INSTALL

REQUIREMENTS
=============

HapCUT2 is written in C and requires a gcc like compiler to compile the source code. HapCUT2 requires the htslib library (> 1.2.1) for reading BAM files. It is assumed that htslib is installed, but otherwise the path can be specified in the Makefile (HTSLIB=path). To install htslib directly from source:

git clone https://github.com/samtools/htslib.git
cd htslib
autoreconf -i
./configure
make

Note that htslib has its own dependencies  (e.g. libssl-dev) that need to be installed. Once htslib is installed, the environment variable LD_LIBRARY_PATH variable should be updated as follows: 

export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/path_to_htslib_directory"

HOW TO COMPILE THE CODE
========================

Run 'make' in the project master directory.


### There is a script "install.sh" that will compile htslib and HapCUT2 from source automatically.