git.arvados.org - lightning.git/history

2023-04-06	Tom Clegg	19995: Add -max-frequency filter. 19995-glm-freq-threshold	blob \| commitdiff \| raw
2023-03-29	Tom Clegg	19995: Report MAF in onehot-columns.npy.	blob \| commitdiff \| raw \| diff to current
2023-03-29	Tom Clegg	19995: Use allele frequency, apply min freq cutoff...	blob \| commitdiff \| raw \| diff to current
2023-03-07	Tom Clegg	Merge branch '19995-glm-freq-threshold'	blob \| commitdiff \| raw \| diff to current
2023-03-06	Tom Clegg	19995: Skip GLM on variants below frequency threshold.	blob \| commitdiff \| raw \| diff to current
2023-02-02	Tom Clegg	Merge branch '19997-glm'	blob \| commitdiff \| raw \| diff to current
2023-02-02	Tom Clegg	Preserve pca components from input when writing samples...	blob \| commitdiff \| raw \| diff to current
2023-02-02	Tom Clegg	Fix validation=0 in samples.csv (should be empty for...	blob \| commitdiff \| raw \| diff to current
2023-01-20	Jiayong Li	Merge branch 'main' into 19868-pca-in-ml	blob \| commitdiff \| raw \| diff to current
2023-01-13	Tom Clegg	Fix GLM p-value calculation when -case-control-only...	blob \| commitdiff \| raw \| diff to current
2023-01-12	Jiayong Li	Merge branch 'main' into 19868-pca-in-ml	blob \| commitdiff \| raw \| diff to current
2023-01-10	Tom Clegg	Fix -min-coverage calculation broken when -case-control...	blob \| commitdiff \| raw \| diff to current
2023-01-03	Tom Clegg	Add column headings to slice-numpy -pca sample list...	blob \| commitdiff \| raw \| diff to current
2023-01-03	Tom Clegg	Fix validation flag in slice-numpy -pca sample list...	blob \| commitdiff \| raw \| diff to current
2022-12-19	Tom Clegg	Merge branch '19566-glm'	blob \| commitdiff \| raw \| diff to current
2022-12-19	Tom Clegg	19566: Preemptible flag.	blob \| commitdiff \| raw \| diff to current
2022-12-19	Tom Clegg	19566: Record number of p-value calculations performed.	blob \| commitdiff \| raw \| diff to current
2022-12-16	Tom Clegg	19566: Silence logging from glm library. 19566-glm	blob \| commitdiff \| raw \| diff to current
2022-12-16	Tom Clegg	19566: Fix chi2 used instead of logistic regression...	blob \| commitdiff \| raw \| diff to current
2022-12-15	Jiayong Li	Merge branch 'main' into 19785-add-cwl 19785-add-cwl	blob \| commitdiff \| raw \| diff to current
2022-12-15	Tom Clegg	19566: Merge branch 'main'	blob \| commitdiff \| raw \| diff to current
2022-12-15	Tom Clegg	Merge branch '19526-manhattan-plot'	blob \| commitdiff \| raw \| diff to current
2022-12-14	Tom Clegg	19566: Precompute cov glm.	blob \| commitdiff \| raw \| diff to current
2022-12-13	Tom Clegg	Merge branch '19566-glm'	blob \| commitdiff \| raw \| diff to current
2022-12-12	Tom Clegg	19566: Test p-value vs. Python.	blob \| commitdiff \| raw \| diff to current
2022-11-29	Tom Clegg	19566: Option to limit pca components used in glm....	blob \| commitdiff \| raw \| diff to current
2022-11-29	Tom Clegg	19566: glm one column at a time.	blob \| commitdiff \| raw \| diff to current
2022-11-29	Tom Clegg	19566: Logistic regression p-value.	blob \| commitdiff \| raw \| diff to current
2022-11-18	Tom Clegg	Check for unparsed command line args.	blob \| commitdiff \| raw \| diff to current
2022-11-18	Tom Clegg	19780: Fix indexing error.	blob \| commitdiff \| raw \| diff to current
2022-11-16	Tom Clegg	19527: slice-numpy accepts samples.csv with or without...	blob \| commitdiff \| raw \| diff to current
2022-11-16	Tom Clegg	19527: Fix odd # columns to pca.	blob \| commitdiff \| raw \| diff to current
2022-11-16	Tom Clegg	19527: Fix one-hot matrix.	blob \| commitdiff \| raw \| diff to current
2022-11-16	Tom Clegg	19527: Fix Χ² calculation.	blob \| commitdiff \| raw \| diff to current
2022-11-16	Tom Clegg	19527: Output samples.csv earlier.	blob \| commitdiff \| raw \| diff to current
2022-11-16	Tom Clegg	19527: Fix crash on tag skipped for min-coverage.	blob \| commitdiff \| raw \| diff to current
2022-11-16	Tom Clegg	19527: Option to exclude non-case/control samples.	blob \| commitdiff \| raw \| diff to current
2022-11-10	Tom Clegg	Merge branch '19527-training-set'	blob \| commitdiff \| raw \| diff to current
2022-11-09	Tom Clegg	19527: Ignore empty line at EOF.	blob \| commitdiff \| raw \| diff to current
2022-11-09	Tom Clegg	Merge branch '19524-pca'	blob \| commitdiff \| raw \| diff to current
2022-11-09	Tom Clegg	19527: Fix p-value calculation.	blob \| commitdiff \| raw \| diff to current
2022-11-09	Tom Clegg	19527: Load training-set flag from samples.csv.	blob \| commitdiff \| raw \| diff to current
2022-11-09	Tom Clegg	19527: choose-samples: training/validation set.	blob \| commitdiff \| raw \| diff to current
2022-11-09	Tom Clegg	19527: Load training-set flag from samples.csv.	blob \| commitdiff \| raw \| diff to current
2022-11-07	Tom Clegg	choose-samples: training/validation set.	blob \| commitdiff \| raw \| diff to current
2022-11-02	Tom Clegg	19524: Fit PCA to specified training set.	blob \| commitdiff \| raw \| diff to current
2022-10-31	Tom Clegg	Merge branch '19524-pca'	blob \| commitdiff \| raw \| diff to current
2022-10-21	Tom Clegg	19524: Fix matrix alloc size. 19524-pca	blob \| commitdiff \| raw \| diff to current
2022-10-20	Tom Clegg	19524: Limit size of PCA input matrix.	blob \| commitdiff \| raw \| diff to current
2022-10-19	Tom Clegg	19524: Limit size of PCA input matrix.	blob \| commitdiff \| raw \| diff to current
2022-10-19	Tom Clegg	19524: configurable vcpus/ram	blob \| commitdiff \| raw \| diff to current
2022-10-14	Tom Clegg	Merge branch '19524-pca'	blob \| commitdiff \| raw \| diff to current
2022-10-12	Tom Clegg	19524: propagate pca-components arg.	blob \| commitdiff \| raw \| diff to current
2022-10-11	Tom Clegg	19524: Output PCA.	blob \| commitdiff \| raw \| diff to current
2022-10-07	Tom Clegg	Update deps, improve error reporting	blob \| commitdiff \| raw \| diff to current
2022-10-07	Tom Clegg	Use min-coverage filter	blob \| commitdiff \| raw \| diff to current
2022-07-20	Tom Clegg	Fix crash when ref tile is dropped due to duplicate...	blob \| commitdiff \| raw \| diff to current
2022-07-15	Tom Clegg	Generate annotations for spanning tiles.	blob \| commitdiff \| raw \| diff to current
2022-07-07	Tom Clegg	Fix wrong index in chunk>0 case.	blob \| commitdiff \| raw \| diff to current
2022-07-01	Tom Clegg	Fix low-coverage tiles counting toward min coverage...	blob \| commitdiff \| raw \| diff to current
2022-04-29	Tom Clegg	Add -log10(pvalue) row to onehot-columns.npy output...	blob \| commitdiff \| raw \| diff to current
2022-03-16	Tom Clegg	Add tilestats cmd.	blob \| commitdiff \| raw \| diff to current
2022-03-16	Tom Clegg	Write chunk-tag-offset.csv with chunked tilevariant...	blob \| commitdiff \| raw \| diff to current
2022-03-04	Tom Clegg	Change zygosity column info from het=1 to hom=1.	blob \| commitdiff \| raw \| diff to current
2022-02-22	Tom Clegg	Encode spanning tile as 0 in tile variant matrix.	blob \| commitdiff \| raw \| diff to current
2022-02-20	Tom Clegg	More debugging info for -debug-tag.	blob \| commitdiff \| raw \| diff to current
2022-02-20	Tom Clegg	Skip input files that aren't needed because -max-tag.	blob \| commitdiff \| raw \| diff to current
2022-02-18	Tom Clegg	Add -debug-tag flag.	blob \| commitdiff \| raw \| diff to current
2022-02-18	Tom Clegg	Fix -include-variant-1	blob \| commitdiff \| raw \| diff to current
2022-02-17	Tom Clegg	Fix -max-tag filter.	blob \| commitdiff \| raw \| diff to current
2022-02-17	Tom Clegg	Fix sparse one-hot coordinates for chunk n>0.	blob \| commitdiff \| raw \| diff to current
2022-02-17	Tom Clegg	Fix -max-tag filter.	blob \| commitdiff \| raw \| diff to current
2022-02-15	Tom Clegg	Option to include variant 1 in one-hot matrix.	blob \| commitdiff \| raw \| diff to current
2022-02-11	Tom Clegg	Include tiles in one-hot matrix even if there is no...	blob \| commitdiff \| raw \| diff to current
2022-02-09	Tom Clegg	Support -max-tag flag for debugging.	blob \| commitdiff \| raw \| diff to current
2022-02-04	Tom Clegg	Don't include het just because corresponding hom passed.	blob \| commitdiff \| raw \| diff to current
2022-02-03	Tom Clegg	Fix log message.	blob \| commitdiff \| raw \| diff to current
2022-02-03	Tom Clegg	Skip tags that appear twice in the same chromosome.	blob \| commitdiff \| raw \| diff to current
2022-01-27	Tom Clegg	Update memory-size log message.	blob \| commitdiff \| raw \| diff to current
2022-01-27	Tom Clegg	Output -single-onehot as coordinates of non-zero values.	blob \| commitdiff \| raw \| diff to current
2022-01-21	Tom Clegg	Fix Χ² calculation.	blob \| commitdiff \| raw \| diff to current
2022-01-17	Tom Clegg	Add -single-onehot output option.	blob \| commitdiff \| raw \| diff to current
2022-01-14	Tom Clegg	Load case/control/neither from csv column, fix Χ² filter.	blob \| commitdiff \| raw \| diff to current
2022-01-13	Tom Clegg	Add -chunked-onehot option.	blob \| commitdiff \| raw \| diff to current
2022-01-07	Tom Clegg	Filter HGVS columns by coverage & p-value threshold.	blob \| commitdiff \| raw \| diff to current
2021-12-30	Tom Clegg	Fix coordinates in hgvs annotations.	blob \| commitdiff \| raw \| diff to current
2021-12-30	Tom Clegg	Fix slice padding.	blob \| commitdiff \| raw \| diff to current
2021-12-30	Tom Clegg	Fix blocking on gob encode.	blob \| commitdiff \| raw \| diff to current
2021-12-29	Tom Clegg	More aggressive GC.	blob \| commitdiff \| raw \| diff to current
2021-12-29	Tom Clegg	Fix index out of bounds error.	blob \| commitdiff \| raw \| diff to current
2021-12-29	Tom Clegg	Refactor chunked-hgvs to use less memory.	blob \| commitdiff \| raw \| diff to current
2021-12-27	Tom Clegg	Separate options to output single/chunked hgvs matrices.	blob \| commitdiff \| raw \| diff to current
2021-12-21	Tom Clegg	Bump slice-numpy memory.	blob \| commitdiff \| raw \| diff to current
2021-12-02	Tom Clegg	Add null csv rows for ref/undiffed. Ensure 0 means...	blob \| commitdiff \| raw \| diff to current
2021-11-30	Tom Clegg	Not a bug when ref is the only variant loaded.	blob \| commitdiff \| raw \| diff to current
2021-11-27	Tom Clegg	Mention undiffable variants in annotations, write ...	blob \| commitdiff \| raw \| diff to current
2021-11-26	Tom Clegg	Write hgvs-oriented matrix and annotations csv.	blob \| commitdiff \| raw \| diff to current
2021-11-26	Tom Clegg	Log exact locations of duplicate tags.	blob \| commitdiff \| raw \| diff to current
2021-11-25	Tom Clegg	Drop duplicate tags, fix ref position tracking.	blob \| commitdiff \| raw \| diff to current
2021-11-25	Tom Clegg	More debug messages and error checks.	blob \| commitdiff \| raw \| diff to current
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