| 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 |
| 2021-09-13 |
Tom Clegg | Always log version at startup. |
commit | commitdiff | tree | snapshot |
| 2021-09-13 |
Tom Clegg | Slice imported data by tag#. |
commit | commitdiff | tree | snapshot |
| 2021-09-09 |
Tom Clegg | Use callbacks in struct instead of args to Load*(). |
commit | commitdiff | tree | snapshot |
| 2021-09-01 |
Tom Clegg | Fix missed TranslatePaths and unreported error. |
commit | commitdiff | tree | snapshot |
| 2021-08-31 |
Tom Clegg | Add -p-value and -cases options for exporting hgvs... |
commit | commitdiff | tree | snapshot |
| 2021-08-31 |
Tom Clegg | Add chi square func. |
commit | commitdiff | tree | snapshot |
| 2021-08-12 |
Tom Clegg | Fix unchecked error. |
commit | commitdiff | tree | snapshot |
| 2021-08-12 |
Tom Clegg | Fix array index out of bounds. |
commit | commitdiff | tree | snapshot |
| 2021-08-11 |
Tom Clegg | Add -match-genome=regexp filter. |
commit | commitdiff | tree | snapshot |
| 2021-08-11 |
Tom Clegg | Export hgvs one-hot numpy: -1 for missing / low quality... |
commit | commitdiff | tree | snapshot |
| 2021-08-10 |
Tom Clegg | Add filter options to export cmd. |
commit | commitdiff | tree | snapshot |
| 2021-08-10 |
Tom Clegg | Add .licenseignore. |
commit | commitdiff | tree | snapshot |
| 2021-08-10 |
Tom Clegg | Memory tweaks. |
commit | commitdiff | tree | snapshot |
| 2021-08-06 |
Tom Clegg | Add copyright headers. |
commit | commitdiff | tree | snapshot |
| 2021-08-06 |
Tom Clegg | Reduce memory use, Limit goroutines when exporting... |
commit | commitdiff | tree | snapshot |
| 2021-08-03 |
Tom Clegg | Reduce lock contention. |
commit | commitdiff | tree | snapshot |
| 2021-08-03 |
Tom Clegg | Write annotations through to conserve memory. |
commit | commitdiff | tree | snapshot |
| 2021-08-02 |
Tom Clegg | Export hgvs one-hot numpy. |
commit | commitdiff | tree | snapshot |
| 2021-07-30 |
Tom Clegg | Use tsv filename when using tab separator. |
commit | commitdiff | tree | snapshot |
| 2021-07-29 |
Tom Clegg | Track which tile variants each hgvs.Variant appeared in. |
commit | commitdiff | tree | snapshot |
| 2021-07-15 |
Tom Clegg | Skip diffs on long ref seqs. |
commit | commitdiff | tree | snapshot |
| 2021-07-13 |
Tom Clegg | Fix some entries skipped by WriteDir. |
commit | commitdiff | tree | snapshot |
| 2021-07-13 |
Tom Clegg | Compress export output. |
commit | commitdiff | tree | snapshot |
| 2021-07-13 |
Tom Clegg | Fix up VCF format. |
commit | commitdiff | tree | snapshot |
| 2021-07-12 |
Tom Clegg | Fix recomputing diffs N times. |
commit | commitdiff | tree | snapshot |
| 2021-07-12 |
Tom Clegg | Separate pvcf/vcf output. |
commit | commitdiff | tree | snapshot |
| 2021-07-09 |
Tom Clegg | Progress indicator for exportSeq. |
commit | commitdiff | tree | snapshot |
| 2021-07-09 |
Tom Clegg | Improve concurrency in export-diff. |
commit | commitdiff | tree | snapshot |
| 2021-07-09 |
Tom Clegg | Include tagset in reference-genome files. |
commit | commitdiff | tree | snapshot |
| 2021-07-08 |
Tom Clegg | Fix missing output. |
commit | commitdiff | tree | snapshot |
| 2021-07-08 |
Tom Clegg | Write ref seqs to their own files. |
commit | commitdiff | tree | snapshot |
| 2021-07-08 |
Tom Clegg | Use more cpus. |
commit | commitdiff | tree | snapshot |
| 2021-07-08 |
Tom Clegg | Fix use of nil writer. |
commit | commitdiff | tree | snapshot |
| 2021-07-08 |
Tom Clegg | Enable network access to get port forwarding. |
commit | commitdiff | tree | snapshot |
| 2021-07-08 |
Tom Clegg | Option to export one vcf/csv file per chromosome. |
commit | commitdiff | tree | snapshot |
| 2021-06-18 |
Tom Clegg | Fix race. |
commit | commitdiff | tree | snapshot |
| 2021-06-17 |
Tom Clegg | Improve concurrency more. |
commit | commitdiff | tree | snapshot |
| 2021-06-17 |
Tom Clegg | Improve loading concurrency. |
commit | commitdiff | tree | snapshot |
| 2021-06-17 |
Tom Clegg | Split sequence data into 64K independently locked parti... |
commit | commitdiff | tree | snapshot |
| 2021-06-17 |
Tom Clegg | Fix exportnumpy test. |
commit | commitdiff | tree | snapshot |
| 2021-06-17 |
Tom Clegg | Add concurrent load to exportnumpy. |
commit | commitdiff | tree | snapshot |
| 2021-06-17 |
Tom Clegg | Skip expensive Tracef. |
commit | commitdiff | tree | snapshot |
| 2021-06-17 |
Tom Clegg | Up load throttle to gomaxprocs. |
commit | commitdiff | tree | snapshot |
| 2021-06-17 |
Tom Clegg | Move alloc/copy out of lock. |
commit | commitdiff | tree | snapshot |
| 2021-06-17 |
Tom Clegg | Limit load goroutines to gomaxprocs/2. |
commit | commitdiff | tree | snapshot |
| 2021-06-17 |
Tom Clegg | Distribute genomes across output files. |
commit | commitdiff | tree | snapshot |
| 2021-06-17 |
Tom Clegg | Fix lock held during getRef. |
commit | commitdiff | tree | snapshot |
| 2021-06-15 |
Tom Clegg | Fixup multiple-file reading. |
commit | commitdiff | tree | snapshot |
| 2021-06-15 |
Tom Clegg | Fix "gob: encoder: message too big" |
commit | commitdiff | tree | snapshot |
| 2021-06-15 |
Tom Clegg | Add "flake" command (read, tidy, write). |
commit | commitdiff | tree | snapshot |
| 2021-06-14 |
Tom Clegg | Add concurrency in Tidy remap phase. |
commit | commitdiff | tree | snapshot |
| 2021-06-14 |
Tom Clegg | Adjust memory. |
commit | commitdiff | tree | snapshot |
| 2021-06-14 |
Tom Clegg | Write hgvs-based numpy matrix. |
commit | commitdiff | tree | snapshot |
| 2021-06-03 |
Tom Clegg | Fix another category of misspelled hgvs diff. |
commit | commitdiff | tree | snapshot |
| 2021-05-25 |
Tom Clegg | Bring memory back down. |
commit | commitdiff | tree | snapshot |
| 2021-05-24 |
Tom Clegg | Limit tile size in export. |
commit | commitdiff | tree | snapshot |
| 2021-05-21 |
Tom Clegg | Save runtime profile data periodically. |
commit | commitdiff | tree | snapshot |
| 2021-05-20 |
Tom Clegg | Don't try to buffer/sort export. |
commit | commitdiff | tree | snapshot |
| 2021-05-19 |
Tom Clegg | More memory, but release buffers. |
commit | commitdiff | tree | snapshot |
| 2021-05-18 |
Tom Clegg | Manage export memory. |
commit | commitdiff | tree | snapshot |
| 2021-05-18 |
Tom Clegg | Add test. |
commit | commitdiff | tree | snapshot |
| 2021-05-11 |
Tom Clegg | Avoid buffering entire output in memory. |
commit | commitdiff | tree | snapshot |
| 2021-05-07 |
Tom Clegg | Export hgvs-onehot. |
commit | commitdiff | tree | snapshot |
| 2021-04-26 |
Tom Clegg | Bump exportnumpy memory. |
commit | commitdiff | tree | snapshot |
| 2021-04-23 |
Tom Clegg | Bump merge memory. |
commit | commitdiff | tree | snapshot |
| 2021-04-23 |
Tom Clegg | Error out early. |
commit | commitdiff | tree | snapshot |
| 2021-04-12 |
Tom Clegg | Bump exportnumpy memory. |
commit | commitdiff | tree | snapshot |
| 2021-04-12 |
Tom Clegg | Bump merge memory. |
commit | commitdiff | tree | snapshot |
| 2021-04-08 |
Tom Clegg | Fix HGVS diff: GGAA>AAAA is GG>AA, not delGG,=AA,insAA. |
commit | commitdiff | tree | snapshot |
| 2021-04-01 |
Tom Clegg | Add -expand-regions flag. |
commit | commitdiff | tree | snapshot |
| 2021-03-24 |
Tom Clegg | Export selected regions. |
commit | commitdiff | tree | snapshot |
| 2021-03-15 |
Tom Clegg | Test numpy annotations. |
commit | commitdiff | tree | snapshot |
| 2021-03-11 |
Tom Clegg | Option to write numpy in chunks (same rows, fewer columns). |
commit | commitdiff | tree | snapshot |
| 2021-03-04 |
Tom Clegg | Bump export RAM. |
commit | commitdiff | tree | snapshot |
| 2021-03-01 |
Tom Clegg | Bump import RAM. |
commit | commitdiff | tree | snapshot |
| 2021-03-01 |
Tom Clegg | Ask for preemptible instances. |
commit | commitdiff | tree | snapshot |
| 2021-03-01 |
Tom Clegg | Reduce import RAM. |
commit | commitdiff | tree | snapshot |
| 2021-03-01 |
Tom Clegg | Throttle goroutines and unflushed bufs to NCPUs. |
commit | commitdiff | tree | snapshot |
| 2021-02-19 |
Tom Clegg | Upgrade to debian bullseye to get bcftools 1.11. |
commit | commitdiff | tree | snapshot |
| 2021-02-08 |
Tom Clegg | Add missing file for batchArgs. |
commit | commitdiff | tree | snapshot |
| 2021-02-08 |
Tom Clegg | Move command line tool to subdir. |
commit | commitdiff | tree | snapshot |
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