[Debian-med-packaging] tophat updated version

[Alex Mestiashvili]

Hi Debian Med Folks,

Could you please check && sponsor the new version of tophat ?
http://anonscm.debian.org/git/debian-med/tophat.git

New tophat depends on bowtie2 and suggests bowtie.

One question: pristine-tar branch still contains tophat source with 
SeqAn distribution, but I removed license statements for SeqAn from 
debian/copyright because we use one distributed in Debian.
Is it acceptable?
For the future I've prepared debian/get-orig-source which suppose to 
strip off seqan from the tarball.

Thank you,
Alex