10 months later... doesn't look like there's much :/ I was actually Googling this question and ended up here.
I have just learned about MMSEQ (http://bgx.org.uk/software/mmseq.html#note1), but it is based on bowtie, and I am looking for possibly faster alternative (such as STAR or HiSat2) as I will have lots of data and time performance is present among my considerations.
Also, I just spotted GeneiASE myself: http://www.nature.com/articles/srep21134
I should be clear that these are just results of Google searches, I haven't used either, and therefore I cannot recommend either yet.
Best wishes, Kevin