Lite v0.1, release candidate 5

Fixes #41

Lite v0.1, release candidate 4

• enable user to specify custom JSON file
• consensus sequence has lower case nucleotides if minimum coverage threshold not met
• fixes StringIO issue with Python 2->3 migration
• fixes maxint to maxsize issue with Python2->3 migration

Lite v0.1, release candidate 3

Fixes #38

Lite v0.1, release candidate 2

• added Stanford HIVdb resistance scoring script (micall/utils/scoreHIVdb.py)
• user can specify custom bowtie2 binaries
• added coverage.R utility script
• added error-metrics.R utility script
• added example files

Release candidate of Lite

See #24