Merge pull request #4 from martinghunt/master

Don't initialize sets, dicts etc in function declarations
Merge pull request #5 from martinghunt/master

Assemble speed increase by using reads more intelligently
Merge pull request #6 from martinghunt/master

Catch mpileup lines with no read bases
Merge pull request #7 from martinghunt/master

Add gage code, make gage defaults more permissive
Add default adapters file