v4.0.0

[4.0.0] - 2022-09-02

Added

• include GIT commit in logs
• script to generate report on closed and unclosed gaps
• script mask2bed that converts Dazzler masks to BED files
• JSON schema for config file
• debugging output to track down issue #31

Changed

• preserve original scaffold headers in output FASTA
• ensure unique scaffold IDs in output
• output FASTA names/coords in AGP
• parallelized alignment filters
• fail early measure against bug in libmaus2

Fixed

• added missing Python installation to Singularity image
• treat long FASTA lines graciously
• fixed rule validate_dentist_config
• fixed install instructions Snakemake profile
• fixed bug with newer versions of Snakemake
• include Python files in GIT repo
• close open LAS file asap
• fixed JSON conversion of AlignmentChain
• workaround for Phobos v2.099.0 bug
• fixed compiler error
• treat compiler warning