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CHANGELOG.md

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Change Log

Version 0.1.7 (10/7/2024)

Added

  • Formally adopted the NumPy + Numba solution in the ordinal mapper. This significantly accelerated the algorithm (#209).
  • Accelerated command-line interface loading (#215).

Changed

  • Changed default output subject coverage (--outcov) coordinates into BED-like (0-based, exclusive end). The output can be directly parsed by programs like bedtools. Also added support for GFF-like and other custom formats, as controled by paramter --outcov-fmt (#204 and #205).
  • Default chunk size is now 1024 for plain and range mapeprs, and 2 ** 20 = 1048576 for ordinal mapper. The latter represents the number of valid query-subject pairs (#209).
  • Updated packaging method (#215).

Version 0.1.6 (2/22/2024)

Changed

  • Improved performance moderately (#192).
  • Parameter --chunk is now the number of unique query sequences instead of the number of lines (#192).
  • Updated GitHub Actions workflow.

Added

  • Added parameter -x|--exclude, which will exclude query sequences that are mapped to given reference sequences (such as host genome, spike-in, vector, etc.) (#192).
  • Added support for interleaved paired-end SAM files (#191).
  • Added native support for PAF file format (#182).

Fixed

  • Updated hyperlinks in documentation.

Version 0.1.5 (12/25/2022)

Changed

  • Modified the command-line interface. Sub-commands under the tools menu were raised to the main menu. For example, woltka tools collapse now becomes woltka collapse (#176). The tools menus is still kept for backward compatibility (#177).
  • Improved efficiency of handling BIOM tables (#171, #175). This significantly reduced the memory consumption and runtime of the collapse command.
  • The --trim-sub parameter now takes underscore (_) as the default separator, if not explicitly specified (#173).
  • Updated installation protocol. Now Woltka can be Conda-installed without explicit pre-installation of biom-format (#174).

Added

  • Upgraded the collapse command. Now it can collapse using internal hierarchies of feature IDs, such as genome-gene pairs, taxonomic lineages, and EC numbers. This upgrade enables stratified taxonomic/functional analysis of coord-matching ORF tables, without explicitly stratifying them during the classification step (which otherwise is time and space-consuming). The output should be identical to the that of the old method (#173).
  • Added a feature to the normalize command, which can extract gene lengths from a gene coordinates file. This enables convenient length-based normalization of an existing gene (ORF) profile. For example, it can convert raw frequencies into RPK (#179).
  • Extended description of stratification and collapsing protocols in the documentation.

Fixed

  • Fixed a bug in parsing sample ID lists (#164).

Version 0.1.4 (04/27/2022)

Changed

  • Used a single integer to store gene and read information in the ordinal mapper; use bitwise operations to parse the information. This significantly reduced memory consumption (#142).
  • Improved alignment file processing efficiency (#153).
  • Updated installation protocol. Currently a single pip install command should suffice (#145).
  • Updated GitHub Actions test from Python 3.6 to Python 3.8. The program itself should continue to support Python 3.6+ (#158).

Added

  • Added a naive algorithm for read-gene matching when the number of reads is small. This improves speed (#148).
  • Added support for stdin as input. This lets the program take a variety of previously unsupported alignment formats (#155).
  • Added or updated several pieces of documentation, such as a RefSeq tutorial (#157).
  • Experimentally added a much accelerated ordinal mapper, powered by NumPy and Numba (branch numba) (#152).

Version 0.1.3 (08/27/2021)

Changed

  • Migrated from Travis CI to GitHub Actions (#127).
  • Made --map-as-rank default when only mapping file(s) are provided (#132).
  • Renamed --normalize|-z as --frac|-f (#128).
  • Modified core algorithm which slightly improved performance (#124).

Added

  • Added tool normalize command, with multiple features (#124).
  • Added the feature to collapse a stratified table (#126).
  • Created an WoL FTP server, and added link to it (#118).
  • Added an WoL standard operating procedure (wolsop.sh) and documentation (#116).
  • Added first citation of Woltka (#111).
  • Added protocols for Bowtie2 / SHOGUN and Fastp (#121).
  • Added discussion about mapping uniqueness (#131).

Fixed

  • Fixed free-rank classification subject not found issue (#120).
  • Corrected paths to example files and directories (#117).

Version 0.1.2 (03/31/2021)

Changed

  • Updated Qiita documentation (#107).
  • Renamed "gOTU" with "OGU" (#104).

Added

  • Published at PyPI. Can be installed by pip install woltka (#108).
  • Added instructions for using MetaCyc and KEGG (#99, #101).
  • Added tool collapse command, which supports one-to-many classification (#99).

Fixed

  • Fixed Handling of zero length alignment (#105).

Version 0.1.1 (02/17/2021)

Added

  • First official release.