Update to version 1.4.0

[EricKutschera]

• Update checks that compare alignment and isoform endpoints
  • Add --internal_boundary_limit and --allow_longer_terminal_exons
  • Check shorter ISM chains against longest novel ISM chains
  • Always check individual ISM reads for endpoint compatibility
  • Use the correct endpoint when checking NCD alignments
• Output a summary file from each step
• Add --sort_buffer_size
• Check that input alignments are sorted
• Give an error if unable to use GTF or FASTA input files
• Specify NIC or NNC in compatible isoforms output
• Add Dockerfile
• Improve thread error handling