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Merge branch '19527-training-set'
[lightning.git] / slicenumpy.go
2022-11-10 Tom CleggMerge branch '19527-training-set' blob | commitdiff | raw
2022-11-09 Tom Clegg19527: Ignore empty line at EOF. blob | commitdiff | raw
2022-11-09 Tom CleggMerge branch '19524-pca' blob | commitdiff | raw | diff to current
2022-11-09 Tom Clegg19527: Fix p-value calculation. blob | commitdiff | raw | diff to current
2022-11-09 Tom Clegg19527: Load training-set flag from samples.csv. blob | commitdiff | raw | diff to current
2022-11-09 Tom Clegg19527: choose-samples: training/validation set. blob | commitdiff | raw | diff to current
2022-11-09 Tom Clegg19527: Load training-set flag from samples.csv. blob | commitdiff | raw | diff to current
2022-11-07 Tom Cleggchoose-samples: training/validation set. blob | commitdiff | raw | diff to current
2022-11-02 Tom Clegg19524: Fit PCA to specified training set. blob | commitdiff | raw | diff to current
2022-10-31 Tom CleggMerge branch '19524-pca' blob | commitdiff | raw | diff to current
2022-10-21 Tom Clegg19524: Fix matrix alloc size. 19524-pca blob | commitdiff | raw | diff to current
2022-10-20 Tom Clegg19524: Limit size of PCA input matrix. blob | commitdiff | raw | diff to current
2022-10-19 Tom Clegg19524: Limit size of PCA input matrix. blob | commitdiff | raw | diff to current
2022-10-19 Tom Clegg19524: configurable vcpus/ram blob | commitdiff | raw | diff to current
2022-10-14 Tom CleggMerge branch '19524-pca' blob | commitdiff | raw | diff to current
2022-10-12 Tom Clegg19524: propagate pca-components arg. blob | commitdiff | raw | diff to current
2022-10-11 Tom Clegg19524: Output PCA. blob | commitdiff | raw | diff to current
2022-10-07 Tom CleggUpdate deps, improve error reporting blob | commitdiff | raw | diff to current
2022-10-07 Tom CleggUse min-coverage filter blob | commitdiff | raw | diff to current
2022-07-20 Tom CleggFix crash when ref tile is dropped due to duplicate... blob | commitdiff | raw | diff to current
2022-07-15 Tom CleggGenerate annotations for spanning tiles. blob | commitdiff | raw | diff to current
2022-07-07 Tom CleggFix wrong index in chunk>0 case. blob | commitdiff | raw | diff to current
2022-07-01 Tom CleggFix low-coverage tiles counting toward min coverage... blob | commitdiff | raw | diff to current
2022-04-29 Tom CleggAdd -log10(pvalue) row to onehot-columns.npy output... blob | commitdiff | raw | diff to current
2022-03-16 Tom CleggAdd tilestats cmd. blob | commitdiff | raw | diff to current
2022-03-16 Tom CleggWrite chunk-tag-offset.csv with chunked tilevariant... blob | commitdiff | raw | diff to current
2022-03-04 Tom CleggChange zygosity column info from het=1 to hom=1. blob | commitdiff | raw | diff to current
2022-02-22 Tom CleggEncode spanning tile as 0 in tile variant matrix. blob | commitdiff | raw | diff to current
2022-02-20 Tom CleggMore debugging info for -debug-tag. blob | commitdiff | raw | diff to current
2022-02-20 Tom CleggSkip input files that aren't needed because -max-tag. blob | commitdiff | raw | diff to current
2022-02-18 Tom CleggAdd -debug-tag flag. blob | commitdiff | raw | diff to current
2022-02-18 Tom CleggFix -include-variant-1 blob | commitdiff | raw | diff to current
2022-02-17 Tom CleggFix -max-tag filter. blob | commitdiff | raw | diff to current
2022-02-17 Tom CleggFix sparse one-hot coordinates for chunk n>0. blob | commitdiff | raw | diff to current
2022-02-17 Tom CleggFix -max-tag filter. blob | commitdiff | raw | diff to current
2022-02-15 Tom CleggOption to include variant 1 in one-hot matrix. blob | commitdiff | raw | diff to current
2022-02-11 Tom CleggInclude tiles in one-hot matrix even if there is no... blob | commitdiff | raw | diff to current
2022-02-09 Tom CleggSupport -max-tag flag for debugging. blob | commitdiff | raw | diff to current
2022-02-04 Tom CleggDon't include het just because corresponding hom passed. blob | commitdiff | raw | diff to current
2022-02-03 Tom CleggFix log message. blob | commitdiff | raw | diff to current
2022-02-03 Tom CleggSkip tags that appear twice in the same chromosome. blob | commitdiff | raw | diff to current
2022-01-27 Tom CleggUpdate memory-size log message. blob | commitdiff | raw | diff to current
2022-01-27 Tom CleggOutput -single-onehot as coordinates of non-zero values. blob | commitdiff | raw | diff to current
2022-01-21 Tom CleggFix Χ² calculation. blob | commitdiff | raw | diff to current
2022-01-17 Tom CleggAdd -single-onehot output option. blob | commitdiff | raw | diff to current
2022-01-14 Tom CleggLoad case/control/neither from csv column, fix Χ² filter. blob | commitdiff | raw | diff to current
2022-01-13 Tom CleggAdd -chunked-onehot option. blob | commitdiff | raw | diff to current
2022-01-07 Tom CleggFilter HGVS columns by coverage & p-value threshold. blob | commitdiff | raw | diff to current
2021-12-30 Tom CleggFix coordinates in hgvs annotations. blob | commitdiff | raw | diff to current
2021-12-30 Tom CleggFix slice padding. blob | commitdiff | raw | diff to current
2021-12-30 Tom CleggFix blocking on gob encode. blob | commitdiff | raw | diff to current
2021-12-29 Tom CleggMore aggressive GC. blob | commitdiff | raw | diff to current
2021-12-29 Tom CleggFix index out of bounds error. blob | commitdiff | raw | diff to current
2021-12-29 Tom CleggRefactor chunked-hgvs to use less memory. blob | commitdiff | raw | diff to current
2021-12-27 Tom CleggSeparate options to output single/chunked hgvs matrices. blob | commitdiff | raw | diff to current
2021-12-21 Tom CleggBump slice-numpy memory. blob | commitdiff | raw | diff to current
2021-12-02 Tom CleggAdd null csv rows for ref/undiffed. Ensure 0 means... blob | commitdiff | raw | diff to current
2021-11-30 Tom CleggNot a bug when ref is the only variant loaded. blob | commitdiff | raw | diff to current
2021-11-27 Tom CleggMention undiffable variants in annotations, write ... blob | commitdiff | raw | diff to current
2021-11-26 Tom CleggWrite hgvs-oriented matrix and annotations csv. blob | commitdiff | raw | diff to current
2021-11-26 Tom CleggLog exact locations of duplicate tags. blob | commitdiff | raw | diff to current
2021-11-25 Tom CleggDrop duplicate tags, fix ref position tracking. blob | commitdiff | raw | diff to current
2021-11-25 Tom CleggMore debug messages and error checks. blob | commitdiff | raw | diff to current
2021-11-24 Tom CleggOption to merge matrices and annotations. blob | commitdiff | raw | diff to current
2021-11-22 Tom CleggImplement -regions and -expand-regions for slice-numpy. blob | commitdiff | raw | diff to current
2021-11-04 Tom CleggFix variant numbering. blob | commitdiff | raw | diff to current
2021-11-01 Tom CleggFix duplicate entries in slice-numpy annotations. blob | commitdiff | raw | diff to current
2021-11-01 Tom CleggAvoid empty "ref" field in anno2vcf output. blob | commitdiff | raw | diff to current
2021-10-28 Tom CleggBump slice-numpy memory. blob | commitdiff | raw | diff to current
2021-10-28 Tom CleggAdd anno2vcf command. blob | commitdiff | raw | diff to current
2021-10-06 Tom CleggImplement -match-genome filter. blob | commitdiff | raw | diff to current
2021-10-06 Tom CleggSave all ref tile data in slice 0. blob | commitdiff | raw | diff to current
2021-09-25 Tom CleggImprove logging. blob | commitdiff | raw | diff to current
2021-09-25 Tom CleggTweak cpu/mem usage. blob | commitdiff | raw | diff to current
2021-09-23 Tom CleggAccept multiple input libraries for slice→slicenumpy. blob | commitdiff | raw | diff to current
2021-09-20 Tom CleggFix array index out of bounds. blob | commitdiff | raw | diff to current
2021-09-17 Tom CleggRenumber variants by allele count. blob | commitdiff | raw | diff to current
2021-09-17 Tom CleggFix reference assembly. blob | commitdiff | raw | diff to current
2021-09-14 Tom CleggFix mem usage, improve logging. blob | commitdiff | raw | diff to current
2021-09-13 Tom CleggGenerate annotations for slices. blob | commitdiff | raw | diff to current
2021-09-13 Tom CleggGenerate numpy matrices from slices. blob | commitdiff | raw | diff to current