git.arvados.org - lightning.git/shortlog

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
2020-03-10	Tom Clegg	Don't try to pass fd 3 to docker.	commit \| commitdiff \| tree \| snapshot
2020-03-10	Tom Clegg	vcf2fasta -mask cont'd.	commit \| commitdiff \| tree \| snapshot
2020-03-10	Tom Clegg	Pass gvcf_regions.py via mount.	commit \| commitdiff \| tree \| snapshot
2020-03-10	Tom Clegg	Container request priority flag.	commit \| commitdiff \| tree \| snapshot
2020-03-09	Tom Clegg	Add vcf2fasta -mask option.	commit \| commitdiff \| tree \| snapshot
2020-03-09	Tom Clegg	Add vcf2fasta command.	commit \| commitdiff \| tree \| snapshot
2020-03-07	Tom Clegg	Remove debug bit.	commit \| commitdiff \| tree \| snapshot
2020-03-05	Tom Clegg	Use more tiling workers than NumCPU.	commit \| commitdiff \| tree \| snapshot
2020-03-05	Tom Clegg	Filter logs by container on client side of ws connection.	commit \| commitdiff \| tree \| snapshot
2020-03-05	Tom Clegg	Less verbose logging.	commit \| commitdiff \| tree \| snapshot
2020-03-05	Tom Clegg	Upgrade deps.	commit \| commitdiff \| tree \| snapshot
2020-03-05	Tom Clegg	Fix up log/event handling.	commit \| commitdiff \| tree \| snapshot
2020-03-05	Tom Clegg	I/O pipeline, show arvados container logs.	commit \| commitdiff \| tree \| snapshot
2020-03-04	Tom Clegg	Add example script.	commit \| commitdiff \| tree \| snapshot
2020-03-04	Tom Clegg	Add plot subcommand.	commit \| commitdiff \| tree \| snapshot
2020-03-04	Tom Clegg	Tidy log messages.	commit \| commitdiff \| tree \| snapshot
2020-03-04	Tom Clegg	Fix input arg in export.	commit \| commitdiff \| tree \| snapshot
2020-03-03	Tom Clegg	Add pca subcommand.	commit \| commitdiff \| tree \| snapshot
2020-03-03	Tom Clegg	Run "filter" and "export" in arvados containers.	commit \| commitdiff \| tree \| snapshot
2020-03-02	Tom Clegg	Run "import" in arvados container.	commit \| commitdiff \| tree \| snapshot
2020-03-02	Tom Clegg	Add import -o argument.	commit \| commitdiff \| tree \| snapshot
2020-03-02	Tom Clegg	Don't require reference data when all inputs are fasta.	commit \| commitdiff \| tree \| snapshot
2020-02-07	Tom Clegg	Update go.sum.	commit \| commitdiff \| tree \| snapshot
2020-02-07	Tom Clegg	Fix typo.	commit \| commitdiff \| tree \| snapshot
2020-02-06	Tom Clegg	Fix zeroing everything if max-variants not specified.	commit \| commitdiff \| tree \| snapshot
2020-02-06	Tom Clegg	Fix copy-paste error in color map.	commit \| commitdiff \| tree \| snapshot
2020-02-05	Tom Clegg	Add filter subcommand.	commit \| commitdiff \| tree \| snapshot
2020-02-04	Tom Clegg	Split gvcf2numpy command into import and export-numpy.	commit \| commitdiff \| tree \| snapshot
2020-02-03	Tom Clegg	Color PCA plot.	commit \| commitdiff \| tree \| snapshot
2020-01-31	Tom Clegg	Compact on the fly to reduce memory use.	commit \| commitdiff \| tree \| snapshot
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