Even though the changes and fixes are minor, it is recommended you update to Salmon 0.8.1 if you are using a previous version.

Bug Fixes

This release includes a fix for a bug that would cause Salmon (in alignment-based mode only) to write the inferential sampling (i.e., Gibbs sampling or bootstrap) files to the current working directory, rather than the quantification directory. This release resolves that bug, and now the inferential samples are properly written to the target quantification directory in both modes.

Changes & improvements

The indexer now computes a signature (SHA256 sum) of both the sequence and headers in the fasta file used to build the index. These signatures are propagated into the quantification estimates in the meta_info.json file. This will allow one to verify the exact index used for quantification, and will be utilized in software we are working on for metadata propagation across RNA-seq pipelines. However, this means that indices built for previous version of Salmon will need to be re-built for v0.8.1.
JEMalloc is now built with the --disable-debug. This avoids spurious zone allocator warnings on MacOS Sierra.
Bumped version of JEMalloc to 4.5.0.
Bumped to the latest version of spdlog.
Bumped included version of libcuckoo.
Bumped included version of sparsepp (via RapMap).
Bumped included version of RapMap.
Internal refactoring and improvement of option parsing and argument handling code. This is the first phase of a larger-scale unification of the quasi-mapping-based and alignment-based modes that will be made over the next few releases.