To build this project run either ./mk.sh or ./mk_04.sh. Building
with ./mk.sh will build task1 and task2 with debugging symbols and no
optimizations. Building with ./mk_04.sh will build task1 and task2 with
no debugging symbols and with all compiler optimizations turned on.
The mk.sh build script will output a t1 and t2 file.
The mk_04.sh script will output a t1_opt and t2_opt file.
Invoke these programs as
./<program> data/alphabets/DNA_alphabet.txt data/dna-inputs/*.fasta
Note that data/dna-inputs/MERS_2012_KF600620.fasta.ignore is not picked up
by the *.fasta glob star, this file is excluded due to its containing
ambiguous reads. We felt that it was easiest to simply exclude this file from our
analysis, rather than substituting arbitrary base pairs into the sequence.