lightning.git
2023-10-26 Tom Clegg21139: Reduce memory usage in tiling. 21139-import-mem
2023-10-24 Tom CleggFix glm test.
2023-08-29 Alex ColemanMerge branch '20645-updating-dockerfiles'
2023-08-11 Tom CleggMerge branch '20753-fix-missing-columns'
2023-08-02 Tom Clegg20461: Add -pprof-dir option to slice subcommand.
2023-08-02 Alex Coleman20645: Updating base images. 20645-updating-dockerfiles
2023-07-21 Tom Clegg20753: Fix column offset in full matrix when ref tile... 20753-fix-missing-columns
2023-07-20 Alex ColemanUpdating lightning Dockerfile to go from `pip3 install...
2023-07-06 Tom CleggDefault to applying min-coverage filter based on traini...
2023-06-30 Alex ColemanRemove Jiayong as Maintainer, update base images from...
2023-06-27 Tom CleggFix error message.
2023-06-26 Tom CleggFix wrong array index in PCA mode.
2023-06-26 Tom CleggFix missing struct field.
2023-05-05 Tom CleggMerge branch '19995-glm-freq-threshold'
2023-04-06 Tom Clegg19995: Add -max-frequency filter. 19995-glm-freq-threshold
2023-03-29 Tom Clegg19995: Report MAF in onehot-columns.npy.
2023-03-29 Tom Clegg19995: Use allele frequency, apply min freq cutoff...
2023-03-07 Tom CleggMerge branch '19995-glm-freq-threshold'
2023-03-06 Tom Clegg19995: Skip GLM on variants below frequency threshold.
2023-02-02 Tom CleggMerge branch '19997-glm'
2023-02-02 Tom CleggPreserve pca components from input when writing samples...
2023-02-02 Tom CleggFix validation=0 in samples.csv (should be empty for...
2023-02-02 Tom CleggTurn off auto-retry.
2023-01-27 Jiayong LiMerge branch '19868-pca-in-ml' into main
2023-01-27 Jiayong LiMerge branch 'main' into 19868-pca-in-ml 19868-pca-in-ml
2023-01-27 Jiayong LiChange resource requirement of gvcf2fasta and imputation
2023-01-20 Tom CleggDarker colors.
2023-01-20 Tom CleggBring back genomewideline/suggestiveline options.
2023-01-20 Jiayong LiMerge branch '19868-pca-in-ml' into main
2023-01-20 Jiayong LiMerge branch 'main' into 19868-pca-in-ml
2023-01-20 Jiayong LiChange slice-numpy-onehot parameter
2023-01-19 Tom CleggGenerate a manhattan plot for each chromosome.
2023-01-13 Tom CleggFix GLM p-value calculation when -case-control-only...
2023-01-12 Jiayong LiMerge branch '19868-pca-in-ml' into main
2023-01-12 Jiayong LiMerge branch 'main' into 19868-pca-in-ml
2023-01-12 Jiayong LiFix shebang and license
2023-01-10 Tom CleggFix -min-coverage calculation broken when -case-control...
2023-01-03 Tom CleggAdd column headings to slice-numpy -pca sample list...
2023-01-03 Tom CleggFix validation flag in slice-numpy -pca sample list...
2022-12-21 Tom CleggMerge branch '19526-manhattan-plot'
2022-12-19 Tom Clegg19526: Output tile locations and pvalues at specified... 19526-manhattan-plot
2022-12-19 Tom CleggMerge branch '19566-glm'
2022-12-19 Tom Clegg19566: Preemptible flag.
2022-12-19 Tom Clegg19566: Record number of p-value calculations performed.
2022-12-16 Tom Clegg19566: Silence logging from glm library. 19566-glm
2022-12-16 Tom Clegg19566: Fix chi2 used instead of logistic regression...
2022-12-15 Jiayong LiMerge branch '19785-add-cwl' into main
2022-12-15 Jiayong LiMerge branch 'main' into 19785-add-cwl 19785-add-cwl
2022-12-15 Jiayong LiChange lightning docker file so that it builds the...
2022-12-15 Tom Clegg19566: Merge branch 'main'
2022-12-15 Tom CleggMerge branch '19526-manhattan-plot'
2022-12-14 Tom Clegg19566: Precompute cov glm.
2022-12-13 Tom CleggMerge branch '19566-glm'
2022-12-12 Tom Clegg19566: Test p-value vs. Python.
2022-12-12 Tom Clegg19566: Normalize pca values before glm.
2022-12-12 Tom Clegg19566: Add constant, check GLM results against Python.
2022-12-09 Jiayong LiMerge branch '19785-add-cwl' into main
2022-12-09 Jiayong LiFix readme
2022-12-09 Jiayong LiMerge branch '19785-add-cwl' into main
2022-12-09 Jiayong LiAdd cwl and docker files
2022-12-01 Tom Clegg19526: Tidy manhattan plot.
2022-11-29 Tom Clegg19566: Option to limit pca components used in glm....
2022-11-29 Tom Clegg19566: glm one column at a time.
2022-11-29 Tom Clegg19566: Logistic regression p-value.
2022-11-28 Tom CleggMerge branch '19526-manhattan-plot'
2022-11-28 Tom Clegg19526: Add manhattan plot.
2022-11-18 Tom CleggCheck for unparsed command line args.
2022-11-18 Tom Clegg19780: Fix indexing error.
2022-11-16 Tom Clegg19527: slice-numpy accepts samples.csv with or without...
2022-11-16 Tom Clegg19527: Update arvados sdk.
2022-11-16 Tom Clegg19527: Fix odd # columns to pca.
2022-11-16 Tom Clegg19527: Fix one-hot matrix.
2022-11-16 Tom Clegg19527: Enable choose-samples to work without case/contr...
2022-11-16 Tom Clegg19527: Fix Χ² calculation.
2022-11-16 Tom Clegg19527: Output samples.csv earlier.
2022-11-16 Tom Clegg19527: Fix crash on tag skipped for min-coverage.
2022-11-16 Tom Clegg19527: Option to exclude non-case/control samples.
2022-11-10 Tom CleggMerge branch '19527-training-set'
2022-11-09 Tom Clegg19527: Accommodate header row in samples csv. 19527-training-set
2022-11-09 Tom Clegg19527: Ignore empty line at EOF.
2022-11-09 Tom CleggMerge branch '19524-pca'
2022-11-09 Tom Clegg19527: Fix p-value calculation.
2022-11-09 Tom Clegg19527: Load training-set flag from samples.csv.
2022-11-09 Tom Clegg19527: choose-samples: training/validation set.
2022-11-09 Tom Clegg19527: Load training-set flag from samples.csv.
2022-11-07 Tom Cleggchoose-samples: training/validation set.
2022-11-02 Tom Clegg19524: Fit PCA to specified training set.
2022-10-31 Tom CleggMerge branch '19524-pca'
2022-10-21 Tom Clegg19524: Fix matrix alloc size. 19524-pca
2022-10-20 Tom Clegg19524: Flags choose which PCA components to plot.
2022-10-20 Tom Clegg19524: Update colors, plot unknown-phenotype behind...
2022-10-20 Tom Clegg19524: Limit size of PCA input matrix.
2022-10-19 Tom Clegg19524: Limit size of PCA input matrix.
2022-10-19 Tom Clegg19524: configurable vcpus/ram
2022-10-14 Tom CleggMerge branch '19524-pca'
2022-10-14 Tom Clegg19524: Use marker shape to indicate second category...
2022-10-14 Tom Clegg19524: Remove obsolete pca cmds.
2022-10-14 Tom Clegg19524: Fix deprecated scipy.load.
2022-10-14 Tom Clegg19524: Read multiple phenotype files.
2022-10-14 Tom Clegg19524: Generalize plot colors a little.
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