git.arvados.org - lightning.git/shortlog

2021-03-15	Tom Clegg	Test numpy annotations.	commit \| commitdiff \| tree \| snapshot
2021-03-11	Tom Clegg	Option to write numpy in chunks (same rows, fewer columns).	commit \| commitdiff \| tree \| snapshot
2021-03-04	Tom Clegg	Bump export RAM.	commit \| commitdiff \| tree \| snapshot
2021-03-01	Tom Clegg	Bump import RAM.	commit \| commitdiff \| tree \| snapshot
2021-03-01	Tom Clegg	Ask for preemptible instances.	commit \| commitdiff \| tree \| snapshot
2021-03-01	Tom Clegg	Reduce import RAM.	commit \| commitdiff \| tree \| snapshot
2021-03-01	Tom Clegg	Throttle goroutines and unflushed bufs to NCPUs.	commit \| commitdiff \| tree \| snapshot
2021-02-19	Tom Clegg	Upgrade to debian bullseye to get bcftools 1.11.	commit \| commitdiff \| tree \| snapshot
2021-02-08	Tom Clegg	Add missing file for batchArgs.	commit \| commitdiff \| tree \| snapshot
2021-02-08	Tom Clegg	Move command line tool to subdir.	commit \| commitdiff \| tree \| snapshot
2021-01-29	Tom Clegg	Fake a complete_genomics_pass_all preset.	commit \| commitdiff \| tree \| snapshot
2021-01-29	Tom Clegg	Log # low quality tile variants during import.	commit \| commitdiff \| tree \| snapshot
2021-01-29	Tom Clegg	Log exported numpy shape.	commit \| commitdiff \| tree \| snapshot
2021-01-18	Tom Clegg	Add dumpgob command.	commit \| commitdiff \| tree \| snapshot
2021-01-14	Tom Clegg	Fix log message.	commit \| commitdiff \| tree \| snapshot
2020-12-18	Tom Clegg	Share a single sitefs for multiple arvados files.	commit \| commitdiff \| tree \| snapshot
2020-12-18	Tom Clegg	Bump import memory.	commit \| commitdiff \| tree \| snapshot
2020-12-17	Tom Clegg	Bump exportnumpy memory.	commit \| commitdiff \| tree \| snapshot
2020-12-16	Tom Clegg	Sort rows by label shown in csv, not full file path.	commit \| commitdiff \| tree \| snapshot
2020-12-15	Tom Clegg	Bump merge memory.	commit \| commitdiff \| tree \| snapshot
2020-12-15	Tom Clegg	Load library with pgzip.	commit \| commitdiff \| tree \| snapshot
2020-12-14	Tom Clegg	Faster merge output.	commit \| commitdiff \| tree \| snapshot
2020-12-08	Tom Clegg	Bigger output buffer for annotate.	commit \| commitdiff \| tree \| snapshot
2020-12-08	Tom Clegg	Save git version in lightning binary collection name...	commit \| commitdiff \| tree \| snapshot
2020-12-04	Tom Clegg	Include numpy matrix filename in labels csv.	commit \| commitdiff \| tree \| snapshot
2020-12-04	Tom Clegg	More memory + direct Keep access for merge and exportnumpy.	commit \| commitdiff \| tree \| snapshot
2020-12-02	Tom Clegg	Update example.	commit \| commitdiff \| tree \| snapshot
2020-12-02	Tom Clegg	Don't pass -gvcf-type="" to gvcf_regions.py.	commit \| commitdiff \| tree \| snapshot
2020-12-02	Tom Clegg	Fix deadlock on error.	commit \| commitdiff \| tree \| snapshot
2020-12-02	Tom Clegg	Improve import and vcf2fasta performance.	commit \| commitdiff \| tree \| snapshot
2020-11-29	Tom Clegg	Increase concurrency, reduce allocs.	commit \| commitdiff \| tree \| snapshot
2020-11-29	Tom Clegg	Reduce lock contention.	commit \| commitdiff \| tree \| snapshot
2020-11-25	Tom Clegg	Use smaller machines for small batches.	commit \| commitdiff \| tree \| snapshot
2020-11-25	Tom Clegg	Use buffered writer to avoid overwhelming arv-mount.	commit \| commitdiff \| tree \| snapshot
2020-11-25	Tom Clegg	Share CR refresh throttle when running multiple containers.	commit \| commitdiff \| tree \| snapshot
2020-11-25	Tom Clegg	Export labels.csv with numpy array.	commit \| commitdiff \| tree \| snapshot
2020-11-24	Tom Clegg	Concurrent-batches mode for vcf2fasta and import.	commit \| commitdiff \| tree \| snapshot
2020-11-23	Tom Clegg	More memory for pca.	commit \| commitdiff \| tree \| snapshot
2020-11-23	Tom Clegg	Propagate -match-chromosome arg to container.	commit \| commitdiff \| tree \| snapshot
2020-11-22	Tom Clegg	Pass gvcf-type to gvcf_regions.	commit \| commitdiff \| tree \| snapshot
2020-11-22	Tom Clegg	Fix fasta sequence names.	commit \| commitdiff \| tree \| snapshot
2020-11-22	Tom Clegg	Accept filter args in pca-go.	commit \| commitdiff \| tree \| snapshot
2020-11-22	Tom Clegg	Let caller set container output name.	commit \| commitdiff \| tree \| snapshot
2020-11-19	Tom Clegg	Fix divide by zero.	commit \| commitdiff \| tree \| snapshot
2020-11-19	Tom Clegg	Configurable chromosome name pattern.	commit \| commitdiff \| tree \| snapshot
2020-11-19	Tom Clegg	Fix wrong container name.	commit \| commitdiff \| tree \| snapshot
2020-11-19	Tom Clegg	Indicate low quality tile variants with -1 in numpy...	commit \| commitdiff \| tree \| snapshot
2020-11-13	Tom Clegg	Gzip gob files.	commit \| commitdiff \| tree \| snapshot
2020-11-13	Tom Clegg	Update example.	commit \| commitdiff \| tree \| snapshot
2020-11-12	Tom Clegg	When not saving incomplete tilevars, still save hashes...	commit \| commitdiff \| tree \| snapshot
2020-11-05	Tom Clegg	Add numpy-common-variants sanity check.	commit \| commitdiff \| tree \| snapshot
2020-11-05	Tom Clegg	Renumber/prune variants for numpy export.	commit \| commitdiff \| tree \| snapshot
2020-11-02	Tom Clegg	Omit refname field in annotation if only one ref exists.	commit \| commitdiff \| tree \| snapshot
2020-11-02	Tom Clegg	Adjust speed knobs.	commit \| commitdiff \| tree \| snapshot
2020-11-02	Tom Clegg	Don't drop ref tile data when filtering.	commit \| commitdiff \| tree \| snapshot
2020-11-02	Tom Clegg	Propagate filters to container.	commit \| commitdiff \| tree \| snapshot
2020-11-02	Tom Clegg	Faster annotate.	commit \| commitdiff \| tree \| snapshot
2020-11-01	Tom Clegg	Write annotations along with numpy.	commit \| commitdiff \| tree \| snapshot
2020-10-31	Tom Clegg	Use tilelib to load for export and pca.	commit \| commitdiff \| tree \| snapshot
2020-10-29	Tom Clegg	Log locations of long tiles.	commit \| commitdiff \| tree \| snapshot
2020-10-29	Tom Clegg	max-tile-size option.	commit \| commitdiff \| tree \| snapshot
2020-10-29	Tom Clegg	Less memory and cpu for annotate.	commit \| commitdiff \| tree \| snapshot
2020-10-29	Tom Clegg	Fix example.	commit \| commitdiff \| tree \| snapshot
2020-10-29	Tom Clegg	Faster annotate.	commit \| commitdiff \| tree \| snapshot
2020-10-29	Tom Clegg	Update example.	commit \| commitdiff \| tree \| snapshot
2020-10-28	Tom Clegg	Log path len and # skipped out-of-order tiles per chrom...	commit \| commitdiff \| tree \| snapshot
2020-10-28	Tom Clegg	Export tile annotations.	commit \| commitdiff \| tree \| snapshot
2020-10-26	Tom Clegg	Continue loop a bit earlier.	commit \| commitdiff \| tree \| snapshot
2020-10-26	Tom Clegg	Better series palette.	commit \| commitdiff \| tree \| snapshot
2020-10-25	Tom Clegg	Fix up example.	commit \| commitdiff \| tree \| snapshot
2020-10-25	Tom Clegg	Plot import stats.	commit \| commitdiff \| tree \| snapshot
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
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