git.arvados.org - lightning.git/shortlog

2021-07-15	Tom Clegg	Skip diffs on long ref seqs.	commit \| commitdiff \| tree \| snapshot
2021-07-13	Tom Clegg	Fix some entries skipped by WriteDir.	commit \| commitdiff \| tree \| snapshot
2021-07-13	Tom Clegg	Compress export output.	commit \| commitdiff \| tree \| snapshot
2021-07-13	Tom Clegg	Fix up VCF format.	commit \| commitdiff \| tree \| snapshot
2021-07-12	Tom Clegg	Fix recomputing diffs N times.	commit \| commitdiff \| tree \| snapshot
2021-07-12	Tom Clegg	Separate pvcf/vcf output.	commit \| commitdiff \| tree \| snapshot
2021-07-09	Tom Clegg	Progress indicator for exportSeq.	commit \| commitdiff \| tree \| snapshot
2021-07-09	Tom Clegg	Improve concurrency in export-diff.	commit \| commitdiff \| tree \| snapshot
2021-07-09	Tom Clegg	Include tagset in reference-genome files.	commit \| commitdiff \| tree \| snapshot
2021-07-08	Tom Clegg	Fix missing output.	commit \| commitdiff \| tree \| snapshot
2021-07-08	Tom Clegg	Write ref seqs to their own files.	commit \| commitdiff \| tree \| snapshot
2021-07-08	Tom Clegg	Use more cpus.	commit \| commitdiff \| tree \| snapshot
2021-07-08	Tom Clegg	Fix use of nil writer.	commit \| commitdiff \| tree \| snapshot
2021-07-08	Tom Clegg	Enable network access to get port forwarding.	commit \| commitdiff \| tree \| snapshot
2021-07-08	Tom Clegg	Option to export one vcf/csv file per chromosome.	commit \| commitdiff \| tree \| snapshot
2021-06-18	Tom Clegg	Fix race.	commit \| commitdiff \| tree \| snapshot
2021-06-17	Tom Clegg	Improve concurrency more.	commit \| commitdiff \| tree \| snapshot
2021-06-17	Tom Clegg	Improve loading concurrency.	commit \| commitdiff \| tree \| snapshot
2021-06-17	Tom Clegg	Split sequence data into 64K independently locked parti...	commit \| commitdiff \| tree \| snapshot
2021-06-17	Tom Clegg	Fix exportnumpy test.	commit \| commitdiff \| tree \| snapshot
2021-06-17	Tom Clegg	Add concurrent load to exportnumpy.	commit \| commitdiff \| tree \| snapshot
2021-06-17	Tom Clegg	Skip expensive Tracef.	commit \| commitdiff \| tree \| snapshot
2021-06-17	Tom Clegg	Up load throttle to gomaxprocs.	commit \| commitdiff \| tree \| snapshot
2021-06-17	Tom Clegg	Move alloc/copy out of lock.	commit \| commitdiff \| tree \| snapshot
2021-06-17	Tom Clegg	Limit load goroutines to gomaxprocs/2.	commit \| commitdiff \| tree \| snapshot
2021-06-17	Tom Clegg	Distribute genomes across output files.	commit \| commitdiff \| tree \| snapshot
2021-06-17	Tom Clegg	Fix lock held during getRef.	commit \| commitdiff \| tree \| snapshot
2021-06-15	Tom Clegg	Fixup multiple-file reading.	commit \| commitdiff \| tree \| snapshot
2021-06-15	Tom Clegg	Fix "gob: encoder: message too big"	commit \| commitdiff \| tree \| snapshot
2021-06-15	Tom Clegg	Add "flake" command (read, tidy, write).	commit \| commitdiff \| tree \| snapshot
2021-06-14	Tom Clegg	Add concurrency in Tidy remap phase.	commit \| commitdiff \| tree \| snapshot
2021-06-14	Tom Clegg	Adjust memory.	commit \| commitdiff \| tree \| snapshot
2021-06-14	Tom Clegg	Write hgvs-based numpy matrix.	commit \| commitdiff \| tree \| snapshot
2021-06-03	Tom Clegg	Fix another category of misspelled hgvs diff.	commit \| commitdiff \| tree \| snapshot
2021-05-25	Tom Clegg	Bring memory back down.	commit \| commitdiff \| tree \| snapshot
2021-05-24	Tom Clegg	Limit tile size in export.	commit \| commitdiff \| tree \| snapshot
2021-05-21	Tom Clegg	Save runtime profile data periodically.	commit \| commitdiff \| tree \| snapshot
2021-05-20	Tom Clegg	Don't try to buffer/sort export.	commit \| commitdiff \| tree \| snapshot
2021-05-19	Tom Clegg	More memory, but release buffers.	commit \| commitdiff \| tree \| snapshot
2021-05-18	Tom Clegg	Manage export memory.	commit \| commitdiff \| tree \| snapshot
2021-05-18	Tom Clegg	Add test.	commit \| commitdiff \| tree \| snapshot
2021-05-11	Tom Clegg	Avoid buffering entire output in memory.	commit \| commitdiff \| tree \| snapshot
2021-05-07	Tom Clegg	Export hgvs-onehot.	commit \| commitdiff \| tree \| snapshot
2021-04-26	Tom Clegg	Bump exportnumpy memory.	commit \| commitdiff \| tree \| snapshot
2021-04-23	Tom Clegg	Bump merge memory.	commit \| commitdiff \| tree \| snapshot
2021-04-23	Tom Clegg	Error out early.	commit \| commitdiff \| tree \| snapshot
2021-04-12	Tom Clegg	Bump exportnumpy memory.	commit \| commitdiff \| tree \| snapshot
2021-04-12	Tom Clegg	Bump merge memory.	commit \| commitdiff \| tree \| snapshot
2021-04-08	Tom Clegg	Fix HGVS diff: GGAA>AAAA is GG>AA, not delGG,=AA,insAA.	commit \| commitdiff \| tree \| snapshot
2021-04-01	Tom Clegg	Add -expand-regions flag.	commit \| commitdiff \| tree \| snapshot
2021-03-24	Tom Clegg	Export selected regions.	commit \| commitdiff \| tree \| snapshot
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
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