The transrate package has been modified to work with Salmon v1.10.1. 

1. The old bin directory has been replaced by a new bin with
 bam-read and snap-aligner (which appear to be stand-alone binaries)
 and symbolic links to the salmon 1.10.1 binary and its associated 
 library files.

2. lib/app/lib/transrate/salmon.rb has been modified to remove 
   deprecated command options that cause errors if used with 
   the current version of salmon. salmon_quant_alignment.help
   in that directory is the output of the salmon quant --help-alignment
   command. 
3. lib/app/deps/deps.yaml has been modified to change the salmon verion
   to 1.10.1