Support GAF alignment files

[adamnovak]

Now that vg supports indexed GAF files, we should be able to support GAF alongside GAM as a file type for read tracks.

[adamnovak]

This might need the -F option to vg chunk when passing it a GAF.

[adamnovak]

To make this work, we need to:

• Add gaf as a recognized extension: https://github.com/vgteam/sequenceTubeMap/blob/afaf98bff4c4162d2507bb7f75287f61a2a2b505/src/config.json#L84
• Change a bunch of code in the server that uses "gam" to refer to the concept of a reads file: https://github.com/vgteam/sequenceTubeMap/blob/56d3c4b5615dcc89466a4f48e796fee552bdb1b8/src/server.mjs#L510-L521 https://github.com/vgteam/sequenceTubeMap/blob/56d3c4b5615dcc89466a4f48e796fee552bdb1b8/src/server.mjs#L620-L631
• Also in that last block, add code to use -F for GAF files. I think this might be a flag to mark the "GAM" files as actually GAF; we might really need to teach vg chunk to mix GAM and GAF files to do this properly.
• Fix some more loactions where we explicitly say we're passing around GAM files: https://github.com/vgteam/sequenceTubeMap/blob/56d3c4b5615dcc89466a4f48e796fee552bdb1b8/src/__mocks__/data/mountedFileNames.js#L4 https://github.com/vgteam/sequenceTubeMap/blob/56d3c4b5615dcc89466a4f48e796fee552bdb1b8/src/api/GBZBaseAPI.mjs#L440
• Adjust the importer scripts to allow GAF files in addition to GAM files.