                                    Bisar
            Pairwise four-letter realignment computation for bisulfite reads

                     http://www.seqan.de/projects/
                                Version 0.1
                                 May, 2014

---------------------------------------------------------------------------
Table of Contents
---------------------------------------------------------------------------
  1.   Overview
  3.   Usage
  4.   Output Format
  5.   Example
  6.   Contact
  7.   References

---------------------------------------------------------------------------
1. Overview
---------------------------------------------------------------------------

This program reads three-letter mappings of bisulfite reads and computes 
local pairwise four-letter realignments using an advanced statistical 
alignment model.


---------------------------------------------------------------------------
3. Usage
---------------------------------------------------------------------------

To get a short usage description of Bisar, you can execute bisar -h or 
bisar --help.

Usage: bisar [OPTION]... <MAPPED READ FILE> <GENOME FILE> <READS FILE>
       bisar [OPTION]... <MAPPED READ FILE> <GENOME FILE> <PE-READS FILE1> <PE-READS FILE2>


---------------------------------------------------------------------------
3.1. Main Options
---------------------------------------------------------------------------




---------------------------------------------------------------------------
4. Output Formats
---------------------------------------------------------------------------


---------------------------------------------------------------------------
5. Example
---------------------------------------------------------------------------



---------------------------------------------------------------------------
6. Contact
---------------------------------------------------------------------------

For questions or comments, contact:
  Sabrina Krakau <sabrina.krakau@fu-berlin.de>

---------------------------------------------------------------------------
7. References
---------------------------------------------------------------------------


