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:

  sequenceTubeMap/src/config.json

  Line 84 in afaf98b

  "read": ".gam"

• Change a bunch of code in the server that uses "gam" to refer to the concept of a reads file:

  sequenceTubeMap/src/server.mjs

  Lines 510 to 521 in 56d3c4b

  	let gamFiles = getGams(req.body.tracks);
  	console.log("graphFile ", graphFile);
  	console.log("gbwtFile ", gbwtFile);
  	console.log("bedFile ", bedFile);
  	console.log("gamFiles ", gamFiles);
  	req.withGam = true;
  	if (!gamFiles || !gamFiles.length) {
  	req.withGam = false;
  	console.log("no gam index provided.");
  	}

  
  

  sequenceTubeMap/src/server.mjs

  Lines 620 to 631 in 56d3c4b

  	// push all gam files
  	for (const gamFile of gamFiles) {
  	if (!gamFile.endsWith(".gam")) {
  	throw new BadRequestError("GAM file doesn't end in .gam: " + gamFile);
  	}
  	if (!isAllowedPath(gamFile)) {
  	throw new BadRequestError("GAM file path not allowed: " + gamFile);
  	}
  	// Use a GAM index
  	console.log("pushing gam file", gamFile);
  	vgChunkParams.push("-a", gamFile, "-g");
  	}

• 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:

  sequenceTubeMap/src/__mocks__/data/mountedFileNames.js

  Line 4 in 56d3c4b

  gamIndices: ["cactus-NA12879.sorted.gam"],

  
  

  sequenceTubeMap/src/api/GBZBaseAPI.mjs

  Line 440 in 56d3c4b

  gam: [],

• Adjust the importer scripts to allow GAF files in addition to GAM files.