This is a HiC short-read alignment pipeline. It will perform an alignment, or read in an external alignment, perform optional duplicate-read marking, perform HiC read classification based on an in-slico restriction digest of reference sequences and finally split the output alignments based on HiC read-type. It can also optionally process and output HiC alignment statistics. Under the hood, it uses bwa mem and samtools to perform and process alignments. It also uses a custom C++ Python extension to perform the in-silico digest (using the Hyperscan (https://github.com/intel/hyperscan) regex library) and subsequent HiC classification.