Prior to "bam2hints" you need to have BAMTools on your system.


--- Installing BAMTools ---

Get the latest version of BAMTools directly from GitHub (https://github.com/pezmaster31/bamtools).
The download link is:
  https://github.com/pezmaster31/bamtools/zipball/master .
Unpack this , for example, into your home directory:
  unzip pezmaster31-bamtools-466bc50.zip
Then follow the instructions under https://github.com/pezmaster31/bamtools/wiki , which are basically:

# installation of "cmake"
# use a package manager, e.g.
sudo apt-get install cmake
# or see http://www.cmake.org/cmake/resources/software.html

# do installation
cd pezmaster31-bamtools-466bc50
mkdir build
cd build
cmake ..

make


--- Installing bam2hints ---

For this step, you only need to adjust one line of the makefile. Open "Makefile" with any editor and search for the line beginning with 'BAMTOOLS = '.
Insert the path to your BAMTools directory here (e.g. 'BAMTOOLS = /home/<user_name>/pezmaster31-bamtools-466bc50', if you unzipped BAMTools to your home directory).
Save and exit the makefile. Then, running the command:
  make clean
should result in a executable named "bam2hints".
