Improves Species and Contamination Estimation

[emarinier]

This pull request improves species and contamination estimation by:

• Having higher requirements for estimating 'all' species. Now: 1x multiplicity, 5% shared k-mers, 0x coverage.
• Calling Mash directory instead of RefSeq Masher. This allows Mash to process multiple files simultaneously (RSM forces each file to be run separately).
• RefSeq Masher's Mash database and Mash output processing are still used to assign species names. This now involves calling the appropriate RSM functions directly.
• Contamination checking is done on up to 5 'chunks' instead of the 5 largest contigs. Each chunk should contain approximately 1/5 of the assembled contigs. This should help reduce false positives for contamination.
• Clarified some variable names in contamination_handler.py that were called "estimations" when they were actually Species.