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Changelog

2.0.1 (2025-04-01)

Bug Fixes

  • ci: use hatch in pypi publishing workflow instead of setup.py (e838f0f)

Miscellaneous Chores

2.0.0 (2025-03-31)

⚠ BREAKING CHANGES

  • change fasta2bed method from fuzzyregex to semi-global alignment based search with parasail

Features

  • .github.workflows.tests - created automatic testing workflow (41e6222)
  • add quiet mode, only prints WARNING and ERROR log messages (16967e7)
  • add support for gzipped fastq output (5b16301)
  • add the --verbose flag and debugging log messages (5b16301)
  • add the 'virtual primer support' to link closely positioned primers to each other in the index for accurate removal (3620f2f)
  • change fasta2bed method from fuzzyregex to semi-global alignment based search with parasail (36c4479)
  • sonar-project.properties - added branch analysis config (41e6222)
  • test-requirements- added seperate test reqs (41e6222)

Bug Fixes

  • .gitignore - added *:Zone.Identifier (2f24ebe)
  • add an explicit import for IUPACData from Bio.Data (instead of the implicit import that didn't always work depending on the interpreter) (5abae9a)
  • Add extra checks to cleanly exit when dealing with corrupted or incomplete inputfiles (2155999)
  • add UTF-8 encoding when opening export primers file when -to is given (c0bfe5f)
  • change the table of IUPAC data to actually reference the IUPACData table in fasta2bed (daed988)
  • disable the progress bar when in debug mode (verbose) (5b16301)
  • do not update per-thread progression when processing very low read counts (will throw zerodivisionerror) (d3bb8b5)
  • fixed a typo in fasta2bed (7968429)
  • improve error message when too little threads are given (57e74b5)
  • improved static type checking, linting, and formatting for all files (2f24ebe)
  • proper grouping of the regex to clean cigar strings (abe1f69)
  • tests: add conditional to handle boolean arguments in test (fc786fe)
  • tests: too short e2e test is expected behaviour. Updated test configuration to include comparison file and correct failure status (c7ab8a7)
  • tests: use relative path for unittest reference file path (03a2ddf)
  • tests: use the correct referenceID in the synthetic bedfile (a5c4d8c)
  • typo in github workflow (fed3c2e)

Performance Improvements

  • perform most alignment-preset related calculations in parallel (multiprocessing with concurrent.futures) (edf23ac)
  • use pgzip for multithreaded writing of gzip file (5b16301)

Dependencies

  • add flake8-pyproject (06cb0cb)
  • add pgzip to the dependency list (cfd25e3)
  • remove intel channel from conda recipe file (ed916b8)
  • update dependencies in env.yml (ed916b8)
  • update dependencies in setup.py (ed916b8)
  • update dependencies in setup.py and env.yml (e09cb10)
  • update minimum required python version in setup.py (0fe1beb)

Documentation

  • add docstring for percentage_representation function in fasta2bed (a625b8b)
  • add virtual primer mode section and related image to user guide (5da3690)
  • expand function docstring to better explain the edge cases (910f75a)
  • improves the docstring for this find_or_read_primers() method (e670d2b)
  • update citation information in CITATION.cff and README.md (7e8e0c6)

1.3.1 (2024-04-03)

Bug Fixes

  • don't replace NA name values when reading BED file (6d0c192)

1.3.0 (2023-08-08)

Features

  • allow multi-fasta reference input (cd4f413)
  • primer removal process now works with reference-specific primer coordinates (7a1a899)

Bug Fixes

  • add a default value of 0 to min() to avoid a ValueError when an empty list is provided (c23301f)

1.2.1 (2023-02-28)

Bug Fixes

  • Fix extension checking for cli arguments (015e10d)
  • fix pandas version string in setup.py install_requires (d0a40f0)
  • split file extension checking for input and output files (c5cc43a)
  • update permissions for GH-actions workflows (59fead2)
  • use log.warning() instead of the deprecated log.warn() (87685f6)

Documentation

  • add citation file (59fead2)
  • update conda installation badge (d88f4f4)

1.2.0 (2022-12-20)

Features

  • add support for fragmented amplicon reads with the --amplicon-type fragmented mode (9d5559b)

Bug Fixes

  • only check the last file extension to see for a fastq or bam file (fixes check for file with multiple dots in the filename) (386fb1f)
  • print the correct coordinates when a primer is found multiple times on the reverse strand (420438c)

Documentation

  • update docstrings (c8af27a)
  • update readme (0287408)
  • update user documentation to include the new "fragmented" amplicon-type (159366e)

1.1.0 (2022-08-11)

Features

  • output some basic stats in the log (c5ad032)
  • use rich as a logging handler to improve logging with timestamps and various information levels. (c5ad032)

Dependencies

  • add rich as a dependency (c5ad032)
  • change parmap version to lenient version 1.5.x (0c4d2a5)
  • remove tqdm as a dependency (c5ad032)
  • update mappy to latest version 2.24 (efed0a1)
  • update pandas to >=1.3 (efed0a1)
  • update parmap to latest version 1.5.3 (efed0a1)
  • update pysam to lenient version 0.19.* (efed0a1)
  • updated environment recipe and setup.py to newest dependencies (efed0a1)

1.0.3 (2022-07-12)

Bug Fixes

  • ci: Use other access key in order to trigger publishing workflow (384625e)

1.0.2 (2022-07-12)

Bug Fixes

  • Fix cutting reverse primers too short (a01c69d)
  • FWSet and RVSet are now different objects (a28d629)

Documentation

  • ci: update mkdocs config to support tabbed content (bdfb52d)
  • restructured user guide page, clarified some sections and added many more example commands for reference (d723b97)
  • rewritten installation page with clarified instructions and added conda instructions (271a0a8)
  • update documentation site landing page (45a3fca)
  • update readme with quick installation instructions (bdfb52d)

1.0.1 (2022-04-14)

Continuous Integration

  • update github actions workflow, split package upload to separate workflow (77c13a1)

1.0.0 (2022-04-14)

⚠ BREAKING CHANGES

  • Export BED file of cut primers

Features

  • Add support for BED file input (eaa60a0)
  • Export BED file of cut primers (f51d222)

Bug Fixes

  • Add seq and revseq to coordinatelist (eb27331)
  • Fix parsing error rate from cli (28976f2)
  • Fix parsing of "." in score column (cc6913b)
  • Fix running fasta2bed script (f8545a4)
  • Output empty bed if no primers are found (ca67b0b)

Dependencies

  • update all python versions mentions to 3.8 (89ced9c)

Documentation

  • add docstrings to AmpliGone.mappreset (6d9c32c)
  • add docstrings to functions in AmpliGone.AmpliGone (54a0a01)
  • add docstrings to functions in AmpliGone.fasta2bed (ea2d5c6)
  • add docstrings to functions in AmpliGone.io_ops (d9c60ae)
  • Update installation instructions (fbb7e0e)
  • Update user guide (071e71f)

0.4.3 (2022-02-03)

Bug Fixes

  • remove unnecessary print statement (c7bd712)

Documentation

  • add --error-rate flag to user guide documentation (9db3848)

0.4.2 (2022-02-03)

Features

  • allow the primer-search error rate to be set by the user (fddd94a)

0.4.1 (2022-02-02)

Bug Fixes

  • don't report duplicate coordinates of same primer when ambiguity-primers are given (f5449e2)
  • use Nonetypes instead of string "None" (f5449e2)

0.4.0 (2022-01-27)

Features

  • find coordinates of primers with mismatches to reference (d6bf925)

Bug Fixes

  • consistently remove reverse primers in end-to-end mode (0c4f621)
  • Fix cutting too many bases (78bd9ea)
  • Make number of iterations variable (62ac2d7)

Documentation

  • update installation instructions and include primer-search changes (5fdc6fa)

0.3.3 (2021-12-08)

Bug Fixes

  • solve preset-sampling crash when less than 3 input reads are provided (29d5624)
  • solve reference before assignment error in end-to-mid mode (14c9d24)

0.3.2 (2021-11-26)

Bug Fixes

  • report removed coordinates from all iterations (f726e9a)

0.3.1 (2021-11-25)

Bug Fixes

  • Distinguish (mis)match and cut soft clips (d4132c1)

Performance Improvements

  • Add minimap scoring to presets (11158e5)

0.3.0 (2021-11-17)

Features

  • Use CIGAR strings to cut end-to-end (ebd2684)

Bug Fixes

  • Fix typo in 75e792fa8d69746 (eca004b)
  • only return data that got an alignment-hit (f9e64e8)

Performance Improvements

  • Improved (fastq)data loading speed (9d1ae23)

Documentation

  • Fix comment in cut_read function (b920738)
  • update docs to match new primer removal process (035be92)
  • update readme (95ff984)

0.2.3 (2021-10-28)

Bug Fixes

  • set correct exit code when -to flag is given (5a93ff0)

0.2.2 (2021-10-27)

Bug Fixes

  • add missing primer-orientation keywords (41a84e6)
  • exit cleanly when primers aren't found (#11) (e927591)
  • Exit cleanly with empty input (#12) (35aae65)

Documentation

  • update user-guide to include newly added flag (4d28ac1)

0.2.1 (2021-10-25)

Documentation