lightning.git
3 weeks ago19073: Fix dup tag detection. main
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>

3 weeks ago19073: Fix dup tag detection.
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>

3 weeks ago19073: Remove dup tags (>1 ref placement) from tilestats bed file.
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>

4 weeks agoAdd -log10(pvalue) row to onehot-columns.npy output from slicenumpy.
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>

2 months agoAdd tilestats cmd.
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>

2 months agoWrite chunk-tag-offset.csv with chunked tilevariant# matrix.
Tom Clegg [Wed, 16 Mar 2022 17:16:22 +0000 (13:16 -0400)]
Write chunk-tag-offset.csv with chunked tilevariant# matrix.

refs #17996

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

2 months agoChange zygosity column info from het=1 to hom=1.
Tom Clegg [Fri, 4 Mar 2022 19:48:35 +0000 (14:48 -0500)]
Change zygosity column info from het=1 to hom=1.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoFix left-most diff cases.
Tom Clegg [Thu, 24 Feb 2022 15:50:13 +0000 (10:50 -0500)]
Fix left-most diff cases.

refs #18721

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoEncode spanning tile as 0 in tile variant matrix.
Tom Clegg [Tue, 22 Feb 2022 19:04:00 +0000 (14:04 -0500)]
Encode spanning tile as 0 in tile variant matrix.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoMore debugging info for -debug-tag.
Tom Clegg [Sun, 20 Feb 2022 03:08:38 +0000 (22:08 -0500)]
More debugging info for -debug-tag.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoSkip input files that aren't needed because -max-tag.
Tom Clegg [Sun, 20 Feb 2022 03:07:14 +0000 (22:07 -0500)]
Skip input files that aren't needed because -max-tag.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoFix left-most diff cases.
Tom Clegg [Fri, 18 Feb 2022 20:11:19 +0000 (15:11 -0500)]
Fix left-most diff cases.

refs #18721

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoAdd -debug-tag flag.
Tom Clegg [Fri, 18 Feb 2022 20:11:17 +0000 (15:11 -0500)]
Add -debug-tag flag.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoFix -include-variant-1
Tom Clegg [Fri, 18 Feb 2022 14:57:01 +0000 (09:57 -0500)]
Fix -include-variant-1

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoUpdate tests (don't include both het+hom if only one passes filter).
Tom Clegg [Thu, 17 Feb 2022 15:07:02 +0000 (10:07 -0500)]
Update tests (don't include both het+hom if only one passes filter).

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoFix -max-tag filter.
Tom Clegg [Thu, 17 Feb 2022 15:06:55 +0000 (10:06 -0500)]
Fix -max-tag filter.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoFix sparse one-hot coordinates for chunk n>0.
Tom Clegg [Thu, 17 Feb 2022 14:23:20 +0000 (09:23 -0500)]
Fix sparse one-hot coordinates for chunk n>0.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoFix -max-tag filter.
Tom Clegg [Thu, 17 Feb 2022 14:22:47 +0000 (09:22 -0500)]
Fix -max-tag filter.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoOption to include variant 1 in one-hot matrix.
Tom Clegg [Tue, 15 Feb 2022 17:54:27 +0000 (12:54 -0500)]
Option to include variant 1 in one-hot matrix.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoInclude tiles in one-hot matrix even if there is no ref tile.
Tom Clegg [Fri, 11 Feb 2022 20:01:57 +0000 (15:01 -0500)]
Include tiles in one-hot matrix even if there is no ref tile.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoSupport -max-tag flag for debugging.
Tom Clegg [Wed, 9 Feb 2022 21:17:10 +0000 (16:17 -0500)]
Support -max-tag flag for debugging.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoDon't include het just because corresponding hom passed.
Tom Clegg [Fri, 4 Feb 2022 21:17:23 +0000 (16:17 -0500)]
Don't include het just because corresponding hom passed.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoUpdate logged stats.
Tom Clegg [Fri, 4 Feb 2022 06:11:58 +0000 (01:11 -0500)]
Update logged stats.

refs #18664

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoDon't use tags that appear more than once per sequence.
Tom Clegg [Fri, 4 Feb 2022 05:41:40 +0000 (00:41 -0500)]
Don't use tags that appear more than once per sequence.

refs #18664

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoFix log message.
Tom Clegg [Thu, 3 Feb 2022 19:25:47 +0000 (14:25 -0500)]
Fix log message.

refs #18664

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoSkip tags that appear twice in the same chromosome.
Tom Clegg [Thu, 3 Feb 2022 02:37:19 +0000 (21:37 -0500)]
Skip tags that appear twice in the same chromosome.

refs #18664

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoAdd dump command.
Tom Clegg [Mon, 31 Jan 2022 18:56:56 +0000 (13:56 -0500)]
Add dump command.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

3 months agoUpdate memory-size log message.
Tom Clegg [Thu, 27 Jan 2022 14:16:35 +0000 (09:16 -0500)]
Update memory-size log message.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 months agoOutput -single-onehot as coordinates of non-zero values.
Tom Clegg [Thu, 27 Jan 2022 05:31:02 +0000 (00:31 -0500)]
Output -single-onehot as coordinates of non-zero values.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 months agoFix Χ² calculation.
Tom Clegg [Fri, 21 Jan 2022 19:05:34 +0000 (14:05 -0500)]
Fix Χ² calculation.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 months agoUse native client to read annotations.csv.
Tom Clegg [Mon, 17 Jan 2022 18:03:44 +0000 (13:03 -0500)]
Use native client to read annotations.csv.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 months agoAdd -single-onehot output option.
Tom Clegg [Mon, 17 Jan 2022 16:04:43 +0000 (11:04 -0500)]
Add -single-onehot output option.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 months agoLoad case/control/neither from csv column, fix Χ² filter.
Tom Clegg [Fri, 14 Jan 2022 20:24:11 +0000 (15:24 -0500)]
Load case/control/neither from csv column, fix Χ² filter.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 months agoFix deadlock at container finish.
Tom Clegg [Thu, 13 Jan 2022 19:47:46 +0000 (14:47 -0500)]
Fix deadlock at container finish.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 months agoAdd -chunked-onehot option.
Tom Clegg [Thu, 13 Jan 2022 19:47:40 +0000 (14:47 -0500)]
Add -chunked-onehot option.

refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 months agoHandle fasta with no line breaks.
Tom Clegg [Fri, 7 Jan 2022 16:20:06 +0000 (11:20 -0500)]
Handle fasta with no line breaks.

fixes #18619

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 months agoFilter HGVS columns by coverage & p-value threshold.
Tom Clegg [Fri, 7 Jan 2022 14:20:29 +0000 (09:20 -0500)]
Filter HGVS columns by coverage & p-value threshold.

refs #18438
refs #18495
refs #18581

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 months agoFix coordinates in hgvs annotations.
Tom Clegg [Thu, 30 Dec 2021 16:24:44 +0000 (11:24 -0500)]
Fix coordinates in hgvs annotations.

refs #18438

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 months agoContainer-watching fixes.
Tom Clegg [Thu, 30 Dec 2021 15:20:30 +0000 (10:20 -0500)]
Container-watching fixes.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 months agoFix slice padding.
Tom Clegg [Thu, 30 Dec 2021 00:19:28 +0000 (19:19 -0500)]
Fix slice padding.

refs #18438

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 months agoFix blocking on gob encode.
Tom Clegg [Thu, 30 Dec 2021 00:19:26 +0000 (19:19 -0500)]
Fix blocking on gob encode.

refs #18438

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 months agoMore aggressive GC.
Tom Clegg [Wed, 29 Dec 2021 18:40:15 +0000 (13:40 -0500)]
More aggressive GC.

refs #18438

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 months agoFix index out of bounds error.
Tom Clegg [Wed, 29 Dec 2021 14:33:09 +0000 (09:33 -0500)]
Fix index out of bounds error.

refs #18438

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

4 months agoRefactor chunked-hgvs to use less memory.
Tom Clegg [Tue, 28 Dec 2021 21:45:39 +0000 (16:45 -0500)]
Refactor chunked-hgvs to use less memory.

refs #18438

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

5 months agoSeparate options to output single/chunked hgvs matrices.
Tom Clegg [Mon, 27 Dec 2021 18:01:24 +0000 (13:01 -0500)]
Separate options to output single/chunked hgvs matrices.

refs #18438

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

5 months agoBump slice-numpy memory.
Tom Clegg [Tue, 21 Dec 2021 15:05:27 +0000 (10:05 -0500)]
Bump slice-numpy memory.

refs #17996

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

5 months agoInclude HGVS IDs in anno2vcf.
Tom Clegg [Mon, 13 Dec 2021 15:29:56 +0000 (10:29 -0500)]
Include HGVS IDs in anno2vcf.

refs #18579

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

5 months agoUse (throttle)Go() convenience.
Tom Clegg [Tue, 7 Dec 2021 16:01:19 +0000 (11:01 -0500)]
Use (throttle)Go() convenience.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

5 months agoCall 2-base deletion-insertion as two adjacent SNPs.
Tom Clegg [Sat, 4 Dec 2021 06:40:19 +0000 (01:40 -0500)]
Call 2-base deletion-insertion as two adjacent SNPs.

refs #18496
refs #18438

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

5 months agoAdd null csv rows for ref/undiffed. Ensure 0 means ref in matrix.
Tom Clegg [Thu, 2 Dec 2021 18:39:36 +0000 (13:39 -0500)]
Add null csv rows for ref/undiffed. Ensure 0 means ref in matrix.

refs #18496

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

5 months agoFix handling of TAG->CA (spell as T>C, =A, delG).
Tom Clegg [Tue, 30 Nov 2021 21:17:09 +0000 (16:17 -0500)]
Fix handling of TAG->CA (spell as T>C, =A, delG).

fixes #18496

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

5 months agoNot a bug when ref is the only variant loaded.
Tom Clegg [Tue, 30 Nov 2021 21:01:44 +0000 (16:01 -0500)]
Not a bug when ref is the only variant loaded.

refs #18438

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

5 months agoFix deadlock in skip-on-error case.
Tom Clegg [Tue, 30 Nov 2021 21:01:19 +0000 (16:01 -0500)]
Fix deadlock in skip-on-error case.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

5 months agoCall SNPs separately when called within 1bp of start/end of indels.
Tom Clegg [Tue, 30 Nov 2021 19:59:45 +0000 (14:59 -0500)]
Call SNPs separately when called within 1bp of start/end of indels.

fixes #18496

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoMention undiffable variants in annotations, write -2 in hgvs matrix.
Tom Clegg [Sat, 27 Nov 2021 03:15:56 +0000 (22:15 -0500)]
Mention undiffable variants in annotations, write -2 in hgvs matrix.

refs #18438

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoWrite hgvs-oriented matrix and annotations csv.
Tom Clegg [Fri, 26 Nov 2021 21:24:31 +0000 (16:24 -0500)]
Write hgvs-oriented matrix and annotations csv.

refs #18438

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoLog exact locations of duplicate tags.
Tom Clegg [Fri, 26 Nov 2021 15:33:32 +0000 (10:33 -0500)]
Log exact locations of duplicate tags.

refs #18438

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoDrop duplicate tags, fix ref position tracking.
Tom Clegg [Thu, 25 Nov 2021 20:13:39 +0000 (15:13 -0500)]
Drop duplicate tags, fix ref position tracking.

refs #18438

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoFix interval tree unused node markers.
Tom Clegg [Thu, 25 Nov 2021 19:41:44 +0000 (14:41 -0500)]
Fix interval tree unused node markers.

refs #18438

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoMore debug messages and error checks.
Tom Clegg [Thu, 25 Nov 2021 19:41:01 +0000 (14:41 -0500)]
More debug messages and error checks.

refs #18438

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoUse non-preemptible instances.
Tom Clegg [Wed, 24 Nov 2021 20:19:27 +0000 (15:19 -0500)]
Use non-preemptible instances.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoOption to merge matrices and annotations.
Tom Clegg [Wed, 24 Nov 2021 20:19:19 +0000 (15:19 -0500)]
Option to merge matrices and annotations.

refs #18438

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoImplement -regions and -expand-regions for slice-numpy.
Tom Clegg [Mon, 22 Nov 2021 15:20:52 +0000 (10:20 -0500)]
Implement -regions and -expand-regions for slice-numpy.

refs #18438

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoAdjust slice memory.
Tom Clegg [Fri, 19 Nov 2021 18:23:16 +0000 (13:23 -0500)]
Adjust slice memory.

refs #18414

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoWrite deletions as "TAA T" instead of "AA .".
Tom Clegg [Thu, 4 Nov 2021 18:11:42 +0000 (14:11 -0400)]
Write deletions as "TAA T" instead of "AA .".

refs #17763

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoFix variant numbering.
Tom Clegg [Thu, 4 Nov 2021 18:10:14 +0000 (14:10 -0400)]
Fix variant numbering.

Renumbering code was incorrectly reserving ranking spots for no-calls.

refs #17763

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoUpdate slice-numpy test.
Tom Clegg [Mon, 1 Nov 2021 14:41:01 +0000 (10:41 -0400)]
Update slice-numpy test.

refs #17763

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoFix duplicate entries in slice-numpy annotations.
Tom Clegg [Mon, 1 Nov 2021 14:27:04 +0000 (10:27 -0400)]
Fix duplicate entries in slice-numpy annotations.

refs #17763

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoAvoid empty "ref" field in anno2vcf output.
Tom Clegg [Mon, 1 Nov 2021 14:00:38 +0000 (10:00 -0400)]
Avoid empty "ref" field in anno2vcf output.

refs #17763

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoSplit anno2vcf output by chromosome.
Tom Clegg [Mon, 1 Nov 2021 13:31:04 +0000 (09:31 -0400)]
Split anno2vcf output by chromosome.

refs #17763

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoFix sort func.
Tom Clegg [Fri, 29 Oct 2021 18:39:42 +0000 (14:39 -0400)]
Fix sort func.

refs #17763

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoBump slice-numpy memory.
Tom Clegg [Thu, 28 Oct 2021 15:28:32 +0000 (11:28 -0400)]
Bump slice-numpy memory.

refs #17763

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoSort input files.
Tom Clegg [Thu, 28 Oct 2021 15:28:04 +0000 (11:28 -0400)]
Sort input files.

refs #17763

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

6 months agoAdd anno2vcf command.
Tom Clegg [Thu, 28 Oct 2021 14:33:43 +0000 (10:33 -0400)]
Add anno2vcf command.

refs #17763

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

7 months agoAccept PDH on command line.
Tom Clegg [Fri, 8 Oct 2021 02:12:06 +0000 (22:12 -0400)]
Accept PDH on command line.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

7 months agoUse arvados client for /any/path/$id/, not just /mnt/$id/.
Tom Clegg [Wed, 6 Oct 2021 20:07:40 +0000 (16:07 -0400)]
Use arvados client for /any/path/$id/, not just /mnt/$id/.

refs #17996

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

7 months agoImplement -match-genome filter.
Tom Clegg [Wed, 29 Sep 2021 18:47:34 +0000 (14:47 -0400)]
Implement -match-genome filter.

refs #17996

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

7 months agoFix namespace types.
Tom Clegg [Wed, 29 Sep 2021 18:46:10 +0000 (14:46 -0400)]
Fix namespace types.

refs #17996

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

7 months agoSave all ref tile data in slice 0.
Tom Clegg [Sun, 26 Sep 2021 02:47:00 +0000 (22:47 -0400)]
Save all ref tile data in slice 0.

refs #17996

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

8 months agoCleanup var name.
Tom Clegg [Sun, 26 Sep 2021 01:56:08 +0000 (21:56 -0400)]
Cleanup var name.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

8 months agoScale keep cache to 2*(openfiles+1).
Tom Clegg [Sat, 25 Sep 2021 13:44:22 +0000 (09:44 -0400)]
Scale keep cache to 2*(openfiles+1).

refs #17966

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

8 months agoImprove logging.
Tom Clegg [Fri, 24 Sep 2021 18:09:16 +0000 (14:09 -0400)]
Improve logging.

refs #17966

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

8 months agoTweak cpu/mem usage.
Tom Clegg [Fri, 24 Sep 2021 18:08:59 +0000 (14:08 -0400)]
Tweak cpu/mem usage.

refs #17966

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

8 months agoAccept multiple input libraries for slice→slicenumpy.
Tom Clegg [Thu, 23 Sep 2021 19:52:42 +0000 (15:52 -0400)]
Accept multiple input libraries for slice→slicenumpy.

refs #17966

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

8 months agoLog total variant/genome/ref counts.
Tom Clegg [Tue, 21 Sep 2021 13:59:03 +0000 (09:59 -0400)]
Log total variant/genome/ref counts.

refs #17966

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

8 months agoFix array index out of bounds.
Tom Clegg [Mon, 20 Sep 2021 13:20:30 +0000 (09:20 -0400)]
Fix array index out of bounds.

refs #17966

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

8 months agoRenumber variants by allele count.
Tom Clegg [Fri, 17 Sep 2021 01:50:45 +0000 (21:50 -0400)]
Renumber variants by allele count.

refs #17966

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

8 months agoFix reference assembly.
Tom Clegg [Fri, 17 Sep 2021 00:33:38 +0000 (20:33 -0400)]
Fix reference assembly.

refs #17966

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

8 months agoFix mem usage, improve logging.
Tom Clegg [Tue, 14 Sep 2021 20:15:35 +0000 (16:15 -0400)]
Fix mem usage, improve logging.

refs #17996

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

8 months agoGenerate annotations for slices.
Tom Clegg [Mon, 13 Sep 2021 15:23:23 +0000 (11:23 -0400)]
Generate annotations for slices.

refs #17996

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

8 months agoGenerate numpy matrices from slices.
Tom Clegg [Mon, 13 Sep 2021 14:01:49 +0000 (10:01 -0400)]
Generate numpy matrices from slices.

refs #17996

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

8 months agoAlways log version at startup.
Tom Clegg [Sun, 12 Sep 2021 19:24:45 +0000 (15:24 -0400)]
Always log version at startup.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

8 months agoSlice imported data by tag#.
Tom Clegg [Sun, 12 Sep 2021 19:24:20 +0000 (15:24 -0400)]
Slice imported data by tag#.

refs #17996

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

8 months agoUse callbacks in struct instead of args to Load*().
Tom Clegg [Thu, 9 Sep 2021 15:28:08 +0000 (11:28 -0400)]
Use callbacks in struct instead of args to Load*().

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

8 months agoFix missed TranslatePaths and unreported error.
Tom Clegg [Wed, 1 Sep 2021 17:44:57 +0000 (13:44 -0400)]
Fix missed TranslatePaths and unreported error.

refs #17562

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

8 months agoAdd -p-value and -cases options for exporting hgvs numpy.
Tom Clegg [Tue, 31 Aug 2021 18:56:04 +0000 (14:56 -0400)]
Add -p-value and -cases options for exporting hgvs numpy.

refs #17562

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

8 months agoAdd chi square func.
Tom Clegg [Tue, 31 Aug 2021 18:55:56 +0000 (14:55 -0400)]
Add chi square func.

refs #17562

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

9 months agoFix unchecked error.
Tom Clegg [Thu, 12 Aug 2021 13:56:50 +0000 (09:56 -0400)]
Fix unchecked error.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

9 months agoFix array index out of bounds.
Tom Clegg [Thu, 12 Aug 2021 03:16:36 +0000 (23:16 -0400)]
Fix array index out of bounds.

refs #17562

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

9 months agoAdd -match-genome=regexp filter.
Tom Clegg [Wed, 11 Aug 2021 22:10:26 +0000 (18:10 -0400)]
Add -match-genome=regexp filter.

refs #17939
refs #17922

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>