HybPiper version 2.3.1

• Re-write of the modules for commands hybpiper stats, hybpiper retrieve_sequences, and hybpiper paralog_retriever, to vastly speed up processing of compressed sample (*.tar.gz) folders.
  • Much improved speed using a single thread (the hard-coded default for HybPiper version 2.3.0)
  • Samples can now be processed in parallel when using these commands; new option --cpu added (default is to use all available CPUs minus one).
• Bugfix: ensure all intron sequences are recovered when running hybpiper retrieve_sequences using the intron option.