* Added multithreading support when aligning reads to the paths and paths to the reference. Setting --nt 2 will add 4 additional threads, --nt 3 will add 6, and so on. The speed improvements are notable but not huge, so the default is 1. Note that the threads currently use spinlocks because context switching proved way too costly. A possible better solution might be to use mutexes or condition variables and just chain the threads together (so at the end of SemiGlobalAlignment, the threads for aligning the reads to the paths are woken). For what it's worth, profiling suggests that speeding up other function will have minimal effect, though it seems that gprof is questionable in the presence of multiple threads.
 * Added a --quiet option, to suppress printing the ROI: ... lines