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lightning.git
2022-11-10 Tom CleggMerge branch '19527-training-set' commit | commitdiff | tree | snapshot
2022-11-09 Tom Clegg19527: Accommodate header row in samples csv. 19527-training-set commit | commitdiff | tree | snapshot
2022-11-09 Tom Clegg19527: Ignore empty line at EOF. commit | commitdiff | tree | snapshot
2022-11-09 Tom CleggMerge branch '19524-pca' commit | commitdiff | tree | snapshot
2022-11-09 Tom Clegg19527: Fix p-value calculation. commit | commitdiff | tree | snapshot
2022-11-09 Tom Clegg19527: Load training-set flag from samples.csv. commit | commitdiff | tree | snapshot
2022-11-09 Tom Clegg19527: choose-samples: training/validation set. commit | commitdiff | tree | snapshot
2022-11-09 Tom Clegg19527: Load training-set flag from samples.csv. commit | commitdiff | tree | snapshot
2022-11-07 Tom Cleggchoose-samples: training/validation set. commit | commitdiff | tree | snapshot
2022-11-02 Tom Clegg19524: Fit PCA to specified training set. commit | commitdiff | tree | snapshot
2022-10-31 Tom CleggMerge branch '19524-pca' commit | commitdiff | tree | snapshot
2022-10-21 Tom Clegg19524: Fix matrix alloc size. 19524-pca commit | commitdiff | tree | snapshot
2022-10-20 Tom Clegg19524: Flags choose which PCA components to plot. commit | commitdiff | tree | snapshot
2022-10-20 Tom Clegg19524: Update colors, plot unknown-phenotype behind... commit | commitdiff | tree | snapshot
2022-10-20 Tom Clegg19524: Limit size of PCA input matrix. commit | commitdiff | tree | snapshot
2022-10-19 Tom Clegg19524: Limit size of PCA input matrix. commit | commitdiff | tree | snapshot
2022-10-19 Tom Clegg19524: configurable vcpus/ram commit | commitdiff | tree | snapshot
2022-10-14 Tom CleggMerge branch '19524-pca' commit | commitdiff | tree | snapshot
2022-10-14 Tom Clegg19524: Use marker shape to indicate second category... commit | commitdiff | tree | snapshot
2022-10-14 Tom Clegg19524: Remove obsolete pca cmds. commit | commitdiff | tree | snapshot
2022-10-14 Tom Clegg19524: Fix deprecated scipy.load. commit | commitdiff | tree | snapshot
2022-10-14 Tom Clegg19524: Read multiple phenotype files. commit | commitdiff | tree | snapshot
2022-10-14 Tom Clegg19524: Generalize plot colors a little. commit | commitdiff | tree | snapshot
2022-10-13 Tom CleggFail if inadvertently using randomness. commit | commitdiff | tree | snapshot
2022-10-12 Tom Clegg19524: Fix colormap. commit | commitdiff | tree | snapshot
2022-10-12 Tom Clegg19524: propagate pca-components arg. commit | commitdiff | tree | snapshot
2022-10-11 Tom Clegg19524: plot: get sample list from csv instead of fasta... commit | commitdiff | tree | snapshot
2022-10-11 Tom Clegg19524: Output PCA. commit | commitdiff | tree | snapshot
2022-10-07 Tom CleggUpdate deps, improve error reporting commit | commitdiff | tree | snapshot
2022-10-07 Tom CleggUse min-coverage filter commit | commitdiff | tree | snapshot
2022-08-05 Tom CleggFix diff case commit | commitdiff | tree | snapshot
2022-08-03 Tom CleggFix diff case commit | commitdiff | tree | snapshot
2022-07-27 Tom CleggFix diff case commit | commitdiff | tree | snapshot
2022-07-27 Tom CleggFix diff case commit | commitdiff | tree | snapshot
2022-07-27 Tom CleggFix diff case commit | commitdiff | tree | snapshot
2022-07-26 Tom CleggFix diff case commit | commitdiff | tree | snapshot
2022-07-20 Tom CleggFix crash when ref tile is dropped due to duplicate... commit | commitdiff | tree | snapshot
2022-07-15 Tom CleggAdd test for variant at right end of spanning tile. commit | commitdiff | tree | snapshot
2022-07-15 Tom CleggGenerate annotations for spanning tiles. commit | commitdiff | tree | snapshot
2022-07-14 Tom CleggUpdate tests. commit | commitdiff | tree | snapshot
2022-07-07 Tom CleggFix wrong index in chunk>0 case. commit | commitdiff | tree | snapshot
2022-07-01 Tom CleggFix low-coverage tiles counting toward min coverage... commit | commitdiff | tree | snapshot
2022-06-03 Tom CleggFix loss of precision in p-value calculation. commit | commitdiff | tree | snapshot
2022-05-04 Tom Clegg19073: Fix dup tag detection. commit | commitdiff | tree | snapshot
2022-05-04 Tom Clegg19073: Fix dup tag detection. commit | commitdiff | tree | snapshot
2022-05-03 Tom Clegg19073: Remove dup tags (>1 ref placement) from tilestat... commit | commitdiff | tree | snapshot
2022-04-29 Tom CleggAdd -log10(pvalue) row to onehot-columns.npy output... commit | commitdiff | tree | snapshot
2022-03-16 Tom CleggAdd tilestats cmd. commit | commitdiff | tree | snapshot
2022-03-16 Tom CleggWrite chunk-tag-offset.csv with chunked tilevariant... commit | commitdiff | tree | snapshot
2022-03-04 Tom CleggChange zygosity column info from het=1 to hom=1. commit | commitdiff | tree | snapshot
2022-02-24 Tom CleggFix left-most diff cases. commit | commitdiff | tree | snapshot
2022-02-22 Tom CleggEncode spanning tile as 0 in tile variant matrix. commit | commitdiff | tree | snapshot
2022-02-20 Tom CleggMore debugging info for -debug-tag. commit | commitdiff | tree | snapshot
2022-02-20 Tom CleggSkip input files that aren't needed because -max-tag. commit | commitdiff | tree | snapshot
2022-02-18 Tom CleggFix left-most diff cases. commit | commitdiff | tree | snapshot
2022-02-18 Tom CleggAdd -debug-tag flag. commit | commitdiff | tree | snapshot
2022-02-18 Tom CleggFix -include-variant-1 commit | commitdiff | tree | snapshot
2022-02-17 Tom CleggUpdate tests (don't include both het+hom if only one... commit | commitdiff | tree | snapshot
2022-02-17 Tom CleggFix -max-tag filter. commit | commitdiff | tree | snapshot
2022-02-17 Tom CleggFix sparse one-hot coordinates for chunk n>0. commit | commitdiff | tree | snapshot
2022-02-17 Tom CleggFix -max-tag filter. commit | commitdiff | tree | snapshot
2022-02-15 Tom CleggOption to include variant 1 in one-hot matrix. commit | commitdiff | tree | snapshot
2022-02-11 Tom CleggInclude tiles in one-hot matrix even if there is no... commit | commitdiff | tree | snapshot
2022-02-09 Tom CleggSupport -max-tag flag for debugging. commit | commitdiff | tree | snapshot
2022-02-04 Tom CleggDon't include het just because corresponding hom passed. commit | commitdiff | tree | snapshot
2022-02-04 Tom CleggUpdate logged stats. commit | commitdiff | tree | snapshot
2022-02-04 Tom CleggDon't use tags that appear more than once per sequence. commit | commitdiff | tree | snapshot
2022-02-03 Tom CleggFix log message. commit | commitdiff | tree | snapshot
2022-02-03 Tom CleggSkip tags that appear twice in the same chromosome. commit | commitdiff | tree | snapshot
2022-01-31 Tom CleggAdd dump command. commit | commitdiff | tree | snapshot
2022-01-27 Tom CleggUpdate memory-size log message. commit | commitdiff | tree | snapshot
2022-01-27 Tom CleggOutput -single-onehot as coordinates of non-zero values. commit | commitdiff | tree | snapshot
2022-01-21 Tom CleggFix Χ² calculation. commit | commitdiff | tree | snapshot
2022-01-17 Tom CleggUse native client to read annotations.csv. commit | commitdiff | tree | snapshot
2022-01-17 Tom CleggAdd -single-onehot output option. commit | commitdiff | tree | snapshot
2022-01-14 Tom CleggLoad case/control/neither from csv column, fix Χ² filter. commit | commitdiff | tree | snapshot
2022-01-13 Tom CleggFix deadlock at container finish. commit | commitdiff | tree | snapshot
2022-01-13 Tom CleggAdd -chunked-onehot option. commit | commitdiff | tree | snapshot
2022-01-07 Tom CleggHandle fasta with no line breaks. commit | commitdiff | tree | snapshot
2022-01-07 Tom CleggFilter HGVS columns by coverage & p-value threshold. commit | commitdiff | tree | snapshot
2021-12-30 Tom CleggFix coordinates in hgvs annotations. commit | commitdiff | tree | snapshot
2021-12-30 Tom CleggContainer-watching fixes. commit | commitdiff | tree | snapshot
2021-12-30 Tom CleggFix slice padding. commit | commitdiff | tree | snapshot
2021-12-30 Tom CleggFix blocking on gob encode. commit | commitdiff | tree | snapshot
2021-12-29 Tom CleggMore aggressive GC. commit | commitdiff | tree | snapshot
2021-12-29 Tom CleggFix index out of bounds error. commit | commitdiff | tree | snapshot
2021-12-29 Tom CleggRefactor chunked-hgvs to use less memory. commit | commitdiff | tree | snapshot
2021-12-27 Tom CleggSeparate options to output single/chunked hgvs matrices. commit | commitdiff | tree | snapshot
2021-12-21 Tom CleggBump slice-numpy memory. commit | commitdiff | tree | snapshot
2021-12-13 Tom CleggInclude HGVS IDs in anno2vcf. commit | commitdiff | tree | snapshot
2021-12-07 Tom CleggUse (throttle)Go() convenience. commit | commitdiff | tree | snapshot
2021-12-04 Tom CleggCall 2-base deletion-insertion as two adjacent SNPs. commit | commitdiff | tree | snapshot
2021-12-02 Tom CleggAdd null csv rows for ref/undiffed. Ensure 0 means... commit | commitdiff | tree | snapshot
2021-11-30 Tom CleggFix handling of TAG->CA (spell as T>C, =A, delG). commit | commitdiff | tree | snapshot
2021-11-30 Tom CleggNot a bug when ref is the only variant loaded. commit | commitdiff | tree | snapshot
2021-11-30 Tom CleggFix deadlock in skip-on-error case. commit | commitdiff | tree | snapshot
2021-11-30 Tom CleggCall SNPs separately when called within 1bp of start... commit | commitdiff | tree | snapshot
2021-11-27 Tom CleggMention undiffable variants in annotations, write ... commit | commitdiff | tree | snapshot
2021-11-26 Tom CleggWrite hgvs-oriented matrix and annotations csv. commit | commitdiff | tree | snapshot
2021-11-26 Tom CleggLog exact locations of duplicate tags. commit | commitdiff | tree | snapshot
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