v1.11.3

Added

• Consensus and variant models for v4.3.0 dorado models.

v1.11.2

Added

• Parsing model information from fastq headers output by Guppy and MinKNOW.

Changed

• Additional explanatory information in VCF INFO fields concerning depth calculations.

v1.11.1

Fixed

• Do not exit if model cannot be interpreted, use the default instead.
• An issue with co-ordinate handling in computing variants from alignments.

Added

• Ability to use basecaller model name as --model argument.
• Better handling or errors when running abpoa.

v1.11.0

Fixed

• Correct suffix of consensus file when medaka_consensus outputs a fastq.

Added

• Choice of model file can be introspected from input files. For BAM files the
  read group (RG) headers are searched according to the dorado
  specification,
  whilst for .fastq files the comment section of a number of reads are checked
  for corresponding read group information. In the latter case see README for
  information on correctly converting basecaller output to .fastq whilst
  maintaining the relevant meta information.
• medaka tools resolve_model can display the model that would automatically
  be used for a given input file.

Changed

• If no model is provided on command-line interface (medaka consensus,
  medaka_consensus, and medaka_haploid_variant) automatic attempts will be made
  to choose the appropriate model.

v1.10.0

Changed

• Tensorflow logging level no longer set from Python.
• spoa and parasail are now strict requirements.

Fixed

• Sort VCF before annotating in medaka_haploid_variant.
• Ignore errors when deleting temporary files.
• The output of the first POA run not being used in the second iteration in smolecule command.

Added

• Support for Python 3.11.
• --spoa_min_coverage option to smolecule command.

Removed

• Support for Python 3.7.

v1.9.1

Fixed

• A long-standing bug in pileup_counts that manifests for single-position pileups on ARM64.

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.