In this extra credit assignment you will write a genome alignment program 
(in Perl or Python) to output high scoring segments in MAF format. 

The input sequences to test your program on are given on the course website. 

1. The first step of your program is to hash each genome with a seed or a set of seeds. 

2. Then output the hits in MAF format. 

Note that your hits will not have gaps in them. 

Evaluate the accuracy of your alignment with the maf comparator program. Use the
command:

mafComparator --maf1 <your MAF file>.maf --maf2 dogA-ratQ-truth-mafFilter.maf --out dogAratQ-UCSC.xml

python comparatorSummarizer.py --xml dogAratQ-UCSC.xml

In your submission make a text file listing your seeds and the accuracy obtained
with each of them. Also submit your accuracy of all seeds combined.

Which seeds gives the highest accuracy? What is your accuracy of all seeds combined? 
 
The due date is midnight Dec 17th 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.