=== README ===

This file was last modified by Katharina J. Hoff on October 9th 2015.

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

--- If you have Ubuntu ---

Make sure that the repository universe is in your '/etc/apt/sources.list'. It should contain a line like:

     deb http://us.archive.ubuntu.com/ubuntu vivid main universe

In case you had to add that line, run (otherwise skip):

   sudo apt-get update

Install bamtools and libbamtools-dev:

   sudo apt-get install bamtools libbamtools-dev

Afterwards, go to the auxprogs/bam2hints directory and run 

   make clean

This produces a bam2hints binary that is located in auxprogs/bam2hints.

--- If for some reason you want to install BAMTools manually ---

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 after manual BAMtools installation ---

For this step, you only need to adjust three lines in the Makefile.

Add:
   BAMTOOLS = /your/path/to/bamtools

Replace:
   INCLUDES = /usr/include/bamtools
By:
   INCLUDES = $(BAMTOOLS)/include

Replace:
   LIBS = -lbamtools -lz
By:
   LIBS = $(BAMTOOLS)/lib/libbamtools.a -lz

Save and exit the Makefile. Then, running the command:
  make clean
should result in a executable named "bam2hints" that is located in auxprogs/bam2hints.