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Recent Releases of coverm

coverm - v0.7.0

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

- Rust
Published by AroneyS about 2 years ago

coverm - v0.6.1

  • 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.

- Rust
Published by wwood about 5 years ago

coverm - v0.6.0

  • 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)

- Rust
Published by wwood about 5 years ago

coverm - v0.5.0

  • 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.

- Rust
Published by wwood over 5 years ago

coverm - v0.4.0

  • 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

- Rust
Published by wwood about 6 years ago

coverm - v0.3.2

  • 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.

- Rust
Published by wwood about 6 years ago

coverm - v0.3.1

  • 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

- Rust
Published by wwood over 6 years ago

coverm - v0.3.0

  • 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.

- Rust
Published by wwood over 6 years ago

coverm - v0.2.0-alpha7

  • 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)

- Rust
Published by wwood almost 7 years ago

coverm - v0.2.0-alpha6

  • 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

- Rust
Published by wwood almost 7 years ago

coverm - v0.2.0-alpha4

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

- Rust
Published by wwood about 7 years ago

coverm - v0.2.0-alpha3

- Rust
Published by wwood about 7 years ago