This is mainly a bug-fix and maintenance release.

Bug Fix

In rare circumstances, when an equal quality mapping existed between the forward and reverse-complement strand, the algorithm would exhibit a preference for the forward mapping. This bug was due to a shadowed variable and has been resolved.

Features

The -c flag enforces co-linearity within chains of hits (i.e. the hits must be monotonically increasing / decreasing with respect to both the reference and query). We're adding the appropriate framework for enforcing different types of filters, so more should be forthcoming in future releases.
Though it has been implemented for a while, here we're documenting the existence of the perfect-hash-based quasi indexing. This replaces the dense hash map with a perfect hash (using the fantastic EMPHF library). This is enabled when building the quasi-index by passing the -p or --perfectHash flag. The tradeoff is that index construction will be slower, but the resulting index will require considerably less space (40 - 50% less) during mapping. Mapping speed is roughly equivalent regardless of whether a "normal" or perfect hash is used.