This is an individual problem set, you can consult with friends but you should all author your code independently. The problem set has a required part and an optional extra credit part.

Part 1: (Required, 9 Points): Overlap Graphs

Solve the Overlap Graphs problem. Your solution should be in the form of a self-contained OCaml program contained in one file named overlap.ml. When compiled from the Unix shell with:

> ocamlc -o overlap overlap.ml

> ./overlap a.fas 3

Notes

1. There is no harness code for this problem set, use SublimeText to create both sample FASTA files as well as the source file overlap.ml. But feel free to use a variation of the following snippet of code for reading the input text from the FASTA file.

   
   (* readLines : string -> string list
    *
    * The call (readLines filename) returns a list of strings with
    * one list-entry for each line in filename.
   *)
   let readLines filename =
     let inch = open_in filename in
     let rec repeat lines =
       try
         repeat ((input_line inch)::lines)
       with
         End_of_file -> close_in inch;
                        lines
     in
     repeat []
   
   

2. Remember that the unix command line inputs to your program can be found in the string array Sys.argv.

3. You'll want to make use of several of the functions in OCaml's String module.

Part 2: (Optional, 3 Points): Locating Restriction Sites