git.arvados.org - lightning.git/shortlog

2022-07-27	Tom Clegg	Fix diff case	commit \| commitdiff \| tree \| snapshot
2022-07-26	Tom Clegg	Fix diff case	commit \| commitdiff \| tree \| snapshot
2022-07-20	Tom Clegg	Fix crash when ref tile is dropped due to duplicate...	commit \| commitdiff \| tree \| snapshot
2022-07-15	Tom Clegg	Add test for variant at right end of spanning tile.	commit \| commitdiff \| tree \| snapshot
2022-07-15	Tom Clegg	Generate annotations for spanning tiles.	commit \| commitdiff \| tree \| snapshot
2022-07-14	Tom Clegg	Update tests.	commit \| commitdiff \| tree \| snapshot
2022-07-07	Tom Clegg	Fix wrong index in chunk>0 case.	commit \| commitdiff \| tree \| snapshot
2022-07-01	Tom Clegg	Fix low-coverage tiles counting toward min coverage...	commit \| commitdiff \| tree \| snapshot
2022-06-03	Tom Clegg	Fix loss of precision in p-value calculation.	commit \| commitdiff \| tree \| snapshot
2022-05-04	Tom Clegg	19073: Fix dup tag detection.	commit \| commitdiff \| tree \| snapshot
2022-05-04	Tom Clegg	19073: Fix dup tag detection.	commit \| commitdiff \| tree \| snapshot
2022-05-03	Tom Clegg	19073: Remove dup tags (>1 ref placement) from tilestat...	commit \| commitdiff \| tree \| snapshot
2022-04-29	Tom Clegg	Add -log10(pvalue) row to onehot-columns.npy output...	commit \| commitdiff \| tree \| snapshot
2022-03-16	Tom Clegg	Add tilestats cmd.	commit \| commitdiff \| tree \| snapshot
2022-03-16	Tom Clegg	Write chunk-tag-offset.csv with chunked tilevariant...	commit \| commitdiff \| tree \| snapshot
2022-03-04	Tom Clegg	Change zygosity column info from het=1 to hom=1.	commit \| commitdiff \| tree \| snapshot
2022-02-24	Tom Clegg	Fix left-most diff cases.	commit \| commitdiff \| tree \| snapshot
2022-02-22	Tom Clegg	Encode spanning tile as 0 in tile variant matrix.	commit \| commitdiff \| tree \| snapshot
2022-02-20	Tom Clegg	More debugging info for -debug-tag.	commit \| commitdiff \| tree \| snapshot
2022-02-20	Tom Clegg	Skip input files that aren't needed because -max-tag.	commit \| commitdiff \| tree \| snapshot
2022-02-18	Tom Clegg	Fix left-most diff cases.	commit \| commitdiff \| tree \| snapshot
2022-02-18	Tom Clegg	Add -debug-tag flag.	commit \| commitdiff \| tree \| snapshot
2022-02-18	Tom Clegg	Fix -include-variant-1	commit \| commitdiff \| tree \| snapshot
2022-02-17	Tom Clegg	Update tests (don't include both het+hom if only one...	commit \| commitdiff \| tree \| snapshot
2022-02-17	Tom Clegg	Fix -max-tag filter.	commit \| commitdiff \| tree \| snapshot
2022-02-17	Tom Clegg	Fix sparse one-hot coordinates for chunk n>0.	commit \| commitdiff \| tree \| snapshot
2022-02-17	Tom Clegg	Fix -max-tag filter.	commit \| commitdiff \| tree \| snapshot
2022-02-15	Tom Clegg	Option to include variant 1 in one-hot matrix.	commit \| commitdiff \| tree \| snapshot
2022-02-11	Tom Clegg	Include tiles in one-hot matrix even if there is no...	commit \| commitdiff \| tree \| snapshot
2022-02-09	Tom Clegg	Support -max-tag flag for debugging.	commit \| commitdiff \| tree \| snapshot
2022-02-04	Tom Clegg	Don't include het just because corresponding hom passed.	commit \| commitdiff \| tree \| snapshot
2022-02-04	Tom Clegg	Update logged stats.	commit \| commitdiff \| tree \| snapshot
2022-02-04	Tom Clegg	Don't use tags that appear more than once per sequence.	commit \| commitdiff \| tree \| snapshot
2022-02-03	Tom Clegg	Fix log message.	commit \| commitdiff \| tree \| snapshot
2022-02-03	Tom Clegg	Skip tags that appear twice in the same chromosome.	commit \| commitdiff \| tree \| snapshot
2022-01-31	Tom Clegg	Add dump command.	commit \| commitdiff \| tree \| snapshot
2022-01-27	Tom Clegg	Update memory-size log message.	commit \| commitdiff \| tree \| snapshot
2022-01-27	Tom Clegg	Output -single-onehot as coordinates of non-zero values.	commit \| commitdiff \| tree \| snapshot
2022-01-21	Tom Clegg	Fix Χ² calculation.	commit \| commitdiff \| tree \| snapshot
2022-01-17	Tom Clegg	Use native client to read annotations.csv.	commit \| commitdiff \| tree \| snapshot
2022-01-17	Tom Clegg	Add -single-onehot output option.	commit \| commitdiff \| tree \| snapshot
2022-01-14	Tom Clegg	Load case/control/neither from csv column, fix Χ² filter.	commit \| commitdiff \| tree \| snapshot
2022-01-13	Tom Clegg	Fix deadlock at container finish.	commit \| commitdiff \| tree \| snapshot
2022-01-13	Tom Clegg	Add -chunked-onehot option.	commit \| commitdiff \| tree \| snapshot
2022-01-07	Tom Clegg	Handle fasta with no line breaks.	commit \| commitdiff \| tree \| snapshot
2022-01-07	Tom Clegg	Filter HGVS columns by coverage & p-value threshold.	commit \| commitdiff \| tree \| snapshot
2021-12-30	Tom Clegg	Fix coordinates in hgvs annotations.	commit \| commitdiff \| tree \| snapshot
2021-12-30	Tom Clegg	Container-watching fixes.	commit \| commitdiff \| tree \| snapshot
2021-12-30	Tom Clegg	Fix slice padding.	commit \| commitdiff \| tree \| snapshot
2021-12-30	Tom Clegg	Fix blocking on gob encode.	commit \| commitdiff \| tree \| snapshot
2021-12-29	Tom Clegg	More aggressive GC.	commit \| commitdiff \| tree \| snapshot
2021-12-29	Tom Clegg	Fix index out of bounds error.	commit \| commitdiff \| tree \| snapshot
2021-12-29	Tom Clegg	Refactor chunked-hgvs to use less memory.	commit \| commitdiff \| tree \| snapshot
2021-12-27	Tom Clegg	Separate options to output single/chunked hgvs matrices.	commit \| commitdiff \| tree \| snapshot
2021-12-21	Tom Clegg	Bump slice-numpy memory.	commit \| commitdiff \| tree \| snapshot
2021-12-13	Tom Clegg	Include HGVS IDs in anno2vcf.	commit \| commitdiff \| tree \| snapshot
2021-12-07	Tom Clegg	Use (throttle)Go() convenience.	commit \| commitdiff \| tree \| snapshot
2021-12-04	Tom Clegg	Call 2-base deletion-insertion as two adjacent SNPs.	commit \| commitdiff \| tree \| snapshot
2021-12-02	Tom Clegg	Add null csv rows for ref/undiffed. Ensure 0 means...	commit \| commitdiff \| tree \| snapshot
2021-11-30	Tom Clegg	Fix handling of TAG->CA (spell as T>C, =A, delG).	commit \| commitdiff \| tree \| snapshot
2021-11-30	Tom Clegg	Not a bug when ref is the only variant loaded.	commit \| commitdiff \| tree \| snapshot
2021-11-30	Tom Clegg	Fix deadlock in skip-on-error case.	commit \| commitdiff \| tree \| snapshot
2021-11-30	Tom Clegg	Call SNPs separately when called within 1bp of start...	commit \| commitdiff \| tree \| snapshot
2021-11-27	Tom Clegg	Mention undiffable variants in annotations, write ...	commit \| commitdiff \| tree \| snapshot
2021-11-26	Tom Clegg	Write hgvs-oriented matrix and annotations csv.	commit \| commitdiff \| tree \| snapshot
2021-11-26	Tom Clegg	Log exact locations of duplicate tags.	commit \| commitdiff \| tree \| snapshot
2021-11-25	Tom Clegg	Drop duplicate tags, fix ref position tracking.	commit \| commitdiff \| tree \| snapshot
2021-11-25	Tom Clegg	Fix interval tree unused node markers.	commit \| commitdiff \| tree \| snapshot
2021-11-25	Tom Clegg	More debug messages and error checks.	commit \| commitdiff \| tree \| snapshot
2021-11-24	Tom Clegg	Use non-preemptible instances.	commit \| commitdiff \| tree \| snapshot
2021-11-24	Tom Clegg	Option to merge matrices and annotations.	commit \| commitdiff \| tree \| snapshot
2021-11-22	Tom Clegg	Implement -regions and -expand-regions for slice-numpy.	commit \| commitdiff \| tree \| snapshot
2021-11-19	Tom Clegg	Adjust slice memory.	commit \| commitdiff \| tree \| snapshot
2021-11-04	Tom Clegg	Write deletions as "TAA T" instead of "AA .".	commit \| commitdiff \| tree \| snapshot
2021-11-04	Tom Clegg	Fix variant numbering.	commit \| commitdiff \| tree \| snapshot
2021-11-01	Tom Clegg	Update slice-numpy test.	commit \| commitdiff \| tree \| snapshot
2021-11-01	Tom Clegg	Fix duplicate entries in slice-numpy annotations.	commit \| commitdiff \| tree \| snapshot
2021-11-01	Tom Clegg	Avoid empty "ref" field in anno2vcf output.	commit \| commitdiff \| tree \| snapshot
2021-11-01	Tom Clegg	Split anno2vcf output by chromosome.	commit \| commitdiff \| tree \| snapshot
2021-11-01	Tom Clegg	Fix sort func.	commit \| commitdiff \| tree \| snapshot
2021-10-28	Tom Clegg	Bump slice-numpy memory.	commit \| commitdiff \| tree \| snapshot
2021-10-28	Tom Clegg	Sort input files.	commit \| commitdiff \| tree \| snapshot
2021-10-28	Tom Clegg	Add anno2vcf command.	commit \| commitdiff \| tree \| snapshot
2021-10-08	Tom Clegg	Accept PDH on command line.	commit \| commitdiff \| tree \| snapshot
2021-10-06	Tom Clegg	Use arvados client for /any/path/$id/, not just /mnt...	commit \| commitdiff \| tree \| snapshot
2021-10-06	Tom Clegg	Implement -match-genome filter.	commit \| commitdiff \| tree \| snapshot
2021-10-06	Tom Clegg	Fix namespace types.	commit \| commitdiff \| tree \| snapshot
2021-10-06	Tom Clegg	Save all ref tile data in slice 0.	commit \| commitdiff \| tree \| snapshot
2021-09-26	Tom Clegg	Cleanup var name.	commit \| commitdiff \| tree \| snapshot
2021-09-25	Tom Clegg	Scale keep cache to 2*(openfiles+1).	commit \| commitdiff \| tree \| snapshot
2021-09-25	Tom Clegg	Improve logging.	commit \| commitdiff \| tree \| snapshot
2021-09-25	Tom Clegg	Tweak cpu/mem usage.	commit \| commitdiff \| tree \| snapshot
2021-09-23	Tom Clegg	Accept multiple input libraries for slice→slicenumpy.	commit \| commitdiff \| tree \| snapshot
2021-09-21	Tom Clegg	Log total variant/genome/ref counts.	commit \| commitdiff \| tree \| snapshot
2021-09-20	Tom Clegg	Fix array index out of bounds.	commit \| commitdiff \| tree \| snapshot
2021-09-17	Tom Clegg	Renumber variants by allele count.	commit \| commitdiff \| tree \| snapshot
2021-09-17	Tom Clegg	Fix reference assembly.	commit \| commitdiff \| tree \| snapshot
2021-09-14	Tom Clegg	Fix mem usage, improve logging.	commit \| commitdiff \| tree \| snapshot
2021-09-13	Tom Clegg	Generate annotations for slices.	commit \| commitdiff \| tree \| snapshot
2021-09-13	Tom Clegg	Generate numpy matrices from slices.	commit \| commitdiff \| tree \| snapshot
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