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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>
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>
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>
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>
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>
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>
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>
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>
projects / lightning.git / log