Nigel

This release provides a number of bug fixes and a number of new features.

New features:

• Core methods for constrained basecalling (given constraints on the sequence space; fixed-length and ambiguity codes within sequence)
• Reference-anchored index decoding and basecall-anchored full-path decoding for modified base calling
  • Added methods do not significantly effect results. Defaults (unchanged) remain the recommendation
• Partial support for CRF models (cannot run modified base or variant calling outputs)

Bug fixes and optimizations:

• Faster runtimes when not outputting flip-flop modified bases or sequence variant outputs (avoid guppy --post_out option)
• Better handling for failed reads from Guppy 5.0+
• Fix bug skipping modified base calls near the ends of reads
• Updates to docs
• Minor bug fixes