Several code cleanups and packages fixes
Merge branch 'pabarcgar-consequence-type-gbpa' into feature/0.3.x
feature/0.3.x: ConsequenceType constructor slightly modified. nc_transcript_variant modified to non_coding_transcript_variant at ConsequenceTypeMappings.java
Merge branch 'feature/0.3.x' of https://github.com/opencb/biodata into feature/0.3.x
Merge branch 'feature/0.3.x' of github.com:opencb/biodata into consequence-type-gbpa