New features

Salmon learned the ability to optionally write quality values in output SAM files. If the --writeQualities flag is passed to salmon when mappings are also being written (i.e. with --writeMappings=), then the SAM records for reads will contain the corresponding quality values. Note: You should not pass this flag to salmon if you are providing FASTA rather than FASTQ files as input; those files have no quality values, and so this flag is not compatible with FASTA input. Note: The default behavior remains to not write quality values, as they are not necessary for many downstream applications and they consume considerable extra space in the output. This addresses the feature request in #756; thanks to @A-N-Other for the suggestion.

Fixes

Addressing #748, raised by @taylorreiter - In single-end mode, all unmapped reads were being reported with the code u, including those mapped to decoys. This release fixes the output so the proper code d, is reported for those fragments best mapping to decoys.

When salmon alevin was being run upstream of alevin-fry for generating a RAD file, it was possible for the file to be truncated if there was insufficient disk space for the output. This release of salmon adds a final check of the ofstream after the call to close to determine if the stream is in a bad state. This should lead to better error reporting and proper exit codes if the RAD output of salmon alevin is unexpectedly truncated. Thanks to @allyhawkins for helping to uncover this issue.
The use of multi-stage builds has greatly reduced the size of the Docker image to ~101MB (from ~1.38G); thanks to @kaczmarj for contributing this improvement.
Improvements to the documentation have been made and some typos fidex thanks to @molecules.

Full Changelog: v1.8.0...v1.9.0