The current version of HapTree is intended for individual connected components of the ReadGraph only. Support for disconnected ReadGraphs will be available shortly.

At this time, HapTree takes in 3 arguments, READS, VCF file, and OUTPUTNAME.
To run HapTree, in terminal type: ./HapTree READS VCF OUTPUTNAME
The order of the arguments matters; they do not have labels.

For the formats of the first two arguments, please see examples. 
The third argument is whatever you wish to name your output folder. If a folder of that name already exists, the code will not run properly; please name these folders uniquely.

As this is a very early version of the code, it is quite possible to tweak the examples slightly so that they are no longer viable. The easiest ways to do this is to disconnect the ReadGraph or to include a different number of SNPs in the VCF file than in the READS. Feel free to generate your own examples but proceed with caution. A more flexible version of the code will available by 10/26/2013.

To check the number of Vector Errors of a particular SOLUTION against a phased_VCF file, in terminal run: ./scoring SOLUTION phased_VCF

For both executables, you may need to update permissions of the file after download.

For Unix, the version information is: glibc 2.11.3
The code is written in Python 2.7.