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2025-10-27Pass `TEXTDIR` configuration on to the script.Frederick Muriuki Muriithi
Pass the `TEXXDIR` configuration variable on to the script.
2025-08-03Fix mypy errors.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-08-03Fix linting errors.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-17Skip blank lines.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-17Skip malformed genotype rows with mismatched data columns.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-16Add kludge comment for "HSNIH-Palmer_true.geno" which has floats.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-16Set a larger map size for the larger genotype files.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-16Add functionality for importing one entire genotype directory.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-16More efficiently and correctly count nrows is genotype.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-16Delete un-used import.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-16Add module doc-string.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-16Improve genotype file parsing.Munyoki Kilyungi
* scripts/lmdb_matrix.py (GenotypeMatrix): Delete transpose. Add "file_info" field. (save_excursion, count_lines): Delete. (get_genotype_dimensions, read_genotype_headers): New function. (read_geno_file): Rename this to... (read_genotype_file): ... this. (genotype_db_put): Put "file_info". (genotype_db_get): Fetch "file_info". (import_genotype): Use read_genotype_file. (print_current_matrix): Remove transpose. Print out file_info metadata. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-16Simplify genotype db script.Munyoki Kilyungi
Hashing and versioning made the script very slow. Now, this script can handle much larger data. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-07-16Add genotype matrix script.Munyoki Kilyungi
* scripts/lmdb_matrix.py: New file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-04-30Revert commit dd9ef90ee89e5c075acbd5ef63cb89518e726ca3.Alexander_Kabui
2025-04-30refactor: For genetic probabilites use cores 0 to use allAlexander_Kabui
available of no cores detected.
2025-04-08refactor: Explicity define no of cores for rqtl2 computation.Alexander_Kabui
2025-04-08refactor: Check for geno_tranposed and founder_geno_transposed.Alexander_Kabui
2025-03-27refactor: Temporary disable checking sex covariates in rqtl2.Alexander_Kabui
2025-03-07refactor: Construct map object from cross with columns (Marker, chr,cM, Mb).Alexander_Kabui
2025-03-07fix: Minor rqtl2 fixes.Alexander_Kabui
2025-03-07refactor rqtl2 script.Alexander_Kabui
2025-03-04Revert "feat: Add Python implementation of Fibonacci number calculation".Munyoki Kilyungi
This reverts commit 280c5e97d21501c03f672ed3576ae3eddfc76420.
2025-03-04feat: Add Python implementation of Fibonacci number calculationMunyoki Kilyungi (aider)
2025-02-28Fix linting errors.Frederick Muriuki Muriithi
2025-02-24Remove "generate_lod_plot" from rqtl2_wrapper.R.Munyoki Kilyungi
* scripts/rqtl2_wrapper.R (generate_lod_plot): Delete function. (output): Remove "lod_plot_path". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2025-02-21feat: Temporary disable performing genome scan with covariates for RQTL2.Alexander_Kabui
2025-02-20refactor: Skip permutation test when NO_OF_PERMUTATION less than 0.Alexander_Kabui
2025-02-20refactor: Use p=0.63 in permutation summary for suggestive threshold.Alexander_Kabui
2025-02-07fix: pass the correct genome probabilites.Alexander_Kabui
2025-02-06feat: Add the physical map file path.Alexander_Kabui
2025-02-06refactor: Rename pheno_map to physical_map .Alexander_Kabui
2025-02-06feat: Pass scan results file and genotype map file as output.Alexander_Kabui
2025-02-06feat: Modify default thresholds and write permutation results to csv file.Alexander_Kabui
2025-01-28Pass in virtuoso ttl directory as a CLI optionFrederick Muriuki Muriithi
Pass in the directory as a command-line option to add flexibility to the deployment. Prior to this commit, the script made the assumption that the TTL directory would show up on the path "/var/lib/data", which is not always the case.
2025-01-06feat: Add print statements for start and end of qtl script run.Alexander_Kabui
2024-12-20feat: Enable verbose for script by default.Alexander_Kabui
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
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-11-22 07:34:03 +0000