This is a program to perform haplotype assembly, with some help from humans.

To use the program, do the following:

1. Run $ python3 team_3_scoreAlignments.py from the command line. This will output two files in your working directory called fragments.txt and overlap.txt, which will be used implicitly in the following step.
2. Run $ python2 team_3_tsp.py from the command line. Note that this requires Python 2 due to the fact that the library which runs the max. TSP algorithm has not been updated for Python 3. This program will write a file called alignmentOrder.txt to your working directory, to be used in the following step.
3. Run $ python3 team_3_prettyPrintTSPAlignments.py from the command line. This will output the best alignment (as determined in the previous step) to the screen, as well as to a file called alignments.csv which you can open in Excel.