Version 0.10.0-alpha.0

0.10.0-alpha.0

Changed

• Denovo discovery is now done by repeatedly polishing the loci's maximum likelihood sequences using the regions of the
  reads that mapped to the loci through Racon;
• Pandora discover CLI heavily changed: parameters -M,--mapped-reads, --clean-dbg, --discover-k, --max-ins,
  --covg-threshold, -l, -L, -d,--merge, -N, --min-dbg-dp removed;

Added

• Pandora map, compare and discover commands now produce SAM files;
• Parameter -K/--debugging-files to pandora map, compare and discover commands to create extra
  debugging files, which are able to describe completely the mapping process of pandora.