In this assignment you will align reads to a reference genome and calculate the 
number of correctly aligned ones.

1. Align the reads given on the course website to the reference chromosome 22 of 
the human genome using the program called BWA. BWA is available on osl machines
after typing "module load bwa". The executable is bwa. 

2. Write a Perl script to obtain the position of each read given by BWA,
the true position of each read, and the number of correctly aligned ones. A 
correctly aligned read is one where the position given by BWA is within
100 base pairs of the true position.

3. BWA outputs aligned reads in SAM format whose specification can be obtained 
from http://samtools.sourceforge.net/SAM1.pdf

Calculate the number of correctly aligned reads for each of the six datasets with a 
Perl script.

Submit the percentage of correctly aligned reads, incorrectly aligned ones, and unmapped ones 
in one file, your output SAM files for each divergence, and your Perl script for calculating 
the accuracy.

The due date is midnight Nov 27th 2018.

Submit your assignment by copying it into the directory
/afs/cad/courses/bnfo/f18/bnfo/601/101/<ucid>.
For example if your ucid is abc12 then copy your Perl script into
/afs/cad/courses/bnfo/f18/bnfo/601/101/abc12.