lightning.git
2021-11-01 Tom CleggAvoid empty "ref" field in anno2vcf output.
2021-11-01 Tom CleggSplit anno2vcf output by chromosome.
2021-11-01 Tom CleggFix sort func.
2021-10-28 Tom CleggBump slice-numpy memory.
2021-10-28 Tom CleggSort input files.
2021-10-28 Tom CleggAdd anno2vcf command.
2021-10-08 Tom CleggAccept PDH on command line.
2021-10-06 Tom CleggUse arvados client for /any/path/$id/, not just /mnt...
2021-10-06 Tom CleggImplement -match-genome filter.
2021-10-06 Tom CleggFix namespace types.
2021-10-06 Tom CleggSave all ref tile data in slice 0.
2021-09-26 Tom CleggCleanup var name.
2021-09-25 Tom CleggScale keep cache to 2*(openfiles+1).
2021-09-25 Tom CleggImprove logging.
2021-09-25 Tom CleggTweak cpu/mem usage.
2021-09-23 Tom CleggAccept multiple input libraries for slice→slicenumpy.
2021-09-21 Tom CleggLog total variant/genome/ref counts.
2021-09-20 Tom CleggFix array index out of bounds.
2021-09-17 Tom CleggRenumber variants by allele count.
2021-09-17 Tom CleggFix reference assembly.
2021-09-14 Tom CleggFix mem usage, improve logging.
2021-09-13 Tom CleggGenerate annotations for slices.
2021-09-13 Tom CleggGenerate numpy matrices from slices.
2021-09-13 Tom CleggAlways log version at startup.
2021-09-13 Tom CleggSlice imported data by tag#.
2021-09-09 Tom CleggUse callbacks in struct instead of args to Load*().
2021-09-01 Tom CleggFix missed TranslatePaths and unreported error.
2021-08-31 Tom CleggAdd -p-value and -cases options for exporting hgvs...
2021-08-31 Tom CleggAdd chi square func.
2021-08-12 Tom CleggFix unchecked error.
2021-08-12 Tom CleggFix array index out of bounds.
2021-08-11 Tom CleggAdd -match-genome=regexp filter.
2021-08-11 Tom CleggExport hgvs one-hot numpy: -1 for missing / low quality...
2021-08-10 Tom CleggAdd filter options to export cmd.
2021-08-10 Tom CleggAdd .licenseignore.
2021-08-10 Tom CleggMemory tweaks.
2021-08-06 Tom CleggAdd copyright headers.
2021-08-06 Tom CleggReduce memory use, Limit goroutines when exporting...
2021-08-03 Tom CleggReduce lock contention.
2021-08-03 Tom CleggWrite annotations through to conserve memory.
2021-08-02 Tom CleggExport hgvs one-hot numpy.
2021-07-30 Tom CleggUse tsv filename when using tab separator.
2021-07-29 Tom CleggTrack which tile variants each hgvs.Variant appeared in.
2021-07-15 Tom CleggSkip diffs on long ref seqs.
2021-07-13 Tom CleggFix some entries skipped by WriteDir.
2021-07-13 Tom CleggCompress export output.
2021-07-13 Tom CleggFix up VCF format.
2021-07-12 Tom CleggFix recomputing diffs N times.
2021-07-12 Tom CleggSeparate pvcf/vcf output.
2021-07-09 Tom CleggProgress indicator for exportSeq.
2021-07-09 Tom CleggImprove concurrency in export-diff.
2021-07-09 Tom CleggInclude tagset in reference-genome files.
2021-07-08 Tom CleggFix missing output.
2021-07-08 Tom CleggWrite ref seqs to their own files.
2021-07-08 Tom CleggUse more cpus.
2021-07-08 Tom CleggFix use of nil writer.
2021-07-08 Tom CleggEnable network access to get port forwarding.
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.
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