Prerequisite:
------------
1. Gnu Scientific Library (GSL) (version >= 1.12)
    http://www.gnu.org/software/gsl/
    Note that cblas library might be required by GSL.

2. Python (version >= 2.5)
    http://www.python.org/

3. SciPy (version >= 0.7)
    http://www.scipy.org/

4. NumPy (version >= 1.3)
    http://numpy.scipy.org/


Installation:
------------
Type "make" in the directory containing the source files.


Usage:
-----
There are two steps to BayesCall.

1) Estimate model parameters

To obtain model parameters, use the following command

  >> python EM.py <intensity_file_names>

It will create a folder named "run_yymmddHHMMSS" where yymmddHHMMSS is
the current time and stores obtained parameters in the folder.  Note
that if your run is not 76bp run, you must specify the run length by

  >> python EM.py --seq_len <run_length> <intensity_file_names>

A detailed help for available options can be obtained by

  >> python EM.py --help

2) Basecall tiles

To call bases, use the following command,

  >> python BayesCall.py -p <run_yymmddHHMMSS>/run.param -o <output_file_names> <intensity_file_name>

where <run_yymmddHHMMSS> is the run directory created by EM.py

A detailed help for available options can be obtained by
 
  >> python BayesCall.py --help


Bug Report:
----------
Wei-Chun Kao <wckao@EECS.Berkeley.EDU>
Department of EECS
UC Berkeley