salmon v0.11.1

Salmon v0.11.1 Release Notes

This version adds no features over v0.11.0, but improves some behavior and fixes a bug that was previously introduced that prevented alevin from properly handling DropSeq data.

Changes:

• This version of salmon (and likely all future versions) drops support for the FMD indexing mode. This considerably reduces the maintenance burden, and paves the way for future additions and engineering improvements. If you need to use the FMD index, please use v0.11.0. In the future, indexing and mapping against large sequence databases will be enabled using the pufferfish index, which will be integrated into salmon.

• This version removes the often-overlooked and potentially confusing behavior of applying an implicit library type to read libraries that appear before a library type flag. Salmon now requires that the library type flag appear on the command line before the library to which it applies. It will also produce more verbose and meaningful error messages if this is overlooked.

Bug fixes:

• This version resolves a couple of bugs in alevin.
  • Resolves issue #258 (thanks to @pophipi) where alevin was erroneously exiting when using dropseq mode, with an error in parsing UMI; which has been fixed.
  • dumpfeatures was previously seg-faulting if all the features were not used for intelligent whitelisting. Now, automatic detection of the number of features is done when alevin is asked to dump the features.