v1.9.0

Added

• Added medaka tandem targeted tandem repeat variant calling.

v1.8.2

Added

• Updated features related to fetching of trimmed reads.

Changed

• Refactored smolecule module.
• Faster inference and stitching of many short contigs.
• Tensorflow version 2.10 (allows for aarch64 wheels).

v1.8.1

Added

• Expose qualities parameter in medaka_consensus script with -q parameter.

v1.8.0

Added

• Consensus and variant models for v4.1 and v4.2 basecallers.

Changed

• Changed default models to be r1041_e8.2_400bps_v4.2 models
• Clip probabilities in _phred() rather than adding smallest float.

v1.7.3

Added

• Consensus polishing models for Version 4 basecallers.
• Wheel builds for newer Python versions.

Fixed

• Deprecated numpy.unicode use.

Changed

• Set minimum Python version to 3.7.
• Updated tensorflow requirement to 2.8.
• Put lower bound on numpy requirement.

Removed

• Dropped support for Python 3.6. Security support for Python 3.6 was ended on 23 Dec 2021;
  as such we have removed support for Python 3.6 and suggest users update their Python version.

v1.7.2

Added

• New models for R10.4.1 E8.2 260bps based sequencing chemistries.

Changed

• Updated Hac and Fast models for R10.4.1 E8.2 400bps based sequencing chemistries.
• Removed models for Fast basecallers from pypi package

v1.7.1

Fixed

• medaka variant IndexError on long insertion

v1.7.0

Added

• capability to fill gaps in consensus sequence with a designated character
  (e.g. 'N') instead of content from a reference sequence.
• option -r in medaka_consensus to set the designated fill character.
• option --fill_char in medaka stitch to set the designated fill character.

Fixed

• CUDA initialization errors during medaka smolecules stitch phase.

v1.6.1

Added

• New models for R10.4.1 E8.2 400bps based sequencing chemistries.

Fixed

• DiploidZygosityLabelScheme renaming.

v1.6.0

Changed

• Updated to tensorflow~=2.7.0.
• Do not always force recreation of minimap2 index in helper scripts.
• PyPI wheel releases now built with libdeflate for faster BAM reading.

Fixed

• Inclusion of inserted bases immediately after deletion in pileup counts.

Added

• Makefile can now build environment for macOS M1.
• Publish ARMv8 wheels compatible with NVIDIA's Jetpack 4.6.1 binary.
• --qualities option for smolecule and stitch to output consensus fastq.