The current isONclust2 code uses a fork of the spoa library at bsipos/spoa which had support for the cereal serialization library ahead of the main spoa repo at rvaser/spoa.
This is not ideal for maintainability and it is no longer necessary as rvaser/spoa now has built-in support for the cereal library. This pull request updates the spoa submodule to point to the main repository, and also makes the following changes:
The googletest submodule is removed, and now its download is handled by cmake.
Updated the cereal, bioparser, parasail submodules to the latest versions.
Updated the isONclust2 code to deal with the various API changes.
A couple of minor fixes.
The PR was compiled using GCC version 11.2.0 and cmake version 3.22.1. I have tested the compiled binary on a SIRV dataset, more thorough testing is probably warranted.
iiSeymour
commented
1 year ago
The current isONclust2 code uses a fork of the spoa library at bsipos/spoa which had support for the cereal serialization library ahead of the main spoa repo at rvaser/spoa. This is not ideal for maintainability and it is no longer necessary as rvaser/spoa now has built-in support for the cereal library. This pull request updates the spoa submodule to point to the main repository, and also makes the following changes:
The PR was compiled using GCC version 11.2.0 and cmake version 3.22.1. I have tested the compiled binary on a SIRV dataset, more thorough testing is probably warranted.