v0.2-alpha

• Added a argument to control the amount of duplication level for the inclusion-specific kmers.
• Replaced bowtie2 with minimap2 because I would run into memory issues if many large inclusion-specific contigs were mapped simultaneously. Using minimap requires each contig to be in a seperate fasta file. Code has been modified accorfingly (dropped the dictionary). Bowtie2 was also causing issues for too long contigs, trying to use the "-c" option (passing sequences as literal strings)
• Extra methods are found in the "methods file" because I attempt to use aho-corasick algorithm to filter the inclusion-specific kmers prior assembly, but that strategy was dropped because it would take too much time to complete when there was lots of kmers.