Fixes

This releases addresses a bug in deserializing the compact_vector (discovered by @jamshed) that could lead to undefined behavior. In fact, this bug was underlying a relatively rare but longstanding issue with the previous biconda build of salmon where a segmentation fault could occur during indexing.
This release addresses #806, where several output counters used 32-bit values and could produce incorrect values if they exceeded the maximum representable 32-bit integer. These counters have been changed to be 64-bits wide. It is worth noting that this was an issue with the reported values with the output report, but not with the internal representations (i.e. the actual quantifications were not affected).
This release incorporates PR #817 by @Gaura that addresses an issue in the processing of some sci-sea 3 data where having a read1 length of 33 or 34 would result in error while being valid lengths. This resulted in salmon refusing to process this data; this has now been fixed (addresses #813).

Improvements

Substantial refactoring has been made to parts of the mapping code to clean up redundant code and to make future additions easier.
Substantial improvements have been made to the CMake files to reduce the need for redundant copies of files and to propagate target properties more faithfully.
Several dependencies have been updated, including libstadenio and itlib.

Full Changelog: v1.9.0...v1.10.0