CoverM: Read coverage calculator for metagenomics

What's Changed

• Add --checkm2-quality-file

• Use strobealign as default mapper, instead of minimap2

• Update Galah to v0.4.0

• Add minimap2-hifi (#122)

• Update to clap command line parser v4

• Support both BWA and BWA-MEM2 (#72). Thanks @jianshu93

• genome: Update --reference help (#111). Thanks @gallardoalba

• genome: Add --use-full-contig-names (#86). Thanks @shafferm

• genome_parsing: Allow compressed genomes

• contig: Always reset after each contig. Thanks @PandengWang

• contig: Fix documented default for --min-covered-fraction. Thanks Jiarui Sun

• make: Detect when output filenames clash. Thanks @akiledal

• filter: Detail --proper-pairs/--invert interactions. Thanks @Rridley7

• release: Drop symbols and use lto (#129). Thanks @jakobnissen

• mapping_index: Allow missing bwa-mem ref when index exists (#112). Thanks @fbeghini

New Contributors

• @rhysnewell made their first contribution in https://github.com/wwood/CoverM/pull/61
• @AroneyS made their first contribution in https://github.com/wwood/CoverM/pull/196

Full Changelog: https://github.com/wwood/CoverM/compare/v0.6.1...v0.7.0