v1.3.1

1.3.1 (2024-04-03)

Bug Fixes

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

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)

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

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

v1.2.0

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)

AmpliGone v1.1.0

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)

AmpliGone v1.0.3

Bug Fixes

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

AmpliGone v1.0.2

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)

AmpliGone v1.0.1

Continuous Integration

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

AmpliGone v1.0.0

⚠ 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)

AmpliGone v0.4.3

Bug Fixes

• remove unnecessary print statement (c7bd712)

Documentation

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