Nanoraw index

[marcus1487]

Create an index file when running genome_resquiggle that is linked to directories and loaded instead of querying all files for all subsequent commands. This should essentially be the parsed files object and should likely be stored as a hidden (or maybe not hidden) file in the most proximal sub directory to the reads. For recursive this will be two levels above the reads and for non recursive it will be one level above the reads. The file should be named: [original_directory].nanoraw.index or something like that and should be created by default with a flag to not produce the index for whatever reason. This will drastically reduce the time for subsequent commands.