broadinstitute/oncotator — pull request #194 by LeeTL1220 (2014-07-01 02:26:27+00:00)
Title: Issue 134 protein rendering fail on non primitive variants

Hotfix to address Oncotator failure when the variant type is incorrect for some non-standard variants generated by GATK. This change will emit a lot of error messages and proceed. The protein change annotation may be incorrect. Previous functionality was to halt.

Additionally, TcgaMAFOutputRenderer was altered to throw exception during a failure to ensure a non-zero return code.