git.arvados.org - lightning.git/shortlog

2021-11-30	Tom Clegg	Call SNPs separately when called within 1bp of start...	commit \| commitdiff \| tree \| snapshot
2021-11-27	Tom Clegg	Mention undiffable variants in annotations, write ...	commit \| commitdiff \| tree \| snapshot
2021-11-26	Tom Clegg	Write hgvs-oriented matrix and annotations csv.	commit \| commitdiff \| tree \| snapshot
2021-11-26	Tom Clegg	Log exact locations of duplicate tags.	commit \| commitdiff \| tree \| snapshot
2021-11-25	Tom Clegg	Drop duplicate tags, fix ref position tracking.	commit \| commitdiff \| tree \| snapshot
2021-11-25	Tom Clegg	Fix interval tree unused node markers.	commit \| commitdiff \| tree \| snapshot
2021-11-25	Tom Clegg	More debug messages and error checks.	commit \| commitdiff \| tree \| snapshot
2021-11-24	Tom Clegg	Use non-preemptible instances.	commit \| commitdiff \| tree \| snapshot
2021-11-24	Tom Clegg	Option to merge matrices and annotations.	commit \| commitdiff \| tree \| snapshot
2021-11-22	Tom Clegg	Implement -regions and -expand-regions for slice-numpy.	commit \| commitdiff \| tree \| snapshot
2021-11-19	Tom Clegg	Adjust slice memory.	commit \| commitdiff \| tree \| snapshot
2021-11-04	Tom Clegg	Write deletions as "TAA T" instead of "AA .".	commit \| commitdiff \| tree \| snapshot
2021-11-04	Tom Clegg	Fix variant numbering.	commit \| commitdiff \| tree \| snapshot
2021-11-01	Tom Clegg	Update slice-numpy test.	commit \| commitdiff \| tree \| snapshot
2021-11-01	Tom Clegg	Fix duplicate entries in slice-numpy annotations.	commit \| commitdiff \| tree \| snapshot
2021-11-01	Tom Clegg	Avoid empty "ref" field in anno2vcf output.	commit \| commitdiff \| tree \| snapshot
2021-11-01	Tom Clegg	Split anno2vcf output by chromosome.	commit \| commitdiff \| tree \| snapshot
2021-11-01	Tom Clegg	Fix sort func.	commit \| commitdiff \| tree \| snapshot
2021-10-28	Tom Clegg	Bump slice-numpy memory.	commit \| commitdiff \| tree \| snapshot
2021-10-28	Tom Clegg	Sort input files.	commit \| commitdiff \| tree \| snapshot
2021-10-28	Tom Clegg	Add anno2vcf command.	commit \| commitdiff \| tree \| snapshot
2021-10-08	Tom Clegg	Accept PDH on command line.	commit \| commitdiff \| tree \| snapshot
2021-10-06	Tom Clegg	Use arvados client for /any/path/$id/, not just /mnt...	commit \| commitdiff \| tree \| snapshot
2021-10-06	Tom Clegg	Implement -match-genome filter.	commit \| commitdiff \| tree \| snapshot
2021-10-06	Tom Clegg	Fix namespace types.	commit \| commitdiff \| tree \| snapshot
2021-10-06	Tom Clegg	Save all ref tile data in slice 0.	commit \| commitdiff \| tree \| snapshot
2021-09-26	Tom Clegg	Cleanup var name.	commit \| commitdiff \| tree \| snapshot
2021-09-25	Tom Clegg	Scale keep cache to 2*(openfiles+1).	commit \| commitdiff \| tree \| snapshot
2021-09-25	Tom Clegg	Improve logging.	commit \| commitdiff \| tree \| snapshot
2021-09-25	Tom Clegg	Tweak cpu/mem usage.	commit \| commitdiff \| tree \| snapshot
2021-09-23	Tom Clegg	Accept multiple input libraries for slice→slicenumpy.	commit \| commitdiff \| tree \| snapshot
2021-09-21	Tom Clegg	Log total variant/genome/ref counts.	commit \| commitdiff \| tree \| snapshot
2021-09-20	Tom Clegg	Fix array index out of bounds.	commit \| commitdiff \| tree \| snapshot
2021-09-17	Tom Clegg	Renumber variants by allele count.	commit \| commitdiff \| tree \| snapshot
2021-09-17	Tom Clegg	Fix reference assembly.	commit \| commitdiff \| tree \| snapshot
2021-09-14	Tom Clegg	Fix mem usage, improve logging.	commit \| commitdiff \| tree \| snapshot
2021-09-13	Tom Clegg	Generate annotations for slices.	commit \| commitdiff \| tree \| snapshot
2021-09-13	Tom Clegg	Generate numpy matrices from slices.	commit \| commitdiff \| tree \| snapshot
2021-09-13	Tom Clegg	Always log version at startup.	commit \| commitdiff \| tree \| snapshot
2021-09-13	Tom Clegg	Slice imported data by tag#.	commit \| commitdiff \| tree \| snapshot
2021-09-09	Tom Clegg	Use callbacks in struct instead of args to Load*().	commit \| commitdiff \| tree \| snapshot
2021-09-01	Tom Clegg	Fix missed TranslatePaths and unreported error.	commit \| commitdiff \| tree \| snapshot
2021-08-31	Tom Clegg	Add -p-value and -cases options for exporting hgvs...	commit \| commitdiff \| tree \| snapshot
2021-08-31	Tom Clegg	Add chi square func.	commit \| commitdiff \| tree \| snapshot
2021-08-12	Tom Clegg	Fix unchecked error.	commit \| commitdiff \| tree \| snapshot
2021-08-12	Tom Clegg	Fix array index out of bounds.	commit \| commitdiff \| tree \| snapshot
2021-08-11	Tom Clegg	Add -match-genome=regexp filter.	commit \| commitdiff \| tree \| snapshot
2021-08-11	Tom Clegg	Export hgvs one-hot numpy: -1 for missing / low quality...	commit \| commitdiff \| tree \| snapshot
2021-08-10	Tom Clegg	Add filter options to export cmd.	commit \| commitdiff \| tree \| snapshot
2021-08-10	Tom Clegg	Add .licenseignore.	commit \| commitdiff \| tree \| snapshot
2021-08-10	Tom Clegg	Memory tweaks.	commit \| commitdiff \| tree \| snapshot
2021-08-06	Tom Clegg	Add copyright headers.	commit \| commitdiff \| tree \| snapshot
2021-08-06	Tom Clegg	Reduce memory use, Limit goroutines when exporting...	commit \| commitdiff \| tree \| snapshot
2021-08-03	Tom Clegg	Reduce lock contention.	commit \| commitdiff \| tree \| snapshot
2021-08-03	Tom Clegg	Write annotations through to conserve memory.	commit \| commitdiff \| tree \| snapshot
2021-08-02	Tom Clegg	Export hgvs one-hot numpy.	commit \| commitdiff \| tree \| snapshot
2021-07-30	Tom Clegg	Use tsv filename when using tab separator.	commit \| commitdiff \| tree \| snapshot
2021-07-29	Tom Clegg	Track which tile variants each hgvs.Variant appeared in.	commit \| commitdiff \| tree \| snapshot
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
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