New usage release

From this version, user can use this tool in a new way. Before this version, user must modify configure file under source code directory in order to create custom pipeline.

Now, the pipeline has been split into two parts:

• preparation: provide input PATH and specify output PATH, generate configure file
• run pipeline: run pipeline, the script will use configuration in file under current directory (generated by preparation part)

Maf to neoantigen can be used now

This release target on predict neoantigen from maf file, then calculate neoantigen quality.