Tom Clegg [Thu, 2 Feb 2023 15:00:01 +0000 (10:00 -0500)]
Turn off auto-retry.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 20 Jan 2023 19:25:02 +0000 (14:25 -0500)]
Darker colors.
refs #19958
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 20 Jan 2023 18:37:34 +0000 (13:37 -0500)]
Bring back genomewideline/suggestiveline options.
refs #19958
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Jiayong Li [Fri, 20 Jan 2023 14:38:41 +0000 (14:38 +0000)]
Merge branch '19868-pca-in-ml' into main
refs #19868
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>
Jiayong Li [Fri, 20 Jan 2023 14:37:58 +0000 (14:37 +0000)]
Merge branch 'main' into 19868-pca-in-ml
refs #19868
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>
Jiayong Li [Fri, 20 Jan 2023 14:36:55 +0000 (14:36 +0000)]
Change slice-numpy-onehot parameter
refs #19868
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>
Tom Clegg [Thu, 19 Jan 2023 21:38:41 +0000 (16:38 -0500)]
Generate a manhattan plot for each chromosome.
refs #19958
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 13 Jan 2023 20:05:27 +0000 (15:05 -0500)]
Fix GLM p-value calculation when -case-control-only=true.
refs #19566
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Jiayong Li [Thu, 12 Jan 2023 16:18:07 +0000 (16:18 +0000)]
Merge branch '19868-pca-in-ml' into main
refs #19868
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>
Jiayong Li [Thu, 12 Jan 2023 16:17:19 +0000 (16:17 +0000)]
Merge branch 'main' into 19868-pca-in-ml
refs #19868
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>
Jiayong Li [Thu, 12 Jan 2023 16:07:42 +0000 (16:07 +0000)]
Fix shebang and license
refs #19868
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>
Tom Clegg [Tue, 10 Jan 2023 15:00:16 +0000 (10:00 -0500)]
Fix -min-coverage calculation broken when -case-control-only=true.
refs #19868
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Tue, 3 Jan 2023 21:29:12 +0000 (16:29 -0500)]
Add column headings to slice-numpy -pca sample list output.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Tue, 3 Jan 2023 21:23:05 +0000 (16:23 -0500)]
Fix validation flag in slice-numpy -pca sample list output.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 21 Dec 2022 19:46:20 +0000 (14:46 -0500)]
Merge branch '19526-manhattan-plot'
refs #19526
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Mon, 19 Dec 2022 21:51:02 +0000 (16:51 -0500)]
19526: Output tile locations and pvalues at specified threshold.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Mon, 19 Dec 2022 19:25:54 +0000 (14:25 -0500)]
Merge branch '19566-glm'
refs #19566
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Mon, 19 Dec 2022 19:22:34 +0000 (14:22 -0500)]
19566: Preemptible flag.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Mon, 19 Dec 2022 15:10:16 +0000 (10:10 -0500)]
19566: Record number of p-value calculations performed.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 16 Dec 2022 19:25:12 +0000 (14:25 -0500)]
19566: Silence logging from glm library.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 16 Dec 2022 15:45:25 +0000 (10:45 -0500)]
19566: Fix chi2 used instead of logistic regression p-value.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Jiayong Li [Thu, 15 Dec 2022 22:21:02 +0000 (22:21 +0000)]
Merge branch '19785-add-cwl' into main
refs #19785
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>
Jiayong Li [Thu, 15 Dec 2022 22:20:16 +0000 (22:20 +0000)]
Merge branch 'main' into 19785-add-cwl
refs #19785
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>
Jiayong Li [Thu, 15 Dec 2022 22:15:13 +0000 (22:15 +0000)]
Change lightning docker file so that it builds the current branch instead of main
refs #19785
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>
Tom Clegg [Thu, 15 Dec 2022 15:59:27 +0000 (10:59 -0500)]
19566: Merge branch 'main'
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Thu, 15 Dec 2022 15:59:03 +0000 (10:59 -0500)]
Merge branch '19526-manhattan-plot'
refs #19526
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 14 Dec 2022 20:00:46 +0000 (15:00 -0500)]
19566: Precompute cov glm.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Tue, 13 Dec 2022 15:03:06 +0000 (10:03 -0500)]
Merge branch '19566-glm'
refs #19566
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Mon, 12 Dec 2022 16:37:21 +0000 (11:37 -0500)]
19566: Test p-value vs. Python.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 2 Dec 2022 19:23:34 +0000 (14:23 -0500)]
19566: Normalize pca values before glm.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 2 Dec 2022 18:59:29 +0000 (13:59 -0500)]
19566: Add constant, check GLM results against Python.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Jiayong Li [Fri, 9 Dec 2022 21:09:17 +0000 (21:09 +0000)]
Merge branch '19785-add-cwl' into main
refs #19785
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>
Jiayong Li [Fri, 9 Dec 2022 21:08:35 +0000 (21:08 +0000)]
Fix readme
refs #19785
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>
Jiayong Li [Fri, 9 Dec 2022 21:05:32 +0000 (21:05 +0000)]
Merge branch '19785-add-cwl' into main
refs #19785
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>
Jiayong Li [Fri, 9 Dec 2022 21:03:13 +0000 (21:03 +0000)]
Add cwl and docker files
refs #19785
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>
Tom Clegg [Thu, 1 Dec 2022 18:13:18 +0000 (13:13 -0500)]
19526: Tidy manhattan plot.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Tue, 29 Nov 2022 16:22:12 +0000 (11:22 -0500)]
19566: Option to limit pca components used in glm. Fix onehot use.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Tue, 29 Nov 2022 16:10:32 +0000 (11:10 -0500)]
19566: glm one column at a time.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Tue, 29 Nov 2022 15:43:29 +0000 (10:43 -0500)]
19566: Logistic regression p-value.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Mon, 28 Nov 2022 20:18:32 +0000 (15:18 -0500)]
Merge branch '19526-manhattan-plot'
refs #19526
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Mon, 28 Nov 2022 18:34:48 +0000 (13:34 -0500)]
19526: Add manhattan plot.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 18 Nov 2022 18:28:36 +0000 (13:28 -0500)]
Check for unparsed command line args.
refs #19780
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 18 Nov 2022 17:50:49 +0000 (12:50 -0500)]
19780: Fix indexing error.
refs #19780
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 16 Nov 2022 20:22:55 +0000 (15:22 -0500)]
19527: slice-numpy accepts samples.csv with or without p-values.
refs #19527
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Mon, 14 Nov 2022 00:06:41 +0000 (19:06 -0500)]
19527: Update arvados sdk.
refs #19527
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 11 Nov 2022 21:04:54 +0000 (16:04 -0500)]
19527: Fix odd # columns to pca.
refs #19527
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 11 Nov 2022 17:44:16 +0000 (12:44 -0500)]
19527: Fix one-hot matrix.
refs #19527
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 11 Nov 2022 17:35:09 +0000 (12:35 -0500)]
19527: Enable choose-samples to work without case/control info.
refs #19527
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 11 Nov 2022 01:55:11 +0000 (20:55 -0500)]
19527: Fix Χ² calculation.
refs #19527
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Thu, 10 Nov 2022 20:49:35 +0000 (15:49 -0500)]
19527: Output samples.csv earlier.
refs #19527
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Thu, 10 Nov 2022 19:40:45 +0000 (14:40 -0500)]
19527: Fix crash on tag skipped for min-coverage.
refs #19527
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Thu, 10 Nov 2022 16:16:59 +0000 (11:16 -0500)]
19527: Option to exclude non-case/control samples.
refs #19527
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Thu, 10 Nov 2022 15:24:53 +0000 (10:24 -0500)]
Merge branch '19527-training-set'
refs #19527
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 9 Nov 2022 23:29:58 +0000 (18:29 -0500)]
19527: Accommodate header row in samples csv.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 9 Nov 2022 23:08:57 +0000 (18:08 -0500)]
19527: Ignore empty line at EOF.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 9 Nov 2022 20:12:33 +0000 (15:12 -0500)]
Merge branch '19524-pca'
refs #19524
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 9 Nov 2022 20:11:48 +0000 (15:11 -0500)]
19527: Fix p-value calculation.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 9 Nov 2022 19:39:31 +0000 (14:39 -0500)]
19527: Load training-set flag from samples.csv.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Mon, 7 Nov 2022 14:29:47 +0000 (09:29 -0500)]
19527: choose-samples: training/validation set.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 9 Nov 2022 19:24:49 +0000 (14:24 -0500)]
19527: Load training-set flag from samples.csv.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Mon, 7 Nov 2022 14:29:47 +0000 (09:29 -0500)]
choose-samples: training/validation set.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 2 Nov 2022 14:49:09 +0000 (10:49 -0400)]
19524: Fit PCA to specified training set.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Mon, 31 Oct 2022 15:53:26 +0000 (11:53 -0400)]
Merge branch '19524-pca'
refs #19524
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 21 Oct 2022 13:23:12 +0000 (09:23 -0400)]
19524: Fix matrix alloc size.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Thu, 20 Oct 2022 17:06:35 +0000 (13:06 -0400)]
19524: Flags choose which PCA components to plot.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Thu, 20 Oct 2022 15:23:08 +0000 (11:23 -0400)]
19524: Update colors, plot unknown-phenotype behind known.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Thu, 20 Oct 2022 14:07:11 +0000 (10:07 -0400)]
19524: Limit size of PCA input matrix.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 19 Oct 2022 20:17:36 +0000 (16:17 -0400)]
19524: Limit size of PCA input matrix.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 19 Oct 2022 19:55:56 +0000 (15:55 -0400)]
19524: configurable vcpus/ram
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 14 Oct 2022 17:34:23 +0000 (13:34 -0400)]
Merge branch '19524-pca'
refs #19524
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Thu, 13 Oct 2022 18:46:46 +0000 (14:46 -0400)]
19524: Use marker shape to indicate second category variable.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Thu, 13 Oct 2022 15:44:05 +0000 (11:44 -0400)]
19524: Remove obsolete pca cmds.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Thu, 13 Oct 2022 14:47:51 +0000 (10:47 -0400)]
19524: Fix deprecated scipy.load.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Thu, 13 Oct 2022 14:47:02 +0000 (10:47 -0400)]
19524: Read multiple phenotype files.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Thu, 13 Oct 2022 14:43:36 +0000 (10:43 -0400)]
19524: Generalize plot colors a little.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Thu, 13 Oct 2022 13:57:37 +0000 (09:57 -0400)]
Fail if inadvertently using randomness.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 12 Oct 2022 18:36:33 +0000 (14:36 -0400)]
19524: Fix colormap.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 12 Oct 2022 05:11:26 +0000 (01:11 -0400)]
19524: propagate pca-components arg.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Tue, 11 Oct 2022 18:40:03 +0000 (14:40 -0400)]
19524: plot: get sample list from csv instead of fasta filenames.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Tue, 11 Oct 2022 14:07:14 +0000 (10:07 -0400)]
19524: Output PCA.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 7 Oct 2022 19:18:39 +0000 (15:18 -0400)]
Update deps, improve error reporting
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 7 Oct 2022 18:11:31 +0000 (14:11 -0400)]
Use min-coverage filter
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 5 Aug 2022 19:45:52 +0000 (15:45 -0400)]
Fix diff case
refs #19236 #note-20
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 3 Aug 2022 20:14:27 +0000 (16:14 -0400)]
Fix diff case
refs #19236 #note-15.7
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 27 Jul 2022 20:56:09 +0000 (16:56 -0400)]
Fix diff case
refs #19236 #note-15.6
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 27 Jul 2022 20:02:40 +0000 (16:02 -0400)]
Fix diff case
refs #19236 #note-15.4, #note-15.5
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 27 Jul 2022 18:48:05 +0000 (14:48 -0400)]
Fix diff case
refs #19236 #note-15.2, #note-15.3
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Tue, 26 Jul 2022 17:16:15 +0000 (13:16 -0400)]
Fix diff case
refs #19236 #note-15.1
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 20 Jul 2022 16:21:32 +0000 (12:21 -0400)]
Fix crash when ref tile is dropped due to duplicate tag.
refs #19236
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 15 Jul 2022 19:21:01 +0000 (15:21 -0400)]
Add test for variant at right end of spanning tile.
refs #19271
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 15 Jul 2022 17:51:56 +0000 (13:51 -0400)]
Generate annotations for spanning tiles.
refs #19271
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Thu, 14 Jul 2022 14:43:48 +0000 (10:43 -0400)]
Update tests.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Thu, 7 Jul 2022 18:28:36 +0000 (14:28 -0400)]
Fix wrong index in chunk>0 case.
refs #19168
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 1 Jul 2022 20:28:23 +0000 (16:28 -0400)]
Fix low-coverage tiles counting toward min coverage threshold.
refs #19168
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 3 Jun 2022 04:05:42 +0000 (00:05 -0400)]
Fix loss of precision in p-value calculation.
refs #19014
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 4 May 2022 05:16:51 +0000 (01:16 -0400)]
19073: Fix dup tag detection.
refs #19073
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 4 May 2022 03:22:31 +0000 (23:22 -0400)]
19073: Fix dup tag detection.
refs #19073
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Tue, 3 May 2022 17:57:01 +0000 (13:57 -0400)]
19073: Remove dup tags (>1 ref placement) from tilestats bed file.
refs #19073
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Fri, 29 Apr 2022 18:57:44 +0000 (14:57 -0400)]
Add -log10(pvalue) row to onehot-columns.npy output from slicenumpy.
closes #19014
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Tom Clegg [Wed, 16 Mar 2022 22:08:31 +0000 (18:08 -0400)]
Add tilestats cmd.
refs #18582
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
projects / lightning.git / log