For all your non-core needs

• removed stack RAM limit issue (via @kloetzl)
• ensure we don't exceeed MAX_SEQ (via @kloetzl )
• by default uppercase all letters and only compare AGTC (via @SionBayliss)
• compare all letters using -a ie. gaps and Ns
• don't auto uppercase using -k
• added TRAVIS support
• removed unused "size estimation" logic