usage
-----
./readingExtension chromosomes.fasta  inputSamFile.sam  seqTotalLength  <delete records with flag!=[0|16](Y/N)>  outputSamFile.sam

Description
-----------

"readingExtension" extends the reading length of inputSamFile.sam using the information from chromosomes.fasta. The final length of each record is seqTotalLength.

Output files
------------
outputSamFile.sam      : File like inputSamFile.sam with their reading extended

Execution Steps
---------------
1) Save the files in a directory
2) type: make
3) Edit executeIt file and verify:
   a) the fasta file is at ../../data/tomatoGenome/S_lycopersicum_chromosomes.2.40.fa  directory. Otherwise edit the executeIt script file.
   b) the sam   file is at ../../data/tomatoGenome/A8.sam                              directory. Otherwise edit the executeIt script file.
4) type: source executeIt

The output will be placed at result directory. 


Included files
--------------
readingExtension.cpp : main code
Tools.cpp            : common routines
Tools.h              : common routines
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
executeIt            : A script to execute the application to generate the paper input data
readme.txt           : This file

