v0.0.1 (thesis version)

Added

• work-around for damapper bug
• histograms generated by check-results include a column for .999 sequence identity
• check-results optionally writes a detailed gap report

Changed

• simplified the coverage bounds interface of mask-repetitive-regions: only max-values and/or the read coverage are required
• improve consensus quality by using lasfilteralignments to remove deteriorating local alignments
• reduced value of --min-reads-per-pile-up to --min-spanning-reads (default: 3) to better work with extremely low coverage
• reduced the default minimum anchor length to 500
• fix & simplify score function for read alignments
• suppress generation of two las files for reads alignment in generate-dazzler-options
• insertion DBs do not include information about existing contigs anymore which makes validation of results easier
• renamed debug-graph → debug-scaffold for clarity
• added logging for discarded pile ups
• check-results counts complementary alignments (inversions) as errors
• remove leading/trailing gaps from all checks by check-results
• improved quality of documentation