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lightning.git
2020-04-08 Tom CleggMore memory for import. commit | commitdiff | tree | snapshot
2020-04-06 Tom CleggFix up websocket locking. commit | commitdiff | tree | snapshot
2020-04-06 Tom CleggPropagate skip-ooo flag to container. commit | commitdiff | tree | snapshot
2020-04-06 Tom CleggExit non-zero if container is cancelled. commit | commitdiff | tree | snapshot
2020-04-06 Tom CleggOutput to arvados storage instead of staging on local... commit | commitdiff | tree | snapshot
2020-04-06 Tom CleggOption to skip/ignore out-of-order tags. commit | commitdiff | tree | snapshot
2020-04-06 Tom CleggFixup tagset collection in example script. commit | commitdiff | tree | snapshot
2020-04-03 Tom CleggRequest more memory when using mask. commit | commitdiff | tree | snapshot
2020-04-03 Tom CleggRead contig sizes from vcf. commit | commitdiff | tree | snapshot
2020-04-02 Tom CleggKill other children and exit early if one child process... commit | commitdiff | tree | snapshot
2020-04-02 Tom CleggSort genome file same way as vcf regions. commit | commitdiff | tree | snapshot
2020-03-12 Tom Cleggs/python/python2/ commit | commitdiff | tree | snapshot
2020-03-12 Tom CleggAdd python2 to docker image. commit | commitdiff | tree | snapshot
2020-03-12 Tom CleggFix example script. commit | commitdiff | tree | snapshot
2020-03-12 Tom CleggPropagate genome arg. commit | commitdiff | tree | snapshot
2020-03-11 Tom CleggRefactor websocket listener. commit | commitdiff | tree | snapshot
2020-03-11 Tom CleggDon't pipe gvcf_regions to bedtools. Avoid short-read... commit | commitdiff | tree | snapshot
2020-03-11 Tom CleggUse named pipe for bcftools --mask data. commit | commitdiff | tree | snapshot
2020-03-11 Tom CleggShow file path in ref2genome -local=false. commit | commitdiff | tree | snapshot
2020-03-11 Tom CleggAdd -priority to example script. commit | commitdiff | tree | snapshot
2020-03-11 Tom CleggFix missing VCPUs. commit | commitdiff | tree | snapshot
2020-03-11 Tom CleggFix unchecked error. commit | commitdiff | tree | snapshot
2020-03-11 Tom CleggConnect stdin/stdout in docker containers. commit | commitdiff | tree | snapshot
2020-03-11 Tom CleggNo O_EXCL. commit | commitdiff | tree | snapshot
2020-03-11 Tom CleggError reporting. commit | commitdiff | tree | snapshot
2020-03-10 Tom CleggUpdate example script. commit | commitdiff | tree | snapshot
2020-03-10 Tom CleggFix docker mounts. commit | commitdiff | tree | snapshot
2020-03-10 Tom CleggGenerate genome file from fasta. commit | commitdiff | tree | snapshot
2020-03-10 Tom CleggFix example collections. commit | commitdiff | tree | snapshot
2020-03-10 Tom CleggInstall bedtools. commit | commitdiff | tree | snapshot
2020-03-10 Tom CleggShow stderr from children. commit | commitdiff | tree | snapshot
2020-03-10 Tom CleggDon't try to pass fd 3 to docker. commit | commitdiff | tree | snapshot
2020-03-10 Tom Cleggvcf2fasta -mask cont'd. commit | commitdiff | tree | snapshot
2020-03-10 Tom CleggPass gvcf_regions.py via mount. commit | commitdiff | tree | snapshot
2020-03-10 Tom CleggContainer request priority flag. commit | commitdiff | tree | snapshot
2020-03-09 Tom CleggAdd vcf2fasta -mask option. commit | commitdiff | tree | snapshot
2020-03-09 Tom CleggAdd vcf2fasta command. commit | commitdiff | tree | snapshot
2020-03-07 Tom CleggRemove debug bit. commit | commitdiff | tree | snapshot
2020-03-05 Tom CleggUse more tiling workers than NumCPU. commit | commitdiff | tree | snapshot
2020-03-05 Tom CleggFilter logs by container on client side of ws connection. commit | commitdiff | tree | snapshot
2020-03-05 Tom CleggLess verbose logging. commit | commitdiff | tree | snapshot
2020-03-05 Tom CleggUpgrade deps. commit | commitdiff | tree | snapshot
2020-03-05 Tom CleggFix up log/event handling. commit | commitdiff | tree | snapshot
2020-03-05 Tom CleggI/O pipeline, show arvados container logs. commit | commitdiff | tree | snapshot
2020-03-04 Tom CleggAdd example script. commit | commitdiff | tree | snapshot
2020-03-04 Tom CleggAdd plot subcommand. commit | commitdiff | tree | snapshot
2020-03-04 Tom CleggTidy log messages. commit | commitdiff | tree | snapshot
2020-03-04 Tom CleggFix input arg in export. commit | commitdiff | tree | snapshot
2020-03-03 Tom CleggAdd pca subcommand. commit | commitdiff | tree | snapshot
2020-03-03 Tom CleggRun "filter" and "export" in arvados containers. commit | commitdiff | tree | snapshot
2020-03-02 Tom CleggRun "import" in arvados container. commit | commitdiff | tree | snapshot
2020-03-02 Tom CleggAdd import -o argument. commit | commitdiff | tree | snapshot
2020-03-02 Tom CleggDon't require reference data when all inputs are fasta. commit | commitdiff | tree | snapshot
2020-02-07 Tom CleggUpdate go.sum. commit | commitdiff | tree | snapshot
2020-02-07 Tom CleggFix typo. commit | commitdiff | tree | snapshot
2020-02-06 Tom CleggFix zeroing everything if max-variants not specified. commit | commitdiff | tree | snapshot
2020-02-06 Tom CleggFix copy-paste error in color map. commit | commitdiff | tree | snapshot
2020-02-05 Tom CleggAdd filter subcommand. commit | commitdiff | tree | snapshot
2020-02-04 Tom CleggSplit gvcf2numpy command into import and export-numpy. commit | commitdiff | tree | snapshot
2020-02-03 Tom CleggColor PCA plot. commit | commitdiff | tree | snapshot
2020-01-31 Tom CleggCompact on the fly to reduce memory use. commit | commitdiff | tree | snapshot
2020-01-31 Tom CleggSkip chr*_*. commit | commitdiff | tree | snapshot
2020-01-31 Tom CleggReduce allocs while tiling. commit | commitdiff | tree | snapshot
2020-01-30 Tom CleggAccount for WIP in progress report. commit | commitdiff | tree | snapshot
2020-01-30 Tom CleggRemove spurious else. commit | commitdiff | tree | snapshot
2020-01-30 Tom CleggUse 2bit-packed uint64 as tagmapKey. commit | commitdiff | tree | snapshot
2020-01-30 Tom CleggFix file mode. commit | commitdiff | tree | snapshot
2020-01-30 Tom CleggAdd -pprof flag. commit | commitdiff | tree | snapshot
2020-01-30 Tom CleggFix writing all variant numbers to npy row 0. commit | commitdiff | tree | snapshot
2020-01-30 Tom CleggSkip extra assignment. commit | commitdiff | tree | snapshot
2020-01-30 Tom CleggAdd example PCA script. commit | commitdiff | tree | snapshot
2020-01-30 Tom CleggFix shadowed var captured in goroutine. commit | commitdiff | tree | snapshot
2020-01-20 Tom CleggTest fasta2numpy. commit | commitdiff | tree | snapshot
2020-01-20 Tom CleggInclude ending tag in tile sequence. commit | commitdiff | tree | snapshot
2020-01-19 Tom CleggUse blake256 sum. commit | commitdiff | tree | snapshot
2020-01-19 Tom CleggAccept fasta inputs. commit | commitdiff | tree | snapshot
2020-01-19 Tom CleggDon't try to match overlapping tags. commit | commitdiff | tree | snapshot
2020-01-17 Tom CleggDrop tiles with no-calls. commit | commitdiff | tree | snapshot
2020-01-17 Tom CleggFix deadlock from unclosed chan. commit | commitdiff | tree | snapshot
2020-01-17 Tom CleggLog tile library size periodically. commit | commitdiff | tree | snapshot
2020-01-16 Tom CleggShow progress / ETA. commit | commitdiff | tree | snapshot
2020-01-16 Tom Cleggint32 -> uint16 in numpy output. commit | commitdiff | tree | snapshot
2020-01-16 Tom CleggFix errs channel race. commit | commitdiff | tree | snapshot
2020-01-16 Tom CleggWrite numpy array. commit | commitdiff | tree | snapshot
2020-01-15 Tom Cleggmd5 -> blake2b commit | commitdiff | tree | snapshot
2020-01-15 Tom CleggAccept directories as vcf source args. commit | commitdiff | tree | snapshot
2020-01-14 Tom Clegglimit concurrency commit | commitdiff | tree | snapshot
2020-01-14 Tom Cleggaccept csi or tbi index commit | commitdiff | tree | snapshot
2020-01-14 Tom CleggFix docker buffering everything. commit | commitdiff | tree | snapshot
2020-01-14 Tom CleggLimit concurrency. commit | commitdiff | tree | snapshot
2020-01-14 Tom CleggOutput tile variant arrays. commit | commitdiff | tree | snapshot
2020-01-13 Tom CleggInitial tiling code. commit | commitdiff | tree | snapshot