Investigate MAF files from the GDC

[agduncan94]

The GDC has both open and controlled MAF files. See below for more information

• https://docs.gdc.cancer.gov/Encyclopedia/pages/Mutation_Annotation_Format/ (see references for some useful information about how MAF files are generated/what they represent)
• https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/

Colin made a MAFviewer for JBrowse, is this something we could build upon? Try out the plugin and see if it works for MAF files from the GDC. If it uses a URL, try with the open access MAF files first.

It may be that the MAF files require some processing.

[GFJHogue]

This was more tricky than expected. MAFviewer requires running commands to convert the MAF files, and the available command options don't support GDC's MAF specification: https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/

Since MAF is BED-like I can use our BaseBEDLikeFeature and possibly see if we can still use the View class provided by MAFViewer.

[GFJHogue]

Okay, now I realize that a "UCSC MAF" (the type for use with MAFViewer) is Multiple Alignment Format, and a "GDC MAF" is Multiple Annotation Format.

These are 2 different genomics file-types with the same abbreviation & file extension... 🤦‍♂️