Support for indexed GAF files

[jmonlong]

The latest versions of vg support GAF indexing, so I added this support here too. I had an old branch with support that I updated. It seems to work

GAF support

• Use the appropriate command-line argument for vg chunk.
• Process the extracted GAF file by converting to GAM before piping to vg view to get the JSON representation.
• Added a test GAF file by converting, sorting and indexing exampleData/cactus-NA12879.gam (removing unmapped reads that tabix doesn't like...).

Limitations

• Can't mix GAMs and GAFs because vg chunk can't handle it. Multiple GAMs or multiple GAFs work fine.

Docker container update

• Bumped the version of vg to 1.59.0.
• Updated the custom config.json for the container
  • Removed the examples bound to dataPath because the container is build so that dataPath points to /data