lightning.git
4 years agoSplit gvcf2numpy command into import and export-numpy.
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>

4 years agoColor PCA plot.
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>

4 years agoCompact on the fly to reduce memory use.
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>

4 years agoSkip chr*_*.
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>

4 years agoReduce allocs while tiling.
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>

4 years agoAccount for WIP in progress report.
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>

4 years agoRemove spurious else.
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>

4 years agoUse 2bit-packed uint64 as tagmapKey.
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>

4 years agoFix file mode.
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>

4 years agoAdd -pprof flag.
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>

4 years agoFix writing all variant numbers to npy row 0.
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>

4 years agoSkip extra assignment.
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>

4 years agoAdd example PCA script.
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>

4 years agoFix shadowed var captured in goroutine.
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>

4 years agoTest fasta2numpy.
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>

4 years agoInclude ending tag in tile sequence.
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>

4 years agoUse blake256 sum.
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>

4 years agoAccept fasta inputs.
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>

4 years agoDon't try to match overlapping tags.
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>

4 years agoDrop tiles with no-calls.
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>

4 years agoFix deadlock from unclosed chan.
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>

4 years agoLog tile library size periodically.
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>

4 years agoShow progress / ETA.
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>

4 years agoint32 -> uint16 in numpy output.
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>

4 years agoFix errs channel race.
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>

4 years agoWrite numpy array.
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>

4 years agomd5 -> blake2b
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>

4 years agoAccept directories as vcf source args.
Tom Clegg [Wed, 15 Jan 2020 16:45:10 +0000 (11:45 -0500)]
Accept directories as vcf source args.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years agolimit concurrency
Tom Clegg [Tue, 14 Jan 2020 17:20:33 +0000 (12:20 -0500)]
limit concurrency

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years agoaccept csi or tbi index
Tom Clegg [Tue, 14 Jan 2020 16:40:18 +0000 (11:40 -0500)]
accept csi or tbi index

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years agoFix docker buffering everything.
Tom Clegg [Tue, 14 Jan 2020 16:19:31 +0000 (11:19 -0500)]
Fix docker buffering everything.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years agoLimit concurrency.
Tom Clegg [Tue, 14 Jan 2020 16:18:30 +0000 (11:18 -0500)]
Limit concurrency.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years agoOutput tile variant arrays.
Tom Clegg [Tue, 14 Jan 2020 16:16:41 +0000 (11:16 -0500)]
Output tile variant arrays.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

4 years agoInitial tiling code.
Tom Clegg [Mon, 13 Jan 2020 17:17:33 +0000 (12:17 -0500)]
Initial tiling code.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>