Releases: ComparativeGenomicsToolkit/hal
Releases · ComparativeGenomicsToolkit/hal
Release V2.3
What's Changed
- patch halReplaceGenomes so dimensions always set before segments by @glennhickey in #236
- Fix PAF so snps and gaps included in cols 10 and 11, resp. by @glennhickey in #237
- fix typo that was hidden by NDEBUG by @glennhickey in #238
- patch halAddToBranch so dimensions always set before segments by @glennhickey in #239
- fix UDC build by @glennhickey in #243
- use --bedType instead of --outBedVersion by @glennhickey in #248
- remove --tab option from halLiftover by @glennhickey in #249
- Add jobstore arg to hal2assemblyHub doc+examples by @glennhickey in #251
- Allow halAppendSubtree to be run with --inMemory by @glennhickey in #252
- More memory fixes for halAppendSubtree by @glennhickey in #253
- Close neighbors in halExtract to better work with --inMemory by @glennhickey in #254
- add halRemoveSubtree by @glennhickey in #255
- Adjust default HDF5 caching behaviour by @glennhickey in #256
- Avoid reading all genome's sequences when possible by @glennhickey in #257
- add halCloseGenome to C interface by @glennhickey in #258
- patch halAppendSubtree so dimensions always set before segments by @thiagogenez in #260
- Don't skip already-seen reference positions in hal2maf unless (--unique used). by @glennhickey in #261
- fix off-by-1 bug when resizing name array by @glennhickey in #267
- Fix bug where hdf5 genome internal caches get out of sync and crash by @glennhickey in #275
- Cleaner Snakes by @glennhickey in #279
New Contributors
- @thiagogenez made their first contribution in #260
Full Changelog: release-V2.2...release-V2.3
Release V2.2
- misc bug fixes
Release V2..1
- Added reserved fields to some mmap structures to make it easier to expand in the future
- update README to remove stale information
Release V2.0
Numerous changes including:
- Addition of mmap format as an alternative to HDF5. The mmap format improves performance at the cost of size in many cases.
- Various optimizations and code simplification.
- Optimization of UCSC browser UDC interface.