Merge branch '19526-manhattan-plot'
[lightning.git] / tilelib.go
2022-07-20 Tom CleggFix crash when ref tile is dropped due to duplicate...
2022-02-04 Tom CleggUpdate logged stats.
2022-02-04 Tom CleggDon't use tags that appear more than once per sequence.
2022-01-14 Tom CleggLoad case/control/neither from csv column, fix Χ² filter.
2022-01-07 Tom CleggHandle fasta with no line breaks.
2021-10-06 Tom CleggSave all ref tile data in slice 0.
2021-09-13 Tom CleggSlice imported data by tag#.
2021-09-09 Tom CleggUse callbacks in struct instead of args to Load*().
2021-08-06 Tom CleggAdd copyright headers.
2021-07-13 Tom CleggFix some entries skipped by WriteDir.
2021-07-09 Tom CleggInclude tagset in reference-genome files.
2021-07-08 Tom CleggWrite ref seqs to their own files.
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 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.
2021-05-07 Tom CleggExport hgvs-onehot.
2021-02-08 Tom CleggMove command line tool to subdir.
2021-01-29 Tom CleggLog # low quality tile variants during import.
2020-12-02 Tom CleggImprove import and vcf2fasta performance.
2020-11-29 Tom CleggIncrease concurrency, reduce allocs.
2020-11-29 Tom CleggReduce lock contention.
2020-11-22 Tom CleggAccept filter args in pca-go.
2020-11-19 Tom CleggConfigurable chromosome name pattern.
2020-11-13 Tom CleggGzip gob files.
2020-11-12 Tom CleggWhen not saving incomplete tilevars, still save hashes...
2020-11-05 Tom CleggRenumber/prune variants for numpy export.
2020-11-01 Tom CleggWrite annotations along with numpy.
2020-10-31 Tom CleggUse tilelib to load for export and pca.
2020-10-28 Tom CleggLog path len and # skipped out-of-order tiles per chrom...
2020-10-25 Tom CleggWrite import stats to stats.json.
2020-10-23 Tom CleggLog input seq/chrom size, input coverage, tile coverage.
2020-10-22 Tom CleggFix var reused in goroutine.
2020-10-21 Tom CleggUse only first field of fasta comment as sequence label.
2020-10-19 Tom CleggHandle variant 0 ("none") in CompactSequences.
2020-10-14 Tom CleggExport HGVS.
2020-10-12 Tom CleggRefactor merge.
2020-10-12 Tom CleggAdd merge command.
2020-10-08 Tom CleggInclude tile variant IDs in library.
2020-09-25 Tom CleggOption to treat tiles with no-calls as regular tiles.
2020-09-25 Tom CleggOption to output tile library when importing.
2020-09-02 Tom CleggFix panic on blank line in fasta.
2020-09-02 Tom CleggUse real longest increasing subsequence algorithm for...
2020-04-24 Tom CleggLog # duplicate tags.
2020-04-24 Tom CleggLog number of skipped tags.
2020-04-24 Tom Clegg-skip-ooo: fix skipping 7 in seq like 0-1-7-0
2020-04-23 Tom CleggLog out-of-order tags if -loglevel=debug.
2020-04-06 Tom CleggOption to skip/ignore out-of-order tags.
2020-03-05 Tom CleggLess verbose logging.
2020-01-31 Tom CleggCompact on the fly to reduce memory use.
2020-01-31 Tom CleggSkip chr*_*.
2020-01-31 Tom CleggReduce allocs while tiling.
2020-01-20 Tom CleggInclude ending tag in tile sequence.
2020-01-19 Tom CleggUse blake256 sum.
2020-01-17 Tom CleggDrop tiles with no-calls.
2020-01-17 Tom CleggLog tile library size periodically.
2020-01-15 Tom Cleggmd5 -> blake2b
2020-01-14 Tom Clegglimit concurrency
2020-01-14 Tom CleggOutput tile variant arrays.
2020-01-13 Tom CleggInitial tiling code.