Update tophat to 2.0.13

Update to `2.0.13` avoids the requirement to install `samtools`[1].
The patch makes `samtools 0.1.18` compilable on Mac. 

[1] "Note: Starting with version 2.0.13 TopHat no longer requires the user to have the SAMtools library (libbam.a), headers or even the samtools program installed, as TopHat2 comes pre-packaged with a stable version of SAMtools which is known to work well with TopHat. Also, TopHat uses the SeqAn library that comes with the TopHat2 source code distribution. It is not necessary for the SeqAn library to be installed separately in order to run TopHat." http://ccb.jhu.edu/software/tophat/tutorial.shtml