Scoring & VDJtools compatibility

Major improvements:

• VDJtools compatibility. Now output of VDJdb annotation can be used for downstream analysis with VDJtools and vice-versa. See README for additional info.
• New scoring scheme: search is performed by first looking up candidate CDR3 sequences with a high number (up to 7) mismatches allowed. The resulting alignments are scored based on substitution matrix and gap scores optimized for precision and recall by running NSGAII for VDJdb alignments (see README). While that slows down VDJdb, we take advantage of suffix tree search that automatically generates alignments and the effect is not that dramatic.

Minor improvements:

• Support all software input formats that are supported by VDJtools
• Some refactoring that should speed-up scored search
• Completely re-wrtitten summary report generation
  • More intuitive summary table
  • Compatibility for sunburst charts in VDJdb-server

Bug fixes:

• Disabled annotation for non-coding clonotypes

Note:

• Search and VDJdb confidence threshold parameters are optimized for latest VDJdb assembly