CoverM

What's Changed

• Add CITATION.cff

• 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

• Croak when minimap2 finds unequal read pairs. (#58). Thanks Robert Hoelzle, Katherine Weigh.
• Standardise documentation to use percentage over fraction (both are still acceptable as paramaters though). Thanks Steve Robbins.
• genome: Fix noisy logging.
• genome, contig: Better error msg for bad -r (#54). Thanks @mcmahon-uw Katherine (Trina) McMahon.

• genome, contig: Add -o/--output-file option. (Thanks @michoug, #30)
• Suggest a solution for dashing install problems (Thanks @gecko1990, #45)
• Add an FAQ section to the manual, showing how to use $TMDIR to change the temporary directory used (Thanks @ShangjinTan, #41)
• genome: Fix -x so it handles a leading dot (Thanks @mcmahon-uw com, #49)
• Include examples in the full help and HTML pages (Thanks @mcmahon-uw com, #49)
• genome: Fix autoconcatenation when contig names clash.
• Add tpm calculation method (Thanks @apcamargo, #22)

• Overhaul the way --full-help is displayed by making it a man page, and publishing HTML versions. Add man as a dependency.
• dereplication: Update to galah 0.2.0 (this changes dereplication results, see https://github.com/wwood/galah), and add new ways to output dereplication results and add thresholding options
• Fix bug is genome when used with --no-zeroes that caused incorrect coverage estimates
• Include supplementary alignments by default (can be reverted with --exclude-supplementary-alignments) (#34)
• Croak when input BAM file is unsorted (#26)
• genome: Add --genome-fasta-list input option

Thanks to Rhys Newell (@rhysnewell), Jianshu Zhao (@jianshu93), Atul Bhosale (@Atul9), and Antônio Pedro Camargo (@apcamargo) for contributions to this release.

• genome mode: Incorporate on the fly dereplication via Galah - use --dereplicate.
• dereplicate: New utility mode
• contig: metabat output: Print 4 decimal places (thanks @apcamargo)
• Documentation improvements

• Fix for samtools 1.10
• More informative error messages when wrapped processes fail
• Logging updates and other minor fixes

Thanks to Rochelle Soo for reporting bugs fixed here.

• Fix integer overflow bug for mean and relative_abundance calculators (Thanks @Thexiyang)
• Fixes for minimap2 for very large databases
• shell-completion: New mode generates shell completions
• Other bugfixes and documentation updates

• Default mapper is now minimap2
• Support for Nanopore and PacBio read mapping
• New coverage method RPKM
• Genomes can now be defined with a TSV file with lines genome_name<tab>contig
• Various documentation improvements and bugfixes

Thanks to Rhys Newell and Mitchell Sullivan for helpful advice, and @ucassee and @jerceyli for useful feature requests.

• Correct bug in counting of total reads when filtering (Thanks Megan Clay)
• Add ability to shard reference sequence database (WIP, experimental, thanks Rhys Newell)
• Documentation and UI improvements (Thanks Megan Clay, Steven Robbins)

• Fix bug in dense output mode, and make it the default output mode (Thanks to Steven Robbins for bug report)
• Change help messages so default is to have short colourful output
• Speed up when mapping due by running samtools sort in a temporary directory
• filter: Introduce --inverse for decontamination uses
• covered_bases and reads_per_base are new coverage statistics (methods)
• When running in genome mode and mapping, genomes are concatenated automatically so -r isn't required
• In genome mode, when a genome has too small a coverage for --min-covered-fraction, reads mapped to that genome are not counted as mapped when calculating relative abundance (same for contig mode).
• Filtering options now have -read to reduce potential confusion
• Other small bug and documentation fixes

• Improve help messages
• Fix bug in dense output mode for genomes