General Usage

Dependencies

The software package has two main dependencies:

 Bowtie2 (Optional, to install separately)
Bowtie 2 is an ultrafast and memory-ecient tool for aligning sequencing reads to long reference sequences. For more and installation instruction go to http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

 Newmat11 (Required, shipped with the package)
Newmat is a C++ library for manipulating a variety of types of matrices using standard matrix operations.
See http://www.robertnz.net/nm intro.htm for more details.

Installation guide

• Follow the following steps to install and run the package:
   - Download the source code at http://sourceforge.net/projects/virhap/files/virhap.tar.gz
   - Unzip the folder
   - Go to the folder and type ”make” to build the newmat libraries and the C++ programs.

Running the program

• The whole process can be run one step after the other (see section 3 ) or one can invoke either the pipeline ’pipeHap’ either the shell script ’virhap.sh’ to run all the commands in one go.

• Type command name -h to see the usage and the help about any of the commands.

• See manual.pdf for the whole manual. A full online documentation is available at: https://sourceforge.net/p/virhap/wiki/Home/