Daniel Edem Kpormegbey
Sareh Assiri
Isaac Shaffer
Tsosie E Schneider

MainLine.cpp --- Main Program takes 5 command line parameters. First 3 are required. Input <reads_file> <reference_genome> <mismatch_tolerance> <seed_size> <cluster_count> Output string to stdout in the format <read_header>$<comma seperated list mapping position to mismatch with ':'>~<comma seperated list mapping reverse complement position to mismath with ':'> prefixtrie.cpp --- PrefixTrie class
Levenshtein.cpp --- Levenshtein distance function

sample_DENV2.fasta --- 100 sequences of 100 bp in fasta format from DENV2 with 1% error and all 'A' line
sample_reads.fasta --- 100 sequences of 100 bp in fasta format from the test_reads.fasta file.
DENV2.txt --- Dengue genome
inf503-notes.pdf --- Some algorithmic background and underlying concepts.