0.7.0

What's Changed

• Support for multiprocessed fastq output by @remiolsen in #65
• Switch CLI over to typer, change command to "anglerfish run" by @remiolsen in #81
• Show closest matching barcodes in unmatched list, allow user to name run folder by @remiolsen in #83
• Readability improvements by @kedhammar in #84
• Misc. improvements, unit tests and mypy proofing by @kedhammar in #85
• Objectify and improve structuring by @kedhammar in #86
• Include edit distance in closest barcode column of non-matching barcodes by @remiolsen in #87

Full Changelog: 0.6.1...0.7.0

0.6.1

What's Changed

• Add my poster from the "Visualize Your Science" course, for fun by @kedhammar in https://github.com/remiolsen/anglerfish/pull/67
• Add UMI support by @remiolsen in https://github.com/remiolsen/anglerfish/pull/72
• First version of the explore command by @alneberg in https://github.com/remiolsen/anglerfish/pull/59
• Implement continous integration practices + formatting and fixes across entire repo by @kedhammar in https://github.com/remiolsen/anglerfish/pull/54
• Changed conda env to development only by @remiolsen in https://github.com/remiolsen/anglerfish/pull/56
• Adapt Dockerfile for arm64 and some requirements changes by @alneberg in https://github.com/remiolsen/anglerfish/pull/58
• Change requirements to python>=3.10 by @remiolsen in https://github.com/remiolsen/anglerfish/pull/55
• Umi format explore fix by @alneberg in https://github.com/remiolsen/anglerfish/pull/73
• Fix debug output by @remiolsen in https://github.com/remiolsen/anglerfish/pull/62
• Bugfix explore again (this time to master) by @alneberg in https://github.com/remiolsen/anglerfish/pull/76
• Bug fix for lenient mode and prepare release of 0.6.1 by @remiolsen in https://github.com/remiolsen/anglerfish/pull/77

Full Changelog: remiolsen/anglerfish@0.6.0...0.6.1

0.6.0

What's Changed

• Add pyyaml as a dependency; used by the samplesheet module by @cbrueffer in https://github.com/remiolsen/anglerfish/pull/36
• Dev 0.6 by @remiolsen in https://github.com/remiolsen/anglerfish/pull/52
  • Added Illumina UDI support
  • Lenient mode for trying all index orientations
  • ONT barcode aware mode
  • Bugfixes and reporting refactoring.
• Added: Force rev. complement and lenient mode scaling by @remiolsen in https://github.com/remiolsen/anglerfish/pull/53

New Contributors

• @cbrueffer made their first contribution in https://github.com/remiolsen/anglerfish/pull/36

Full Changelog: remiolsen/anglerfish@0.5.0...0.6.0

0.5.0

What's Changed

• Add max unknown indices parameter
• Changed .format() strings to f-strings where applicable.
• Adaptors no-longer hard-coded, read from .yaml file.
• Parse globs in samplesheet

New Contributors

• @kedhammar made their first contribution in https://github.com/remiolsen/anglerfish/pull/33

Full Changelog: remiolsen/anglerfish@0.4.2...0.5.0

0.4.2

What's Changed

• 0.4.2-rc.1 by @remiolsen in https://github.com/remiolsen/anglerfish/pull/22
• Bump numpy from 1.19.2 to 1.21.0 by @dependabot in https://github.com/remiolsen/anglerfish/pull/23
• Finalise 0.4.2 by @remiolsen in https://github.com/remiolsen/anglerfish/pull/24

New Contributors

• @dependabot made their first contribution in https://github.com/remiolsen/anglerfish/pull/23

Full Changelog: remiolsen/anglerfish@0.4.1...0.4.2

0.4.2-rc.1

What's Changed

• 0.4.2-rc.1 by @remiolsen in https://github.com/remiolsen/anglerfish/pull/22

Full Changelog: remiolsen/anglerfish@0.4.1...0.4.2-rc.1

Anglerfish v0.4.1

What's Changed

• Dev -> version 0.4.1 by @remiolsen in https://github.com/remiolsen/anglerfish/pull/18
• Fix apt change release by @remiolsen in https://github.com/remiolsen/anglerfish/pull/19

Full Changelog: remiolsen/anglerfish@0.4.0...0.4.1

Anglerfish v0.4.0

Changes

#7 Screen for all known illumina adapters
#10 Independently calculate read lengths enhancement
#11 Automatically adjust minimum mismatches allowed
#12 Output the commandline arguments
#13 Output csv file

Anglerfish v0.3.0

Changes

#4 Possibility have multiple Ilmn index types in one samplesheet
#5 Redesign input samplesheet
#6 Summarize all anglerfish sample read counts in one table

Anglerfish v0.2.0

First release!