git.arvados.org - lightning.git/shortlog

2020-10-25	Tom Clegg	Write import stats to stats.json.	commit \| commitdiff \| tree \| snapshot
2020-10-25	Tom Clegg	Turn off timestamps in logs when not logging to a tty.	commit \| commitdiff \| tree \| snapshot
2020-10-23	Tom Clegg	Log input seq/chrom size, input coverage, tile coverage.	commit \| commitdiff \| tree \| snapshot
2020-10-23	Tom Clegg	Add CalledBases to stats.	commit \| commitdiff \| tree \| snapshot
2020-10-22	Tom Clegg	Fix coverage score.	commit \| commitdiff \| tree \| snapshot
2020-10-22	Tom Clegg	Update example.	commit \| commitdiff \| tree \| snapshot
2020-10-22	Tom Clegg	More RAM for export.	commit \| commitdiff \| tree \| snapshot
2020-10-22	Tom Clegg	Split big func.	commit \| commitdiff \| tree \| snapshot
2020-10-22	Tom Clegg	Assemble sequences concurrently.	commit \| commitdiff \| tree \| snapshot
2020-10-22	Tom Clegg	Update test.	commit \| commitdiff \| tree \| snapshot
2020-10-22	Tom Clegg	Fix divide by zero.	commit \| commitdiff \| tree \| snapshot
2020-10-22	Tom Clegg	Update test.	commit \| commitdiff \| tree \| snapshot
2020-10-22	Tom Clegg	Fix chr pos after chr1.	commit \| commitdiff \| tree \| snapshot
2020-10-22	Tom Clegg	Fix var reused in goroutine.	commit \| commitdiff \| tree \| snapshot
2020-10-21	Tom Clegg	Use only first field of fasta comment as sequence label.	commit \| commitdiff \| tree \| snapshot
2020-10-21	Tom Clegg	Handle N in ref.	commit \| commitdiff \| tree \| snapshot
2020-10-21	Tom Clegg	Merge more than two consecutive del/ins.	commit \| commitdiff \| tree \| snapshot
2020-10-21	Tom Clegg	Export bed file.	commit \| commitdiff \| tree \| snapshot
2020-10-20	Tom Clegg	Export VCF-ish.	commit \| commitdiff \| tree \| snapshot
2020-10-19	Tom Clegg	Handle variant 0 ("none") in CompactSequences.	commit \| commitdiff \| tree \| snapshot
2020-10-19	Tom Clegg	Add PadLeft func to help avoid empty ref/new fields.	commit \| commitdiff \| tree \| snapshot
2020-10-16	Tom Clegg	Add merge cmd.	commit \| commitdiff \| tree \| snapshot
2020-10-14	Tom Clegg	Export HGVS.	commit \| commitdiff \| tree \| snapshot
2020-10-12	Tom Clegg	Refactor merge.	commit \| commitdiff \| tree \| snapshot
2020-10-12	Tom Clegg	Delete dead code.	commit \| commitdiff \| tree \| snapshot
2020-10-12	Tom Clegg	Improve error message.	commit \| commitdiff \| tree \| snapshot
2020-10-12	Tom Clegg	Fix missed error check.	commit \| commitdiff \| tree \| snapshot
2020-10-12	Tom Clegg	Fix log message.	commit \| commitdiff \| tree \| snapshot
2020-10-12	Tom Clegg	Add merge command.	commit \| commitdiff \| tree \| snapshot
2020-10-08	Tom Clegg	Include tile variant IDs in library.	commit \| commitdiff \| tree \| snapshot
2020-10-08	Tom Clegg	Option to output full list of unplaced tags.	commit \| commitdiff \| tree \| snapshot
2020-10-08	Tom Clegg	Allow importing all-hom (reference) data from single...	commit \| commitdiff \| tree \| snapshot
2020-10-07	Tom Clegg	Add TagsPlacedNTimes stat.	commit \| commitdiff \| tree \| snapshot
2020-10-07	Tom Clegg	Increase library read buffer size.	commit \| commitdiff \| tree \| snapshot
2020-10-07	Tom Clegg	When writing library, write tags too.	commit \| commitdiff \| tree \| snapshot
2020-10-07	Tom Clegg	Add stats command.	commit \| commitdiff \| tree \| snapshot
2020-09-25	Tom Clegg	Option to treat tiles with no-calls as regular tiles.	commit \| commitdiff \| tree \| snapshot
2020-09-25	Tom Clegg	Option to output tile library when importing.	commit \| commitdiff \| tree \| snapshot
2020-09-25	Tom Clegg	Less memory for pca.	commit \| commitdiff \| tree \| snapshot
2020-09-18	Tom Clegg	Fix -max-coverage=1.	commit \| commitdiff \| tree \| snapshot
2020-09-18	Tom Clegg	More logs.	commit \| commitdiff \| tree \| snapshot
2020-09-17	Tom Clegg	Log dimensions.	commit \| commitdiff \| tree \| snapshot
2020-09-17	Tom Clegg	Logs.	commit \| commitdiff \| tree \| snapshot
2020-09-17	Tom Clegg	Transpose.	commit \| commitdiff \| tree \| snapshot
2020-09-17	Tom Clegg	More memory for plot.	commit \| commitdiff \| tree \| snapshot
2020-09-17	Tom Clegg	Do PCA in Go.	commit \| commitdiff \| tree \| snapshot
2020-09-15	Tom Clegg	More memory for export-numpy.	commit \| commitdiff \| tree \| snapshot
2020-09-11	Tom Clegg	More memory for pca.	commit \| commitdiff \| tree \| snapshot
2020-09-11	Tom Clegg	Show container mem stats.	commit \| commitdiff \| tree \| snapshot
2020-09-11	Tom Clegg	Option to recode as one-hot for numpy output.	commit \| commitdiff \| tree \| snapshot
2020-09-09	Tom Clegg	Sort numpy output by label.	commit \| commitdiff \| tree \| snapshot
2020-09-09	Tom Clegg	Enable -skip-ooo in example.	commit \| commitdiff \| tree \| snapshot
2020-09-02	Tom Clegg	Clean up tests.	commit \| commitdiff \| tree \| snapshot
2020-09-02	Tom Clegg	Fix panic on blank line in fasta.	commit \| commitdiff \| tree \| snapshot
2020-09-02	Tom Clegg	Use real longest increasing subsequence algorithm for...	commit \| commitdiff \| tree \| snapshot
2020-08-06	Tom Clegg	Increase max fasta line length from 64KiB to 64MiB.	commit \| commitdiff \| tree \| snapshot
2020-07-16	Tom Clegg	Add "timed out?" column to diff output.	commit \| commitdiff \| tree \| snapshot
2020-07-09	Tom Clegg	Add diff -timeout flag.	commit \| commitdiff \| tree \| snapshot
2020-05-21	Tom Clegg	Update git path, update deps.	commit \| commitdiff \| tree \| snapshot
2020-05-13	Tom Clegg	Update git path.	commit \| commitdiff \| tree \| snapshot
2020-05-13	Tom Clegg	Update git path.	commit \| commitdiff \| tree \| snapshot
2020-05-12	Tom Clegg	Add diff-fasta command.	commit \| commitdiff \| tree \| snapshot
2020-04-24	Tom Clegg	Log # duplicate tags.	commit \| commitdiff \| tree \| snapshot
2020-04-24	Tom Clegg	Log number of skipped tags.	commit \| commitdiff \| tree \| snapshot
2020-04-24	Tom Clegg	-skip-ooo: fix skipping 7 in seq like 0-1-7-0	commit \| commitdiff \| tree \| snapshot
2020-04-23	Tom Clegg	Log out-of-order tags if -loglevel=debug.	commit \| commitdiff \| tree \| snapshot
2020-04-21	Tom Clegg	Use black marker instead of crashing on inputs with...	commit \| commitdiff \| tree \| snapshot
2020-04-21	Tom Clegg	More memory for pca.	commit \| commitdiff \| tree \| snapshot
2020-04-21	Tom Clegg	Don't log token in websocket url.	commit \| commitdiff \| tree \| snapshot
2020-04-08	Tom Clegg	More memory for import.	commit \| commitdiff \| tree \| snapshot
2020-04-06	Tom Clegg	Fix up websocket locking.	commit \| commitdiff \| tree \| snapshot
2020-04-06	Tom Clegg	Propagate skip-ooo flag to container.	commit \| commitdiff \| tree \| snapshot
2020-04-06	Tom Clegg	Exit non-zero if container is cancelled.	commit \| commitdiff \| tree \| snapshot
2020-04-06	Tom Clegg	Output to arvados storage instead of staging on local...	commit \| commitdiff \| tree \| snapshot
2020-04-06	Tom Clegg	Option to skip/ignore out-of-order tags.	commit \| commitdiff \| tree \| snapshot
2020-04-06	Tom Clegg	Fixup tagset collection in example script.	commit \| commitdiff \| tree \| snapshot
2020-04-03	Tom Clegg	Request more memory when using mask.	commit \| commitdiff \| tree \| snapshot
2020-04-03	Tom Clegg	Read contig sizes from vcf.	commit \| commitdiff \| tree \| snapshot
2020-04-02	Tom Clegg	Kill other children and exit early if one child process...	commit \| commitdiff \| tree \| snapshot
2020-04-02	Tom Clegg	Sort genome file same way as vcf regions.	commit \| commitdiff \| tree \| snapshot
2020-03-12	Tom Clegg	s/python/python2/	commit \| commitdiff \| tree \| snapshot
2020-03-12	Tom Clegg	Add python2 to docker image.	commit \| commitdiff \| tree \| snapshot
2020-03-12	Tom Clegg	Fix example script.	commit \| commitdiff \| tree \| snapshot
2020-03-12	Tom Clegg	Propagate genome arg.	commit \| commitdiff \| tree \| snapshot
2020-03-11	Tom Clegg	Refactor websocket listener.	commit \| commitdiff \| tree \| snapshot
2020-03-11	Tom Clegg	Don't pipe gvcf_regions to bedtools. Avoid short-read...	commit \| commitdiff \| tree \| snapshot
2020-03-11	Tom Clegg	Use named pipe for bcftools --mask data.	commit \| commitdiff \| tree \| snapshot
2020-03-11	Tom Clegg	Show file path in ref2genome -local=false.	commit \| commitdiff \| tree \| snapshot
2020-03-11	Tom Clegg	Add -priority to example script.	commit \| commitdiff \| tree \| snapshot
2020-03-11	Tom Clegg	Fix missing VCPUs.	commit \| commitdiff \| tree \| snapshot
2020-03-11	Tom Clegg	Fix unchecked error.	commit \| commitdiff \| tree \| snapshot
2020-03-11	Tom Clegg	Connect stdin/stdout in docker containers.	commit \| commitdiff \| tree \| snapshot
2020-03-11	Tom Clegg	No O_EXCL.	commit \| commitdiff \| tree \| snapshot
2020-03-11	Tom Clegg	Error reporting.	commit \| commitdiff \| tree \| snapshot
2020-03-10	Tom Clegg	Update example script.	commit \| commitdiff \| tree \| snapshot
2020-03-10	Tom Clegg	Fix docker mounts.	commit \| commitdiff \| tree \| snapshot
2020-03-10	Tom Clegg	Generate genome file from fasta.	commit \| commitdiff \| tree \| snapshot
2020-03-10	Tom Clegg	Fix example collections.	commit \| commitdiff \| tree \| snapshot
2020-03-10	Tom Clegg	Install bedtools.	commit \| commitdiff \| tree \| snapshot
2020-03-10	Tom Clegg	Show stderr from children.	commit \| commitdiff \| tree \| snapshot
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