Recent Releases of ampligone
ampligone - v2.0.0
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
-tois 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 findorread_primers() method (e670d2b)
- update citation information in CITATION.cff and README.md (7e8e0c6)
- Python
Published by ids-bioinformatics 11 months ago
ampligone - v1.3.0
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)
- Python
Published by ids-bioinformatics over 2 years ago
ampligone - v1.2.1
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
- Python
Published by ids-bioinformatics almost 3 years ago
ampligone - v1.2.0
1.2.0 (2022-12-20)
Features
- add support for fragmented amplicon reads with the
--amplicon-type fragmentedmode (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)
- Python
Published by ids-bioinformatics about 3 years ago
ampligone - AmpliGone v1.1.0
Features
- output some basic stats in the log (c5ad032)
- use
richas a logging handler to improve logging with timestamps and various information levels. (c5ad032)
Dependencies
- add
richas a dependency (c5ad032) - change parmap version to lenient version 1.5.x (0c4d2a5)
- remove
tqdmas 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)
- Python
Published by ids-bioinformatics over 3 years ago
ampligone - AmpliGone v1.0.3
Bug Fixes
- ci: Use other access key in order to trigger publishing workflow (384625e)
- Python
Published by ids-bioinformatics over 3 years ago
ampligone - AmpliGone v1.0.2
Bug Fixes
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)
- Python
Published by github-actions[bot] over 3 years ago
ampligone - AmpliGone v1.0.1
Continuous Integration
- update github actions workflow, split package upload to separate workflow (77c13a1)
- Python
Published by github-actions[bot] almost 4 years ago
ampligone - AmpliGone v1.0.0
⚠ BREAKING CHANGES
- Export BED file of cut primers
Features
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)
- Python
Published by github-actions[bot] almost 4 years ago
ampligone - AmpliGone v0.4.3
Bug Fixes
- remove unnecessary print statement (c7bd712)
Documentation
- add
--error-rateflag to user guide documentation (9db3848)
- Python
Published by github-actions[bot] about 4 years ago
ampligone - AmpliGone v0.4.2
Features
- allow the primer-search error rate to be set by the user (fddd94a)
- Python
Published by github-actions[bot] about 4 years ago
ampligone - AmpliGone v0.4.1
Bug Fixes
- don't report duplicate coordinates of same primer when ambiguity-primers are given (f5449e2)
- use Nonetypes instead of string "None" (f5449e2)
- Python
Published by github-actions[bot] about 4 years ago
ampligone - AmpliGone v0.4.0
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)
- Python
Published by github-actions[bot] about 4 years ago
ampligone - AmpliGone v0.3.3
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)
- Python
Published by github-actions[bot] about 4 years ago
ampligone - AmpliGone v0.3.2
Bug Fixes
- report removed coordinates from all iterations (f726e9a)
- Python
Published by github-actions[bot] about 4 years ago
ampligone - AmpliGone v0.3.1
Bug Fixes
- Distinguish (mis)match and cut soft clips (d4132c1)
Performance Improvements
- Add minimap scoring to presets (11158e5)
- Python
Published by github-actions[bot] about 4 years ago
ampligone - AmpliGone v0.3.0
Features
- Use CIGAR strings to cut end-to-end (ebd2684)
Bug Fixes
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)
- Python
Published by github-actions[bot] over 4 years ago
ampligone - AmpliGone v0.2.3
Bug Fixes
- set correct exit code when
-toflag is given (5a93ff0)
- Python
Published by github-actions[bot] over 4 years ago
ampligone - AmpliGone v0.2.2
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)
- Python
Published by github-actions[bot] over 4 years ago
ampligone - AmpliGone v0.2.1
Documentation
- add changelog link (4b62a92)
- Python
Published by github-actions[bot] over 4 years ago
ampligone - First release: AmpliGone v0.2.0
Initial versioned release of AmpliGone with version 0.2.0
AmpliGone is a tool which accurately finds and removes primer sequences from NGS reads in an amplicon experiment. AmpliGone is compatible with both Nanopore and Illumina data (fastq) and is able to accurately remove primer sequences for various amplicon-NGS experiment designs
- Python
Published by florianzwagemaker over 4 years ago