v1.0.0-beta.2 - 2020-07-23 (public beta)

Added

• Allow use of environment variables in Snakemake workflow config
• Avoid appending to DBs by design
• Improved README:
  • Advice on how to choose parameters
  • Advice on how to run DENTIST with different read types
  • Version information to dependencies
• Log level information to log messages
• More logging on failed gap closing

Changed

• Simplified usage of --workdir: no need to manually create
  the designated directory
• Improvements to close more gaps:
  • Custom pre-consensus alignment filtering
  • Add support sequence to cropped reads to ensure daligner finds alignments
  • Allow cropping in masked region if necessary
  • Selectively ignore repeat mask to allow post consensus alignments
  • Increased sensitivity in pileup alignments by adding the bridging option
    of daligner
• Select reference read for consensus by intrinsic QVs → better
  consensus quality
• Moved flag --max-insertion-error from process to output stage so
  trying different values becomes much faster
• Automatically deduce trace point spacing in all places
• Faster check if .las files are empty → faster CLI options checking
• Naming of temporary files for easier inspection
• Use DBdust for post consensus alignment
• Produce .db for cropped pileups (temporary files) to make DAScover
  and DASqv work
• Removed -I option from daligner calls (avoid useless alignment)

Fixed

• Several bugs in Snakemake workflow
• Significantly improved number of closed gaps
• Coordinates in AGP output
• Bug in procedure that identifies a good cropping position
• Error that caused --proper-alignment-allowance to have no effect by default