[avocado-110] Fixing issues with logging and coverage check.
Merge pull request #110 from fnothaft/fix-logging

[avocado-110] Fixing issues with logging and coverage check.
[avocado-112] Fixing ADAM-prefixed dependencies.

Fixes #112, by updating the names of the ADAM-prefixed classes from the
adam repo that avocado depends on here.
Merge pull request #113 from tdanford/adam-prefixes

[avocado-112] Fixing ADAM-prefixed dependencies.
[avocado-98] Add somatic genotyper
Merge pull request #102 from fnothaft/somatic-caller

[avocado-98] Add somatic genotyper
Merge remote-tracking branch 'upstream/master'