Release Salmon 1.6.0 · COMBINE-lab/salmon

New features

This release introduces specific flags for two new single-cell protocols (which can be processed using either alevin or that can be used to produce a RAD file for alevin-fry). Specifically, these new protocols are special because they mark the initial support within this framework for variable-length barcodes. In the next release, we hope to have an update to our generic barcode, umi, read geometry specification mini-language to expose this feature more generally there, but for the time being, these are implemented as new single-cell protocol flags. The new protocols supported are sci-RNA-seq3 and inDrop v2. These are exposed, respectively with the --sciseq3 and --indropV2 flags. In addition to the custom geometry specification, the list of geometries / protocols with pre-specified flags has now been added to the documentation.

This release fixes #691, where an extra : was present in the cmd_info.json file in rad and sketch mode where the salmon_version was recored. Thanks to @allyhawkins for reporting this issue.
This releases fixes a rare corner case in cell barcode rescue (recovering cell barcodes with an N) where, if a barcode could not be properly extracted, a rescue attempt would be made for the previous barcode, which could result in the wrong barcode / umi pairing for that read. Thanks to @Gaura for finding this bug and the PR to fix it.

Full Changelog: v1.5.2...v1.6.0