git.arvados.org - lightning.git/history

2023-11-09	Alex Coleman	Merge branch '20765-moving-gvcf-regions'	blob \| commitdiff \| raw
2023-11-03	Tom Clegg	21139: Reduce lock contention.	blob \| commitdiff \| raw
2023-11-03	Tom Clegg	21139: Remove excess concurrency to reduce mutex/gorout...	blob \| commitdiff \| raw \| diff to current
2023-10-27	Tom Clegg	Merge branch '21139-import-mem'	blob \| commitdiff \| raw \| diff to current
2023-10-26	Tom Clegg	21139: Reduce memory usage in tiling. 21139-import-mem	blob \| commitdiff \| raw \| diff to current
2022-07-20	Tom Clegg	Fix crash when ref tile is dropped due to duplicate...	blob \| commitdiff \| raw \| diff to current
2022-02-04	Tom Clegg	Update logged stats.	blob \| commitdiff \| raw \| diff to current
2022-02-04	Tom Clegg	Don't use tags that appear more than once per sequence.	blob \| commitdiff \| raw \| diff to current
2022-01-14	Tom Clegg	Load case/control/neither from csv column, fix Χ² filter.	blob \| commitdiff \| raw \| diff to current
2022-01-07	Tom Clegg	Handle fasta with no line breaks.	blob \| commitdiff \| raw \| diff to current
2021-10-06	Tom Clegg	Save all ref tile data in slice 0.	blob \| commitdiff \| raw \| diff to current
2021-09-13	Tom Clegg	Slice imported data by tag#.	blob \| commitdiff \| raw \| diff to current
2021-09-09	Tom Clegg	Use callbacks in struct instead of args to Load*().	blob \| commitdiff \| raw \| diff to current
2021-08-06	Tom Clegg	Add copyright headers.	blob \| commitdiff \| raw \| diff to current
2021-07-13	Tom Clegg	Fix some entries skipped by WriteDir.	blob \| commitdiff \| raw \| diff to current
2021-07-09	Tom Clegg	Include tagset in reference-genome files.	blob \| commitdiff \| raw \| diff to current
2021-07-08	Tom Clegg	Write ref seqs to their own files.	blob \| commitdiff \| raw \| diff to current
2021-07-08	Tom Clegg	Option to export one vcf/csv file per chromosome.	blob \| commitdiff \| raw \| diff to current
2021-06-18	Tom Clegg	Fix race.	blob \| commitdiff \| raw \| diff to current
2021-06-17	Tom Clegg	Improve concurrency more.	blob \| commitdiff \| raw \| diff to current
2021-06-17	Tom Clegg	Improve loading concurrency.	blob \| commitdiff \| raw \| diff to current
2021-06-17	Tom Clegg	Split sequence data into 64K independently locked parti...	blob \| commitdiff \| raw \| diff to current
2021-06-17	Tom Clegg	Skip expensive Tracef.	blob \| commitdiff \| raw \| diff to current
2021-06-17	Tom Clegg	Up load throttle to gomaxprocs.	blob \| commitdiff \| raw \| diff to current
2021-06-17	Tom Clegg	Move alloc/copy out of lock.	blob \| commitdiff \| raw \| diff to current
2021-06-17	Tom Clegg	Limit load goroutines to gomaxprocs/2.	blob \| commitdiff \| raw \| diff to current
2021-06-17	Tom Clegg	Distribute genomes across output files.	blob \| commitdiff \| raw \| diff to current
2021-06-17	Tom Clegg	Fix lock held during getRef.	blob \| commitdiff \| raw \| diff to current
2021-06-15	Tom Clegg	Fixup multiple-file reading.	blob \| commitdiff \| raw \| diff to current
2021-06-15	Tom Clegg	Fix "gob: encoder: message too big"	blob \| commitdiff \| raw \| diff to current
2021-06-15	Tom Clegg	Add "flake" command (read, tidy, write).	blob \| commitdiff \| raw \| diff to current
2021-06-14	Tom Clegg	Add concurrency in Tidy remap phase.	blob \| commitdiff \| raw \| diff to current
2021-05-07	Tom Clegg	Export hgvs-onehot.	blob \| commitdiff \| raw \| diff to current
2021-02-08	Tom Clegg	Move command line tool to subdir.	blob \| commitdiff \| raw \| diff to current
2021-01-29	Tom Clegg	Log # low quality tile variants during import.	blob \| commitdiff \| raw \| diff to current
2020-12-02	Tom Clegg	Improve import and vcf2fasta performance.	blob \| commitdiff \| raw \| diff to current
2020-11-29	Tom Clegg	Increase concurrency, reduce allocs.	blob \| commitdiff \| raw \| diff to current
2020-11-29	Tom Clegg	Reduce lock contention.	blob \| commitdiff \| raw \| diff to current
2020-11-22	Tom Clegg	Accept filter args in pca-go.	blob \| commitdiff \| raw \| diff to current
2020-11-19	Tom Clegg	Configurable chromosome name pattern.	blob \| commitdiff \| raw \| diff to current
2020-11-13	Tom Clegg	Gzip gob files.	blob \| commitdiff \| raw \| diff to current
2020-11-12	Tom Clegg	When not saving incomplete tilevars, still save hashes...	blob \| commitdiff \| raw \| diff to current
2020-11-05	Tom Clegg	Renumber/prune variants for numpy export.	blob \| commitdiff \| raw \| diff to current
2020-11-01	Tom Clegg	Write annotations along with numpy.	blob \| commitdiff \| raw \| diff to current
2020-10-31	Tom Clegg	Use tilelib to load for export and pca.	blob \| commitdiff \| raw \| diff to current
2020-10-28	Tom Clegg	Log path len and # skipped out-of-order tiles per chrom...	blob \| commitdiff \| raw \| diff to current
2020-10-25	Tom Clegg	Write import stats to stats.json.	blob \| commitdiff \| raw \| diff to current
2020-10-23	Tom Clegg	Log input seq/chrom size, input coverage, tile coverage.	blob \| commitdiff \| raw \| diff to current
2020-10-22	Tom Clegg	Fix var reused in goroutine.	blob \| commitdiff \| raw \| diff to current
2020-10-21	Tom Clegg	Use only first field of fasta comment as sequence label.	blob \| commitdiff \| raw \| diff to current
2020-10-19	Tom Clegg	Handle variant 0 ("none") in CompactSequences.	blob \| commitdiff \| raw \| diff to current
2020-10-14	Tom Clegg	Export HGVS.	blob \| commitdiff \| raw \| diff to current
2020-10-12	Tom Clegg	Refactor merge.	blob \| commitdiff \| raw \| diff to current
2020-10-12	Tom Clegg	Add merge command.	blob \| commitdiff \| raw \| diff to current
2020-10-08	Tom Clegg	Include tile variant IDs in library.	blob \| commitdiff \| raw \| diff to current
2020-09-25	Tom Clegg	Option to treat tiles with no-calls as regular tiles.	blob \| commitdiff \| raw \| diff to current
2020-09-25	Tom Clegg	Option to output tile library when importing.	blob \| commitdiff \| raw \| diff to current
2020-09-02	Tom Clegg	Fix panic on blank line in fasta.	blob \| commitdiff \| raw \| diff to current
2020-09-02	Tom Clegg	Use real longest increasing subsequence algorithm for...	blob \| commitdiff \| raw \| diff to current
2020-04-24	Tom Clegg	Log # duplicate tags.	blob \| commitdiff \| raw \| diff to current
2020-04-24	Tom Clegg	Log number of skipped tags.	blob \| commitdiff \| raw \| diff to current
2020-04-24	Tom Clegg	-skip-ooo: fix skipping 7 in seq like 0-1-7-0	blob \| commitdiff \| raw \| diff to current
2020-04-23	Tom Clegg	Log out-of-order tags if -loglevel=debug.	blob \| commitdiff \| raw \| diff to current
2020-04-06	Tom Clegg	Option to skip/ignore out-of-order tags.	blob \| commitdiff \| raw \| diff to current
2020-03-05	Tom Clegg	Less verbose logging.	blob \| commitdiff \| raw \| diff to current
2020-01-31	Tom Clegg	Compact on the fly to reduce memory use.	blob \| commitdiff \| raw \| diff to current
2020-01-31	Tom Clegg	Skip chr_.	blob \| commitdiff \| raw \| diff to current
2020-01-31	Tom Clegg	Reduce allocs while tiling.	blob \| commitdiff \| raw \| diff to current
2020-01-20	Tom Clegg	Include ending tag in tile sequence.	blob \| commitdiff \| raw \| diff to current
2020-01-19	Tom Clegg	Use blake256 sum.	blob \| commitdiff \| raw \| diff to current
2020-01-17	Tom Clegg	Drop tiles with no-calls.	blob \| commitdiff \| raw \| diff to current
2020-01-17	Tom Clegg	Log tile library size periodically.	blob \| commitdiff \| raw \| diff to current
2020-01-15	Tom Clegg	md5 -> blake2b	blob \| commitdiff \| raw \| diff to current
2020-01-14	Tom Clegg	limit concurrency	blob \| commitdiff \| raw \| diff to current
2020-01-14	Tom Clegg	Output tile variant arrays.	blob \| commitdiff \| raw \| diff to current
2020-01-13	Tom Clegg	Initial tiling code.	blob \| commitdiff \| raw \| diff to current

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