INSTALL

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

HapCUT is written in C and requires a gcc like compiler to compile the source code. HapCUT also requires the SAMtools package (http://samtools.sourceforge.net/) to read BAM files.


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

07/04/2015: The code can now be compiled by running 'make all' in the hapcut-master directory 


OLD INSTRUCTIONS TO COMPILE CODE
================================

1. Download the SAMtools package from sourceforge: http://sourceforge.net/projects/samtools/files/samtools/0.1.18/
2. Unzip files in the directory 'samtools' and run 'make' in the 'samtools' directory
3. Download the hapcut-master source code and unzip to create hapcut-master directory 
4. Copy the samtools directory to the hapcut-master directory or modify the Makefile to point to the location of the 'samtools' directory
5. run 'make hairs' in the hapcut-master directory and 'make HAPCUT' in the hapcut-master/hapcut-src' directory