pileup_parser 
Author: Thomas Harrison
Purpose: Takes a .csv file in pileup format from samtools and outputs a .csv file that gives the user information about individual reads. Used for small sequences and short reads.
	Information includes:
 	      * Starting points and ending points of each read
              * The Polarity of each reads
              * The Reference sequence of the read (What nucleotides that the reads should cover)
              * The The actual Sequence of the read (snips are marked with a '*' beforehand and capitalized)
              * The Quantity of the reads matching a given read.
	      * The length of each read.		
  Version 0
  Date Last Modified 6/21/2012 

to compile:
type "make" in the program's directory

*Note* Needs JDK to compile.


to run:
	
1. Save the samtools .xls spread sheet as a .csv file (delimit by spaces).  Do not modify/delete anything in the excel file or the .csv file.
 
the csv file will be your input file. 

2. type "java pileup_parser" in the directory that the parser is in.

you will get prompted for the input file. Type the class path of the .csv file you created.
ex:
/some/class/path/input.csv

it will create an output .csv file in the same directory with .out appended to the name. 
ex: if the input is: "foo.csv" the new file will be named "foo.out.csv".  

  
  
