v1.0.4

• --clean totally removed in preparation for when we bring in quake or another cleaning tool
• --fast: downsamples, samples variant sites, does not find phages, does not use a sample assembly when testing, snap
• Fixed launch_snap a bit more, for stability and for unambiguous matches
• Better documentation including tips and tricks, FAQ, and a different installation document
• --singleend for when you have mixed datasets of PE and SE reads