Support not removing matching bases and sticking with original input

[leexgh]

Fix: https://github.com/genome-nexus/genome-nexus-annotation-pipeline/issues/232 Support removing matching bases and sticking with the original input

• [x] Add a new parameter -s to strip off matching bases, options are all, first and none
• [x] Add a new parameter -d to stick with original input (columns with prefix IGNORE_Genome_Nexus_Original_)
• [x] Add a new parameter -a to add original genomic location input columns to MAF file
• [x] Updating test files
• [x] Update documentation to add more explanations of new parameters

[leexgh]

Also I noticed the tests have been failing for a while, https://app.circleci.com/pipelines/github/genome-nexus/genome-nexus-annotation-pipeline?branch=master, some tests are failed because #genome_nexus_version: 0-unknown-version-SNAPSHOT changed to #genome_nexus_version: null. Not sure why would this happen?

[leexgh]

Merge to build an image for testing