lightning.git
2022-05-04 Tom Clegg19073: Fix dup tag detection. main
2022-05-04 Tom Clegg19073: Fix dup tag detection.
2022-05-03 Tom Clegg19073: Remove dup tags (>1 ref placement) from tilestat...
2022-04-29 Tom CleggAdd -log10(pvalue) row to onehot-columns.npy output...
2022-03-16 Tom CleggAdd tilestats cmd.
2022-03-16 Tom CleggWrite chunk-tag-offset.csv with chunked tilevariant...
2022-03-04 Tom CleggChange zygosity column info from het=1 to hom=1.
2022-02-24 Tom CleggFix left-most diff cases.
2022-02-22 Tom CleggEncode spanning tile as 0 in tile variant matrix.
2022-02-20 Tom CleggMore debugging info for -debug-tag.
2022-02-20 Tom CleggSkip input files that aren't needed because -max-tag.
2022-02-18 Tom CleggFix left-most diff cases.
2022-02-18 Tom CleggAdd -debug-tag flag.
2022-02-18 Tom CleggFix -include-variant-1
2022-02-17 Tom CleggUpdate tests (don't include both het+hom if only one...
2022-02-17 Tom CleggFix -max-tag filter.
2022-02-17 Tom CleggFix sparse one-hot coordinates for chunk n>0.
2022-02-17 Tom CleggFix -max-tag filter.
2022-02-15 Tom CleggOption to include variant 1 in one-hot matrix.
2022-02-11 Tom CleggInclude tiles in one-hot matrix even if there is no...
2022-02-09 Tom CleggSupport -max-tag flag for debugging.
2022-02-04 Tom CleggDon't include het just because corresponding hom passed.
2022-02-04 Tom CleggUpdate logged stats.
2022-02-04 Tom CleggDon't use tags that appear more than once per sequence.
2022-02-03 Tom CleggFix log message.
2022-02-03 Tom CleggSkip tags that appear twice in the same chromosome.
2022-01-31 Tom CleggAdd dump command.
2022-01-27 Tom CleggUpdate memory-size log message.
2022-01-27 Tom CleggOutput -single-onehot as coordinates of non-zero values.
2022-01-21 Tom CleggFix Χ² calculation.
2022-01-17 Tom CleggUse native client to read annotations.csv.
2022-01-17 Tom CleggAdd -single-onehot output option.
2022-01-14 Tom CleggLoad case/control/neither from csv column, fix Χ² filter.
2022-01-13 Tom CleggFix deadlock at container finish.
2022-01-13 Tom CleggAdd -chunked-onehot option.
2022-01-07 Tom CleggHandle fasta with no line breaks.
2022-01-07 Tom CleggFilter HGVS columns by coverage & p-value threshold.
2021-12-30 Tom CleggFix coordinates in hgvs annotations.
2021-12-30 Tom CleggContainer-watching fixes.
2021-12-30 Tom CleggFix slice padding.
2021-12-30 Tom CleggFix blocking on gob encode.
2021-12-29 Tom CleggMore aggressive GC.
2021-12-29 Tom CleggFix index out of bounds error.
2021-12-29 Tom CleggRefactor chunked-hgvs to use less memory.
2021-12-27 Tom CleggSeparate options to output single/chunked hgvs matrices.
2021-12-21 Tom CleggBump slice-numpy memory.
2021-12-13 Tom CleggInclude HGVS IDs in anno2vcf.
2021-12-07 Tom CleggUse (throttle)Go() convenience.
2021-12-04 Tom CleggCall 2-base deletion-insertion as two adjacent SNPs.
2021-12-02 Tom CleggAdd null csv rows for ref/undiffed. Ensure 0 means...
2021-11-30 Tom CleggFix handling of TAG->CA (spell as T>C, =A, delG).
2021-11-30 Tom CleggNot a bug when ref is the only variant loaded.
2021-11-30 Tom CleggFix deadlock in skip-on-error case.
2021-11-30 Tom CleggCall SNPs separately when called within 1bp of start...
2021-11-27 Tom CleggMention undiffable variants in annotations, write ...
2021-11-26 Tom CleggWrite hgvs-oriented matrix and annotations csv.
2021-11-26 Tom CleggLog exact locations of duplicate tags.
2021-11-25 Tom CleggDrop duplicate tags, fix ref position tracking.
2021-11-25 Tom CleggFix interval tree unused node markers.
2021-11-25 Tom CleggMore debug messages and error checks.
2021-11-24 Tom CleggUse non-preemptible instances.
2021-11-24 Tom CleggOption to merge matrices and annotations.
2021-11-22 Tom CleggImplement -regions and -expand-regions for slice-numpy.
2021-11-19 Tom CleggAdjust slice memory.
2021-11-04 Tom CleggWrite deletions as "TAA T" instead of "AA .".
2021-11-04 Tom CleggFix variant numbering.
2021-11-01 Tom CleggUpdate slice-numpy test.
2021-11-01 Tom CleggFix duplicate entries in slice-numpy annotations.
2021-11-01 Tom CleggAvoid empty "ref" field in anno2vcf output.
2021-11-01 Tom CleggSplit anno2vcf output by chromosome.
2021-11-01 Tom CleggFix sort func.
2021-10-28 Tom CleggBump slice-numpy memory.
2021-10-28 Tom CleggSort input files.
2021-10-28 Tom CleggAdd anno2vcf command.
2021-10-08 Tom CleggAccept PDH on command line.
2021-10-06 Tom CleggUse arvados client for /any/path/$id/, not just /mnt...
2021-10-06 Tom CleggImplement -match-genome filter.
2021-10-06 Tom CleggFix namespace types.
2021-10-06 Tom CleggSave all ref tile data in slice 0.
2021-09-26 Tom CleggCleanup var name.
2021-09-25 Tom CleggScale keep cache to 2*(openfiles+1).
2021-09-25 Tom CleggImprove logging.
2021-09-25 Tom CleggTweak cpu/mem usage.
2021-09-23 Tom CleggAccept multiple input libraries for slice→slicenumpy.
2021-09-21 Tom CleggLog total variant/genome/ref counts.
2021-09-20 Tom CleggFix array index out of bounds.
2021-09-17 Tom CleggRenumber variants by allele count.
2021-09-17 Tom CleggFix reference assembly.
2021-09-14 Tom CleggFix mem usage, improve logging.
2021-09-13 Tom CleggGenerate annotations for slices.
2021-09-13 Tom CleggGenerate numpy matrices from slices.
2021-09-13 Tom CleggAlways log version at startup.
2021-09-13 Tom CleggSlice imported data by tag#.
2021-09-09 Tom CleggUse callbacks in struct instead of args to Load*().
2021-09-01 Tom CleggFix missed TranslatePaths and unreported error.
2021-08-31 Tom CleggAdd -p-value and -cases options for exporting hgvs...
2021-08-31 Tom CleggAdd chi square func.
2021-08-12 Tom CleggFix unchecked error.
2021-08-12 Tom CleggFix array index out of bounds.
2021-08-11 Tom CleggAdd -match-genome=regexp filter.
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