usage
-----
 ./consensusCounter chromosomes.fasta peaks.txt consensusSequence

Description
-----------
The application process each peak sequence seq(p) from peaks.txt (sequence from peak start to peak end) counting the times consensusSequences appear in that sequence.

Execution Steps
---------------
1) Save the files in a directory
2) type: make
3) Edit executeIt file and verify the fasta file is at ../../../data/tomatoGenome/S_lycopersicum_chromosomes.2.40.fa directory. Otherwise edit the executeIt script file.
4) type: source executeIt

The output will be placed at result directory. 


Included files
--------------
consensusCounter.cpp : main code
FastaElement.h       : code to work with fasta file
FastaElement.cpp     : code to work with fasta file
Makefile             : file to automatize the compilation of the application
peaks.txt            : data file with peaks data
executeIt            : A script to execute the application to generate the paper input data
readme.txt           : This file
results.xls          : A summary of results from executeIt execution.

