Update BCFtools to use stable sort #1813
Open
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Outdated suggestions cannot be applied.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.
Was looking around at some
bcftools sortcode because of the CI fail in #1809, and noticed that in bcftools v1.21 the sort function was made stable (although it doesn't appear in the release notes, see samtools/bcftools#2252). I tested this builds in docker and am currently running it on a previous graph to see if it works, as making sure thecactus_callis right is a bit finickity.As a separate note, the samtools/htslib in downloadMafTools didn't appear to do anything (although it exports HTSLIB variable), so I removed that and nothing broke (hopefully docker didn't cache anything that would stop this breaking). This seems to save a reasonable amount of build time as htslib is big.