v1.0.0-beta.1] - 2020-03-17 (public beta)

Added

• post-consensus alignment and validation with new parameter
  --max-insertion-error
• inserted sequences are highlighted by upper-case letters which can be
  turned off with --no-highlight-insertions
• batch ranges may end with a $ indicating the end of the pileup DB
• some mechanisms for early error detection
• write duplicate contig IDs to contig alignment cache for easier debugging
• added support for complementary contig alignments in check-results
• allow .db databases as reference
• improved version reporting
• updated README with additional instructions

Changed

• integrated Snakemake workflow into a single file and removed "testing"
  workflow
• cropping and splicing of insertions:
  • existing sequence is completely retained
  • moved from process-pile-ups to output
  • binary format of insertions DBs (breaking change) to gain more freedom
    in later steps
  • splice sites are chosen based on the post-consensus alignments
• ambiguities in the alignment of reads are now detected globally
• weakly anchored alignments are discarded early in the filtering pipeline
• the self- and read-alignment-based masks are now computed separately
• coverage values may now be fractional
• improved README by adhering to Standard Readme
• better (error) reporting
• temporary files have more informative names
• many minor refactorings and extensions

Removed

• combined self- and read-alignment-based masking: old behvaiour can be copied
  by using the --mask parameter and supplying both masks to all commands

Fixed

• trying all possible reference reads for consensus in order to find a
  non-failing reference
• corrected insertion splicing in case of reverse-complement alignment of the
  consensus
• bug that caused check-results to discard all alignments in certain loci
• added missing logic for cropped contigs in getGapState in check-results