add zstd compression support for hal output#1913
Merged
glennhickey merged 1 commit intomasterfrom Apr 23, 2026
Merged
Conversation
glennhickey
force-pushed
the
docker-fixes
branch
2 times, most recently
from
191f9d7 to
6257b13
Compare
Update hal submodule to compression branch (PR #330) which adds LZ4 and Zstd HDF5 compression codec support. Add hdf5Codec option to cactus config XML (defaulting to deflate for compatibility) and pass it through to halAppendCactusSubtree during hal creation. Add --hdf5Codec CLI option to cactus, cactus-align and cactus-prepare to override the config. Update Dockerfile, CI and static build to link against liblz4 and libzstd. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
glennhickey
force-pushed
the
docker-fixes
branch
from
6257b13 to
0758ed6
Compare
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Add
--hdf5Codecto toggle the hdf5 compression codec (ComparativeGenomicsToolkit/hal#330) used to create the output hal.By default it will use the same old gzip, but you can now use
--hdf5Codec zstdto get a smaller and faster hal (but will only be readable by halTools compiled with the updated support.Will consider changing the default to zstd in the future...