v0.11.0

[0.11.0]

Added

• Added emmtyper and parser
• Added pytests for emmtyper

Fixed

Changed

• Changed Shigapass models to be consistent with other typing models
• Changed Shigapass parsers to be consistent with other typing parsers
• Changed ref genome related variables to be optional in quast

v0.10.1

What's Changed

• Updated parsing of chewbbaca cgMLST error codes by @mhkc in #88

Full Changelog: v0.10.0...v0.10.1

v0.10.0

[0.10.0]

Added

• Added flag to set verbosity level.
• Validate TbProfiler schema version.
• Added CLI command for adding IGV annotation tracks
• Added indel_variants to json result and ability to filter vcf into various categories

Fixed

• Fixed genome_annotation appending bug
• Fixed variant sorting as reference_sequence can be None

Changed

• Updated sample metadata in the output format. RunMetadata was split into two fields, one for sequencing and one for pipeline information. Lims id and sample name are now included in the SampleBase object.
• Split SV and SNV from tbprofiler output
• Update annotate_delly to extract SVs from vcf

v0.9.3

[0.9.3]

Added

• Add sample_id to prp output

Fixed

Changed

v0.9.2

[0.9.2]

Added

Fixed

• Changed --symlink_dir to --symlink-dir for consistency

Changed

• Use basename when symlink_dir provided

v0.9.1

Added

• Added additional tests to ensure that Bonsai input data can be re-cast into a PipelineResult data format.

Fixed

Changed

• Fixed some Pylint warnings.
• Pylint ignores pysam functions since they are generated.

v0.9.0

[0.9.0]

Added

• Added Shigapass output
• Added tests for the Shigapass parser.

Fixed

• Fixed minor issues with the ShigaPass parser.

Changed

v0.8.3

[0.8.3]

Added

Fixed

• Reordered lineage data models in the method index.

Changed

v0.8.2

[0.8.2]

Added

Fixed

• Updated lineage parser to work with TbProfiler v6.2

Changed

• Changes lineage datamodel to reflect changes in TbProfiler output

v0.8.1

[0.8.1]

Added

• Added species prediction and phylo group from Mykrobe.

Fixed

Changed

• Changed species_prediction field to be a key-value indexed array to support multiple SPP predictions.