute editingzsloan
2024-11-14Fix case attribute queryzsloan
2024-11-12Remove unused setting.Frederick Muriuki Muriithi
The BCRYPT_SALT setting is not used anywhere in GN3 or GN2
2024-11-12Remove unused import.Frederick Muriuki Muriithi
2024-11-12mypy: Rename and annotate variables to silence mypyFrederick Muriuki Muriithi
2024-11-12Pure aesthetics: No functional change.Frederick Muriuki Muriithi
This commit has no functional change it implements. It is purely a aesthetics change to please Frederick.
2024-11-11Allow extra database connection options on URIFrederick Muriuki Muriithi
Update the database URI parsing to allow setting of extra connection option on the URI string.
2024-11-11feat: add step to insert pseudomarkers to the gmap.Alexander_Kabui
2024-11-11fix: fix issue fetching covar:Alexander_Kabui
2024-11-11refactor: rename dataset to cross.Alexander_Kabui
2024-11-11feat: add a threshold argument for lod score peak with default 1.Alexander_Kabui
2024-11-11feat: print_help when certain parameters are not provided.Alexander_Kabui
2024-11-11Refactor: remove requirement for input and output file to be in theAlexander_Kabui
same directory.
2024-11-11Refactor: add better message for computation steps.Alexander_Kabui
2024-11-11refactor: refactor output for preprocessing steps.Alexander_Kabui
2024-11-11Refactor: refactor checks for working directory, input and output file.Alexander_Kabui
2024-11-11refactor: remove stringr as a script dependency:Alexander_Kabui
refactor: refactor use of str_glue to cat.
2024-11-11refactor: refactor for using cat and new line.Alexander_Kabui
2024-11-11refactor: use NO_OF_CORES as default and pass control file to arguments.Alexander_Kabui
2024-11-11refactor: adding pseudomarkers o genetic probabilites map.Alexander_Kabui
2024-11-11refactor: refactor printing out lod thresholds.Alexander_Kabui
2024-11-11export qtl effect plots for multi parent populations.Alexander_Kabui
2024-11-11feat: add plots for qtl effect multi parent population.Alexander_Kabui
2024-11-11feat: implementation for getting meffects for multiparent population.Alexander_Kabui
2024-11-11feat: implementation for multiparent genome scan.Alexander_Kabui
2024-11-11feat: export chromosome names and qtl effects.Alexander_Kabui
2024-11-08feat: init add functionality to estimate qtl effect.Alexander_Kabui
2024-10-30feat: add option for using pstrata for permutation.Alexander_Kabui
2024-10-30Refactor: Remove reduntant code.Alexander_Kabui
Fix issue when computing the kinship
2024-10-29Refactor: pre compute kinship for both permutation and genome scan.Alexander_Kabui
2024-10-29Refactor: remove hardcoded dir_path for control files.Alexander_Kabui
2024-10-29Refactor: make plot in the temp directory passed in the script arguments.Alexander_Kabui
2024-10-29feat: add output_file as a command line argument.Alexander_Kabui
2024-10-29Refactor: ensure the temp directory is not null.Alexander_Kabui
ensure the input_file exists in the working directory.
2024-10-29feat: add optparse for the arguments.Alexander_Kabui
2024-10-29feat: write output results as json.Alexander_Kabui
2024-10-29Refactor: refactor code to find lod peaks.Alexander_Kabui
2024-10-29Refactor: refactoring for code to perform permutation tests.Alexander_Kabui
2024-10-29Refactor: refactor function to generate plots from scan1 function.Alexander_Kabui
2024-10-29Refactor: refactor method to compute scan 1.Alexander_Kabui
2024-10-29Refactor: refactor function to calculate error LOD scores.Alexander_Kabui
2024-10-29Refactor: refactor functions to compute genetic probabilities:Alexander_Kabui
2024-10-29Refactor: cleanup comments.Alexander_Kabui