| 2021-06-17 |
Tom Clegg | Improve concurrency more. |
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| 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. |
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| 2021-06-17 |
Tom Clegg | Skip expensive Tracef. |
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| 2021-06-17 |
Tom Clegg | Up load throttle to gomaxprocs. |
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| 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. |
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| 2021-06-17 |
Tom Clegg | Distribute genomes across output files. |
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| 2021-06-17 |
Tom Clegg | Fix lock held during getRef. |
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| 2021-06-15 |
Tom Clegg | Fixup multiple-file reading. |
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| 2021-06-15 |
Tom Clegg | Fix "gob: encoder: message too big" |
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| 2021-06-15 |
Tom Clegg | Add "flake" command (read, tidy, write). |
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| 2021-06-14 |
Tom Clegg | Add concurrency in Tidy remap phase. |
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| 2021-06-14 |
Tom Clegg | Adjust memory. |
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| 2021-06-14 |
Tom Clegg | Write hgvs-based numpy matrix. |
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| 2021-06-03 |
Tom Clegg | Fix another category of misspelled hgvs diff. |
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| 2021-05-25 |
Tom Clegg | Bring memory back down. |
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| 2021-05-24 |
Tom Clegg | Limit tile size in export. |
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| 2021-05-21 |
Tom Clegg | Save runtime profile data periodically. |
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| 2021-05-20 |
Tom Clegg | Don't try to buffer/sort export. |
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| 2021-05-19 |
Tom Clegg | More memory, but release buffers. |
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| 2021-05-18 |
Tom Clegg | Manage export memory. |
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| 2021-05-18 |
Tom Clegg | Add test. |
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| 2021-05-11 |
Tom Clegg | Avoid buffering entire output in memory. |
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| 2021-05-07 |
Tom Clegg | Export hgvs-onehot. |
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| 2021-04-26 |
Tom Clegg | Bump exportnumpy memory. |
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| 2021-04-23 |
Tom Clegg | Bump merge memory. |
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| 2021-04-23 |
Tom Clegg | Error out early. |
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| 2021-04-12 |
Tom Clegg | Bump exportnumpy memory. |
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| 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. |
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| 2021-04-01 |
Tom Clegg | Add -expand-regions flag. |
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| 2021-03-24 |
Tom Clegg | Export selected regions. |
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| 2021-03-15 |
Tom Clegg | Test numpy annotations. |
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| 2021-03-11 |
Tom Clegg | Option to write numpy in chunks (same rows, fewer columns). |
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| 2021-03-04 |
Tom Clegg | Bump export RAM. |
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| 2021-03-01 |
Tom Clegg | Bump import RAM. |
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| 2021-03-01 |
Tom Clegg | Ask for preemptible instances. |
commit | commitdiff | tree | snapshot |
| 2021-03-01 |
Tom Clegg | Reduce import RAM. |
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| 2021-03-01 |
Tom Clegg | Throttle goroutines and unflushed bufs to NCPUs. |
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| 2021-02-19 |
Tom Clegg | Upgrade to debian bullseye to get bcftools 1.11. |
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| 2021-02-08 |
Tom Clegg | Add missing file for batchArgs. |
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| 2021-02-08 |
Tom Clegg | Move command line tool to subdir. |
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| 2021-01-29 |
Tom Clegg | Fake a complete_genomics_pass_all preset. |
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| 2021-01-29 |
Tom Clegg | Log # low quality tile variants during import. |
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| 2021-01-29 |
Tom Clegg | Log exported numpy shape. |
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| 2021-01-18 |
Tom Clegg | Add dumpgob command. |
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| 2021-01-14 |
Tom Clegg | Fix log message. |
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| 2020-12-18 |
Tom Clegg | Share a single sitefs for multiple arvados files. |
commit | commitdiff | tree | snapshot |
| 2020-12-18 |
Tom Clegg | Bump import memory. |
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| 2020-12-17 |
Tom Clegg | Bump exportnumpy memory. |
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| 2020-12-16 |
Tom Clegg | Sort rows by label shown in csv, not full file path. |
commit | commitdiff | tree | snapshot |
| 2020-12-15 |
Tom Clegg | Bump merge memory. |
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| 2020-12-15 |
Tom Clegg | Load library with pgzip. |
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| 2020-12-14 |
Tom Clegg | Faster merge output. |
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| 2020-12-08 |
Tom Clegg | Bigger output buffer for annotate. |
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| 2020-12-08 |
Tom Clegg | Save git version in lightning binary collection name... |
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| 2020-12-04 |
Tom Clegg | Include numpy matrix filename in labels csv. |
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| 2020-12-04 |
Tom Clegg | More memory + direct Keep access for merge and exportnumpy. |
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| 2020-12-02 |
Tom Clegg | Update example. |
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| 2020-12-02 |
Tom Clegg | Don't pass -gvcf-type="" to gvcf_regions.py. |
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| 2020-12-02 |
Tom Clegg | Fix deadlock on error. |
commit | commitdiff | tree | snapshot |
| 2020-12-02 |
Tom Clegg | Improve import and vcf2fasta performance. |
commit | commitdiff | tree | snapshot |
| 2020-11-29 |
Tom Clegg | Increase concurrency, reduce allocs. |
commit | commitdiff | tree | snapshot |
| 2020-11-29 |
Tom Clegg | Reduce lock contention. |
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| 2020-11-25 |
Tom Clegg | Use smaller machines for small batches. |
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| 2020-11-25 |
Tom Clegg | Use buffered writer to avoid overwhelming arv-mount. |
commit | commitdiff | tree | snapshot |
| 2020-11-25 |
Tom Clegg | Share CR refresh throttle when running multiple containers. |
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| 2020-11-25 |
Tom Clegg | Export labels.csv with numpy array. |
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| 2020-11-24 |
Tom Clegg | Concurrent-batches mode for vcf2fasta and import. |
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| 2020-11-23 |
Tom Clegg | More memory for pca. |
commit | commitdiff | tree | snapshot |
| 2020-11-23 |
Tom Clegg | Propagate -match-chromosome arg to container. |
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| 2020-11-22 |
Tom Clegg | Pass gvcf-type to gvcf_regions. |
commit | commitdiff | tree | snapshot |
| 2020-11-22 |
Tom Clegg | Fix fasta sequence names. |
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| 2020-11-22 |
Tom Clegg | Accept filter args in pca-go. |
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| 2020-11-22 |
Tom Clegg | Let caller set container output name. |
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| 2020-11-19 |
Tom Clegg | Fix divide by zero. |
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| 2020-11-19 |
Tom Clegg | Configurable chromosome name pattern. |
commit | commitdiff | tree | snapshot |
| 2020-11-19 |
Tom Clegg | Fix wrong container name. |
commit | commitdiff | tree | snapshot |
| 2020-11-19 |
Tom Clegg | Indicate low quality tile variants with -1 in numpy... |
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| 2020-11-13 |
Tom Clegg | Gzip gob files. |
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| 2020-11-13 |
Tom Clegg | Update example. |
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| 2020-11-12 |
Tom Clegg | When not saving incomplete tilevars, still save hashes... |
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| 2020-11-05 |
Tom Clegg | Add numpy-common-variants sanity check. |
commit | commitdiff | tree | snapshot |
| 2020-11-05 |
Tom Clegg | Renumber/prune variants for numpy export. |
commit | commitdiff | tree | snapshot |
| 2020-11-02 |
Tom Clegg | Omit refname field in annotation if only one ref exists. |
commit | commitdiff | tree | snapshot |
| 2020-11-02 |
Tom Clegg | Adjust speed knobs. |
commit | commitdiff | tree | snapshot |
| 2020-11-02 |
Tom Clegg | Don't drop ref tile data when filtering. |
commit | commitdiff | tree | snapshot |
| 2020-11-02 |
Tom Clegg | Propagate filters to container. |
commit | commitdiff | tree | snapshot |
| 2020-11-02 |
Tom Clegg | Faster annotate. |
commit | commitdiff | tree | snapshot |
| 2020-11-01 |
Tom Clegg | Write annotations along with numpy. |
commit | commitdiff | tree | snapshot |
| 2020-10-31 |
Tom Clegg | Use tilelib to load for export and pca. |
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| 2020-10-29 |
Tom Clegg | Log locations of long tiles. |
commit | commitdiff | tree | snapshot |
| 2020-10-29 |
Tom Clegg | max-tile-size option. |
commit | commitdiff | tree | snapshot |
| 2020-10-29 |
Tom Clegg | Less memory and cpu for annotate. |
commit | commitdiff | tree | snapshot |
| 2020-10-29 |
Tom Clegg | Fix example. |
commit | commitdiff | tree | snapshot |
| 2020-10-29 |
Tom Clegg | Faster annotate. |
commit | commitdiff | tree | snapshot |
| 2020-10-29 |
Tom Clegg | Update example. |
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