* Changed default k-mer size to 25. This slows things down but works better in practice (finding an optimal value is on the "to do list").
 * You can now specify different k-mer sizes for the TargetCreator and the realigner
 * If a realignment has a larger edit distance across the entire alignment length than that of the original then it's rejected. This prevents sub-optimal realignments due to using a k-mer size that's not long enough (e.g., when an ROI is surrounded by repeat sequence).
 * Added a clean-all option, which is needed to clean htslib (this is for my convenience while developing the package, since compiling htslib takes a little time).
 * Tweaked the global alignment algorithm to start at the most likely position. This results in a significant speed increase (single-threaded, the realigner is now faster than BisSNP).
 * The BFS algorithm now only returns paths with a given minimum depth. The maximum and minimum values are determined by the maximum and minimum insert/deletion sizes of the alignments covering a given ROI. This bounds the size of paths and allows cycles to be followed, since we'll never loop infinitely.
 * Cycles in paths are now allowed by default. This can be changed during running with the --noCycles option.