Tom Clegg [Wed, 2 Sep 2020 02:22:30 +0000 (22:22 -0400)]
Use real longest increasing subsequence algorithm for -skip-ooo.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 6 Aug 2020 18:01:07 +0000 (14:01 -0400)]
Increase max fasta line length from 64KiB to 64MiB.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 16 Jul 2020 17:47:42 +0000 (13:47 -0400)]
Add "timed out?" column to diff output.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 9 Jul 2020 18:05:07 +0000 (14:05 -0400)]
Add diff -timeout flag.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 21 May 2020 17:17:48 +0000 (13:17 -0400)]
Update git path, update deps.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 13 May 2020 13:42:55 +0000 (09:42 -0400)]
Update git path.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 13 May 2020 13:27:03 +0000 (09:27 -0400)]
Update git path.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 12 May 2020 23:56:43 +0000 (19:56 -0400)]
Add diff-fasta command.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Fri, 24 Apr 2020 20:03:10 +0000 (16:03 -0400)]
Log # duplicate tags.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Fri, 24 Apr 2020 17:36:55 +0000 (13:36 -0400)]
Log number of skipped tags.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Fri, 24 Apr 2020 17:28:08 +0000 (13:28 -0400)]
-skip-ooo: fix skipping 7 in seq like 0-1-7-0
0-1-7-2 -> skip 7 because we will accept 2
0-1-7-0 -> keep 7 because we won't accept 0
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 23 Apr 2020 19:13:35 +0000 (15:13 -0400)]
Log out-of-order tags if -loglevel=debug.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 21 Apr 2020 22:20:40 +0000 (18:20 -0400)]
Use black marker instead of crashing on inputs with no label info.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 21 Apr 2020 20:55:18 +0000 (16:55 -0400)]
More memory for pca.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 21 Apr 2020 20:55:03 +0000 (16:55 -0400)]
Don't log token in websocket url.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 8 Apr 2020 18:52:10 +0000 (14:52 -0400)]
More memory for import.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 6 Apr 2020 19:53:34 +0000 (15:53 -0400)]
Fix up websocket locking.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 6 Apr 2020 15:10:02 +0000 (11:10 -0400)]
Propagate skip-ooo flag to container.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 6 Apr 2020 14:57:08 +0000 (10:57 -0400)]
Exit non-zero if container is cancelled.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 6 Apr 2020 14:13:22 +0000 (10:13 -0400)]
Output to arvados storage instead of staging on local disk.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 6 Apr 2020 14:09:46 +0000 (10:09 -0400)]
Option to skip/ignore out-of-order tags.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 6 Apr 2020 14:08:44 +0000 (10:08 -0400)]
Fixup tagset collection in example script.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Fri, 3 Apr 2020 16:36:53 +0000 (12:36 -0400)]
Request more memory when using mask.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Fri, 3 Apr 2020 00:14:30 +0000 (20:14 -0400)]
Read contig sizes from vcf.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 2 Apr 2020 20:14:12 +0000 (16:14 -0400)]
Kill other children and exit early if one child process fails.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 2 Apr 2020 20:11:08 +0000 (16:11 -0400)]
Sort genome file same way as vcf regions.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 12 Mar 2020 03:26:11 +0000 (23:26 -0400)]
s/python/python2/
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 12 Mar 2020 01:45:30 +0000 (21:45 -0400)]
Add python2 to docker image.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 12 Mar 2020 01:06:19 +0000 (21:06 -0400)]
Fix example script.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 12 Mar 2020 01:06:09 +0000 (21:06 -0400)]
Propagate genome arg.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 11 Mar 2020 20:43:37 +0000 (16:43 -0400)]
Refactor websocket listener.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 11 Mar 2020 19:34:52 +0000 (15:34 -0400)]
Don't pipe gvcf_regions to bedtools. Avoid short-read race bug.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 11 Mar 2020 18:53:49 +0000 (14:53 -0400)]
Use named pipe for bcftools --mask data.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 11 Mar 2020 14:57:22 +0000 (10:57 -0400)]
Show file path in ref2genome -local=false.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 11 Mar 2020 14:20:33 +0000 (10:20 -0400)]
Add -priority to example script.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 11 Mar 2020 14:09:10 +0000 (10:09 -0400)]
Fix missing VCPUs.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 11 Mar 2020 14:08:17 +0000 (10:08 -0400)]
Fix unchecked error.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 11 Mar 2020 14:02:55 +0000 (10:02 -0400)]
Connect stdin/stdout in docker containers.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 11 Mar 2020 13:52:49 +0000 (09:52 -0400)]
No O_EXCL.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 11 Mar 2020 05:49:28 +0000 (01:49 -0400)]
Error reporting.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 21:11:25 +0000 (17:11 -0400)]
Update example script.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 21:11:17 +0000 (17:11 -0400)]
Fix docker mounts.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 21:01:00 +0000 (17:01 -0400)]
Generate genome file from fasta.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 20:15:36 +0000 (16:15 -0400)]
Fix example collections.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 20:15:18 +0000 (16:15 -0400)]
Install bedtools.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 20:11:55 +0000 (16:11 -0400)]
Show stderr from children.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 20:08:50 +0000 (16:08 -0400)]
Don't try to pass fd 3 to docker.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 19:55:17 +0000 (15:55 -0400)]
vcf2fasta -mask cont'd.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 14:21:48 +0000 (10:21 -0400)]
Pass gvcf_regions.py via mount.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 10 Mar 2020 13:33:27 +0000 (09:33 -0400)]
Container request priority flag.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 9 Mar 2020 19:28:31 +0000 (15:28 -0400)]
Add vcf2fasta -mask option.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 9 Mar 2020 14:34:28 +0000 (10:34 -0400)]
Add vcf2fasta command.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Sat, 7 Mar 2020 07:06:20 +0000 (02:06 -0500)]
Remove debug bit.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 5 Mar 2020 19:18:08 +0000 (14:18 -0500)]
Use more tiling workers than NumCPU.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 5 Mar 2020 18:55:03 +0000 (13:55 -0500)]
Filter logs by container on client side of ws connection.
(arvados-ws currently ignores object_uuid filters.)
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 5 Mar 2020 18:52:10 +0000 (13:52 -0500)]
Less verbose logging.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 5 Mar 2020 18:24:42 +0000 (13:24 -0500)]
Upgrade deps.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 5 Mar 2020 15:19:14 +0000 (10:19 -0500)]
Fix up log/event handling.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 5 Mar 2020 03:18:26 +0000 (22:18 -0500)]
I/O pipeline, show arvados container logs.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 4 Mar 2020 20:31:43 +0000 (15:31 -0500)]
Add example script.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 4 Mar 2020 20:19:39 +0000 (15:19 -0500)]
Add plot subcommand.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 4 Mar 2020 01:57:28 +0000 (20:57 -0500)]
Tidy log messages.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 4 Mar 2020 01:54:03 +0000 (20:54 -0500)]
Fix input arg in export.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 3 Mar 2020 20:30:01 +0000 (15:30 -0500)]
Add pca subcommand.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 3 Mar 2020 16:41:23 +0000 (11:41 -0500)]
Run "filter" and "export" in arvados containers.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 2 Mar 2020 21:49:48 +0000 (16:49 -0500)]
Run "import" in arvados container.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 2 Mar 2020 14:53:12 +0000 (09:53 -0500)]
Add import -o argument.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 2 Mar 2020 14:36:03 +0000 (09:36 -0500)]
Don't require reference data when all inputs are fasta.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Fri, 7 Feb 2020 18:28:14 +0000 (13:28 -0500)]
Update go.sum.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Fri, 7 Feb 2020 17:17:48 +0000 (12:17 -0500)]
Fix typo.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 6 Feb 2020 20:40:13 +0000 (15:40 -0500)]
Fix zeroing everything if max-variants not specified.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 6 Feb 2020 15:01:39 +0000 (10:01 -0500)]
Fix copy-paste error in color map.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 5 Feb 2020 21:05:55 +0000 (16:05 -0500)]
Add filter subcommand.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Tue, 4 Feb 2020 21:28:51 +0000 (16:28 -0500)]
Split gvcf2numpy command into import and export-numpy.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 3 Feb 2020 15:25:20 +0000 (10:25 -0500)]
Color PCA plot.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Fri, 31 Jan 2020 18:20:00 +0000 (13:20 -0500)]
Compact on the fly to reduce memory use.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Fri, 31 Jan 2020 07:39:02 +0000 (02:39 -0500)]
Skip chr*_*.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Fri, 31 Jan 2020 07:28:23 +0000 (02:28 -0500)]
Reduce allocs while tiling.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 30 Jan 2020 23:05:26 +0000 (18:05 -0500)]
Account for WIP in progress report.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 30 Jan 2020 23:05:10 +0000 (18:05 -0500)]
Remove spurious else.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 30 Jan 2020 22:53:23 +0000 (17:53 -0500)]
Use 2bit-packed uint64 as tagmapKey.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 30 Jan 2020 21:04:49 +0000 (16:04 -0500)]
Fix file mode.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 30 Jan 2020 21:04:02 +0000 (16:04 -0500)]
Add -pprof flag.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 30 Jan 2020 15:01:57 +0000 (10:01 -0500)]
Fix writing all variant numbers to npy row 0.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 30 Jan 2020 14:55:20 +0000 (09:55 -0500)]
Skip extra assignment.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 30 Jan 2020 07:08:10 +0000 (02:08 -0500)]
Add example PCA script.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 30 Jan 2020 07:03:22 +0000 (02:03 -0500)]
Fix shadowed var captured in goroutine.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 20 Jan 2020 15:40:09 +0000 (10:40 -0500)]
Test fasta2numpy.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Mon, 20 Jan 2020 14:54:26 +0000 (09:54 -0500)]
Include ending tag in tile sequence.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Sun, 19 Jan 2020 02:54:07 +0000 (21:54 -0500)]
Use blake256 sum.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Sun, 19 Jan 2020 02:53:59 +0000 (21:53 -0500)]
Accept fasta inputs.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Sun, 19 Jan 2020 02:53:34 +0000 (21:53 -0500)]
Don't try to match overlapping tags.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Fri, 17 Jan 2020 19:03:29 +0000 (14:03 -0500)]
Drop tiles with no-calls.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Fri, 17 Jan 2020 18:54:24 +0000 (13:54 -0500)]
Fix deadlock from unclosed chan.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Fri, 17 Jan 2020 18:20:03 +0000 (13:20 -0500)]
Log tile library size periodically.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 16 Jan 2020 16:40:08 +0000 (11:40 -0500)]
Show progress / ETA.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 16 Jan 2020 16:24:47 +0000 (11:24 -0500)]
int32 -> uint16 in numpy output.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 16 Jan 2020 15:03:33 +0000 (10:03 -0500)]
Fix errs channel race.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Thu, 16 Jan 2020 00:16:14 +0000 (19:16 -0500)]
Write numpy array.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
Tom Clegg [Wed, 15 Jan 2020 19:37:43 +0000 (14:37 -0500)]
md5 -> blake2b
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
projects / lightning.git / log