This file and the script were written by Mahmoud Dondet. The script will extract the coordinates of mapped reads from the SAM file. It will produce two files, one file for the coordinates of the mapped reads as a tab-limited three-column file, chromosome, start, and end, and the other file will have more information about both the mapped reads and the reference, it is a tab-limited eight-column file with a header. Usage: python get_coordinates.py SAM_file