Use basenames for input file identifiers in output

[ondovb]

Mash output (and sketches) currently represent the input file names as given, with paths:

/path/to/input.fasta

It would probably be better to strip them to basenames:

input.fasta

We would just have to watch out for potential collisions and figure out what to do about those. Some options for resolving:

• error out
• rename
• leave paths
  • strip off longest common path

[tseemann]

@ondovb A common layout that is used is /some/path/SEQNAME/contigs.fa for example, where the file name itself is always the same, but it's folder is the unqiue identifier.

So maybe you could also add this too the suggestions:

• strip off common suffix