Support OncoKB Authentication

OncoKB API

When you run MafAnnotator.py, FusionAnnotator.py and CnaAnnotator.py, you need a token before accessing the OncoKB data via its web API. Please visit OncoKB Data Access Page for more information about how to register an account and get an OncoKB API token.
With the token listed under OncoKB Account Settings Page, you could use it in the following format.

python ${FILE_NAME.py} -i ${INPUT_FILE} -o ${OUTPUT_FILE} -b ${ONCOKB_API_TOKEN}

v1.1.2

Fix a typo in the script generating README file

v1.1.1

Script for generating README file.

Use new annotation endpoints to annotate variants

New Annotation Service

We recently added annotation endpoints which are designed base on variant type and common use cases.
In this new version, all oncokb calls have been separated based on the variant type.

Bug Fix

Intragenic events are now annotated correctly. In the previous implementation, we annotate intragenic on fusions which should not be the case.

v1.0.7

Annotating cancer hotspots and 3d hotspots is optional now and by default turned off.

v1.0.6

Fixed #13 and supported OncoKB levels R2 and R3.

v1.0.5

Fixed #19

v1.0.4

Added mutation effect and citations columns

v1.0.3

Various fixes.

v1.0.2

• Add an option for specifying levels for plotting