lightning.git
2021-07-08 Tom CleggOption to export one vcf/csv file per chromosome.
2021-06-18 Tom CleggFix race.
2021-06-17 Tom CleggImprove concurrency more.
2021-06-17 Tom CleggImprove loading concurrency.
2021-06-17 Tom CleggSplit sequence data into 64K independently locked parti...
2021-06-17 Tom CleggFix exportnumpy test.
2021-06-17 Tom CleggAdd concurrent load to exportnumpy.
2021-06-17 Tom CleggSkip expensive Tracef.
2021-06-17 Tom CleggUp load throttle to gomaxprocs.
2021-06-17 Tom CleggMove alloc/copy out of lock.
2021-06-17 Tom CleggLimit load goroutines to gomaxprocs/2.
2021-06-17 Tom CleggDistribute genomes across output files.
2021-06-17 Tom CleggFix lock held during getRef.
2021-06-15 Tom CleggFixup multiple-file reading.
2021-06-15 Tom CleggFix "gob: encoder: message too big"
2021-06-15 Tom CleggAdd "flake" command (read, tidy, write).
2021-06-14 Tom CleggAdd concurrency in Tidy remap phase.
2021-06-14 Tom CleggAdjust memory.
2021-06-14 Tom CleggWrite hgvs-based numpy matrix.
2021-06-03 Tom CleggFix another category of misspelled hgvs diff.
2021-05-25 Tom CleggBring memory back down.
2021-05-24 Tom CleggLimit tile size in export.
2021-05-21 Tom CleggSave runtime profile data periodically.
2021-05-20 Tom CleggDon't try to buffer/sort export.
2021-05-19 Tom CleggMore memory, but release buffers.
2021-05-18 Tom CleggManage export memory.
2021-05-18 Tom CleggAdd test.
2021-05-11 Tom CleggAvoid buffering entire output in memory.
2021-05-07 Tom CleggExport hgvs-onehot.
2021-04-26 Tom CleggBump exportnumpy memory.
2021-04-23 Tom CleggBump merge memory.
2021-04-23 Tom CleggError out early.
2021-04-12 Tom CleggBump exportnumpy memory.
2021-04-12 Tom CleggBump merge memory.
2021-04-08 Tom CleggFix HGVS diff: GGAA>AAAA is GG>AA, not delGG,=AA,insAA.
2021-04-01 Tom CleggAdd -expand-regions flag.
2021-03-24 Tom CleggExport selected regions.
2021-03-15 Tom CleggTest numpy annotations.
2021-03-11 Tom CleggOption to write numpy in chunks (same rows, fewer columns).
2021-03-04 Tom CleggBump export RAM.
2021-03-01 Tom CleggBump import RAM.
2021-03-01 Tom CleggAsk for preemptible instances.
2021-03-01 Tom CleggReduce import RAM.
2021-03-01 Tom CleggThrottle goroutines and unflushed bufs to NCPUs.
2021-02-19 Tom CleggUpgrade to debian bullseye to get bcftools 1.11.
2021-02-08 Tom CleggAdd missing file for batchArgs.
2021-02-08 Tom CleggMove command line tool to subdir.
2021-01-29 Tom CleggFake a complete_genomics_pass_all preset.
2021-01-29 Tom CleggLog # low quality tile variants during import.
2021-01-29 Tom CleggLog exported numpy shape.
2021-01-18 Tom CleggAdd dumpgob command.
2021-01-14 Tom CleggFix log message.
2020-12-18 Tom CleggShare a single sitefs for multiple arvados files.
2020-12-18 Tom CleggBump import memory.
2020-12-17 Tom CleggBump exportnumpy memory.
2020-12-16 Tom CleggSort rows by label shown in csv, not full file path.
2020-12-15 Tom CleggBump merge memory.
2020-12-15 Tom CleggLoad library with pgzip.
2020-12-14 Tom CleggFaster merge output.
2020-12-08 Tom CleggBigger output buffer for annotate.
2020-12-08 Tom CleggSave git version in lightning binary collection name...
2020-12-04 Tom CleggInclude numpy matrix filename in labels csv.
2020-12-04 Tom CleggMore memory + direct Keep access for merge and exportnumpy.
2020-12-02 Tom CleggUpdate example.
2020-12-02 Tom CleggDon't pass -gvcf-type="" to gvcf_regions.py.
2020-12-02 Tom CleggFix deadlock on error.
2020-12-02 Tom CleggImprove import and vcf2fasta performance.
2020-11-29 Tom CleggIncrease concurrency, reduce allocs.
2020-11-29 Tom CleggReduce lock contention.
2020-11-25 Tom CleggUse smaller machines for small batches.
2020-11-25 Tom CleggUse buffered writer to avoid overwhelming arv-mount.
2020-11-25 Tom CleggShare CR refresh throttle when running multiple containers.
2020-11-25 Tom CleggExport labels.csv with numpy array.
2020-11-24 Tom CleggConcurrent-batches mode for vcf2fasta and import.
2020-11-23 Tom CleggMore memory for pca.
2020-11-23 Tom CleggPropagate -match-chromosome arg to container.
2020-11-22 Tom CleggPass gvcf-type to gvcf_regions.
2020-11-22 Tom CleggFix fasta sequence names.
2020-11-22 Tom CleggAccept filter args in pca-go.
2020-11-22 Tom CleggLet caller set container output name.
2020-11-19 Tom CleggFix divide by zero.
2020-11-19 Tom CleggConfigurable chromosome name pattern.
2020-11-19 Tom CleggFix wrong container name.
2020-11-19 Tom CleggIndicate low quality tile variants with -1 in numpy...
2020-11-13 Tom CleggGzip gob files.
2020-11-13 Tom CleggUpdate example.
2020-11-12 Tom CleggWhen not saving incomplete tilevars, still save hashes...
2020-11-05 Tom CleggAdd numpy-common-variants sanity check.
2020-11-05 Tom CleggRenumber/prune variants for numpy export.
2020-11-02 Tom CleggOmit refname field in annotation if only one ref exists.
2020-11-02 Tom CleggAdjust speed knobs.
2020-11-02 Tom CleggDon't drop ref tile data when filtering.
2020-11-02 Tom CleggPropagate filters to container.
2020-11-02 Tom CleggFaster annotate.
2020-11-01 Tom CleggWrite annotations along with numpy.
2020-10-31 Tom CleggUse tilelib to load for export and pca.
2020-10-29 Tom CleggLog locations of long tiles.
2020-10-29 Tom Cleggmax-tile-size option.
2020-10-29 Tom CleggLess memory and cpu for annotate.
2020-10-29 Tom CleggFix example.
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