msbwt 0.1.3

Introduction
============

TODO: INTRO

TODO: PAPER REF

For detailed usage, please type after installation:

msbwt -h

System Requirements
===================

Msbwt and its modules have been tested under Python 2.7.

Several python modules are required to run the code.

*[pysam] - Tested with pysam 0.7.4

As a wrapper of Samtools, the pysam module facilitates the manipulation of SAM/BAM files in Python. Its latest
package can be downloaded from:

http://code.google.com/p/pysam/


*[argparse] - Tested with argparse 1.2.1

The argparse module is used to parse the command line arguments of the module. It has been maintained in Python
Standard Library since Python 2.7. Its latest package can be downloaded from:

http://code.google.com/p/argparse/

Installation
============

It is recommended to use easy-install (http://packages.python.org/distribute/easy_install.html) for the
installation.

easy_install msbwt

Alternatively, users can download the tarball of source from

http://code.google.com/p/msbwt/

and then type:

easy_install msbwt-<version>.tar.gz

By default, the package will be installed under the directory of Python dist-packages, and the executable of
msbwt can be found under '/usr/local/bin/'.

If you don't have permission to install it in the system-owned directory, you can install it in locally following
the next steps:

(1) Create a local package directory for python:

mkdir -p <local_dir>

(2) Add the absolute path of <local_dir> to the environment variable PYTHONPATH:

export PYTHONPATH=$PYTHONPATH:<local_dir>

(3) Use easy_install to install the package in that directory:

easy_install -d <local_dir> msbwt-<version>.tar.gz

For example, if you want to install the package under the home directory in
a Linux system, you can type:

mkdir -p /home/$USER/.local/lib/python/dist-packages/
export PYTHONPATH=$PYTHONPATH:/home/$USER/.local/lib/python/dist-packages/
easy_install -d /home/$USER/.local/lib/python/dist-packages/ msbwt-<version>.tar.gz

After installation, msbwt will be located in '/home/$USER/.local/lib/python/dist-packages/'.


Detailed Description
===========
TODO