Better handling of assembled contigs as input

[nspies]

• [x] need to be able to specify the alignment distance
• [ ] check whether the alignments actually make sense - probably comparison between bwa and ssw would be informative
• [ ] deal with multiple aligning segments better? this may not be trivial though
• #24

[nspies]

@jzook when you're back on the job, can you email me some contigs and commands you've tried to use here? ideally so it runs on our cluster here so I don't have to move data around