Salmon 1.7.0

New features & improvements

• This release includes a refactoring and optimization of the mapping code in --sketch mode, further increasing speed; output should remain identical.

• This release adds the --splitSeqV1 and --splitSeqV2 flags, that have been the development release for a bit, as simple alternatives to custom geometry when processing SPLiT-seq data for alevin-fry or alevin processing.

Fixes

• No particular bug fixes are noted for this release.

Other changes / enhancements

• Explicitly check for valid value of k before calling out to the indexer. This leads to a more informative error message and exit if the user passes an unacceptable value of k.

Notes

• The Intel TBB library used internally by salmon (and used as well in TwoPaCo that is relied upon for compacted reference de Bruijn graph construction) has evolved into the oneAPI TBB. Recent releases of this library (2021.1 and forward) make certain backward incompatible changes and therefore cannot be used to build salmon. We anticipate working toward replacing the deprecated and removed functions with the corresponding oneAPI replacements and idioms, hopefully in the next release of salmon. Therefore, we anticipate that this will be the last — or close to the last —salmon release to use (and be compatible with) the legacy Intel TBB library. Future releases will likely require a newer version of the oneAPI TBB library instead.

Full Changelog: v1.6.0...v1.7.0