I have a problem building tophat 2.1.0 on Debian jessie. Running configure does not seem to produce errors (see below) but running make causes fails with

```
#some output omitted here

Makefile:1347: recipe for target 'reads.o' failed
make[2]: *** [reads.o] Error 1
make[2]: Leaving directory '/home/pommy/inst/tophat-2.1.0/src'
Makefile:313: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/pommy/inst/tophat-2.1.0'
Makefile:253: recipe for target 'all' failed
make: *** [all] Error 2
```

Here are the configuration results

- tophat 2.1.0 Configuration Results

```
  C++ compiler:        g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3  -DNDEBUG -I./samtools-0.1.18 -pthread -I/home/pommy/include -I./SeqAn-1.3
  Linker flags:        -L./samtools-0.1.18 -L/home/pommy/lib
  BOOST libraries:     -lboost_thread -lboost_system
  GCC version:         gcc (Debian 4.9.2-10) 4.9.2
  Host System type:    x86_64-unknown-linux-gnu
  Install prefix:      /home/pommy
  Install eprefix:     ${prefix}
```
Solution found here: https://github.com/infphilo/tophat/pull/13

I managed compiling a fork that uses a newer SeqAn version:

```
git clone https://github.com/wookietreiber/tophat.git
cd tophat
git checkout update-seqan
./bootstrap
./configure <insert your options here>
make
make install
```

(See also https://groups.google.com/forum/#!topic/tuxedo-tools-users/M7Z9zLuu8o4)