Primalscheme Versions Save

Changed

• Dropped support for python 3.6
• Updated click dependency to latest

Fixed

• pyproject.toml requirements, language version
• README

Added

• Primer sequence column in BED file output.
• PRIMER_MAX_BASE_PENALTY in conf.

Changed

• Tuned some penalty weightings.
• Drop standalone homodimer check; use same method as for heterodimers.
• Improved indel handling.

Fixed

• Bug where left/right primers are not checked against one another for interactions.

Added

• Add primary_only to run report config section
• Allow inputs with IUPAC ambiguity codes

Fixed

• Fix unintended high-gc mode persistance when run as Celery task
• Fix incorrect parameter name in run report json

Added

• Implement high-GC config option
• Warn user if high-GC detected (without --high-gc option)
• Include ref counts in run report

Changed

• Widen default primer size range (min 19, max 34 bp)

Fixed

• Fix bug where last region could be a duplicate amplicon in opposite pool (no progress)

Added

• Add MultiplexScheme parameters to debug log output
• Add version number to debug log and run report

Changed

• Improve --amplicon-size help text
• Move reference info logging into cli

Fixed

• Fix outpath option in README
• Fix --amplicon-size % variation in help text

Removed

• Remove logger name from log file output

Added

• Add --pinned, -p option: reverts to designing primers exclusively from first reference
• Add short option names
• Add option to pass single target amplicon size and auto-determine a suitable range
• Add web interface link to README

Changed

• Switch from Argparse to Click
• Rename options
• Allow --amplicon-size, -a to be passed once to set a target size, or twice to set an exact size range
• Refactor test_cli.py to use CliRunner throughout

Removed

• Remove argparse
• Remove non-functional --step-distance option
• Remove automatic reference sort on length (no longer serves a purpose)

Fixed

• Fix edge case where last-but-one region steps right, putting last region out of bounds
• Fix (usually) inconsequential out-by-one error to make Window.slice_end coord inclusive

Fixed

• Fix number of reported candidates considered
• Fix missing exception message where no suitable pair found
• Fix incorrect logging of --no-sort

Added

• Define ProgressTracker interface as abstract base class (to facilitate web interface progress)

Changed

• Reorganise Region and Window into region.py

Added

• Drop secondary references on repeated flank alignment failure
• Add primary_ref, secondary_refs and excluded_refs to json run report

Changed

• Reduce complexity of Region find_primers() method
• Use progress library
• Add region and considered primers to progress message

Removed

• DIY progress bar