v0.8.0

[0.8.0]

Added

• Added rerun_bonsai_input to rerun bonsai-prp outputs when output format changes
• Added symlink_dir as possible filepaths prefix for IGV inputs
• Added kraken cutoff whereby species prediction needs to have >= 0.01% of read hits
• Added phylogenetic statistics to result for tb
• Added source of variant to output

Fixed

• Handling of tbprofiler v6.2.0 results

Changed

• Changed all click types to click.Path()
• Removed ref_accession != bam_ref_genome check

v0.7.1

[0.7.1]

Added

Fixed

• Fixed ins_size, ins_size_dev & coverage_uniformity parsing and models
• Check first 1000 reads if paired instead of just first read

Changed

v0.7.0

[0.7.0]

Added

• Added sequencing_run and lims_id to output (bonsai input)
• Added function for annotating delly variants intersecting with resistance targets
• Added capability of handling empty dictionaries from serotypefinder output
• Added pytest for prp annotate-delly
• Added pyyaml to docker image

Fixed

• Fixed --output arg re annotate delly

Changed

• Removed sample id from Sample object
• Changed annotate delly output type

v0.6.0

[0.6.0]

Added

• Add optional SNV and structural variants to sample output
• Add n_read_pairs

Fixed

• Calculation of iqr_median (now called coverage_uniformity)

Changed

• Renamed variables to be more informative (median to median_cov, tot_reads to n_reads & mapped_reads to n_mapped_reads)

v0.5.0

[0.5.0]

Added

• Add models for serotypefinder results
• Add fx to parse serotypefinder results
• Add --serotypefinder arg to cli
• Add files for pytest re serotypefinder results for ecoli

Fixed

• Handle amrfinder --organism output

Changed

• Update pytest functions to incl. serotypefinder results for ecoli

v0.4.0

[0.4.0]

Added

• Add create-qc-result as sub arguement
• Add QC class and parse_alignment_results to qc.py
• Add picard, sambamba, java and r-base to Dockerfile
• Add quartile1, median & quartile3 to postalignqc results and respective model
• Add fx for formatting datetime for manually generated tbdbs

Fixed

• Dockerfile python version
• Pydantic models
• Python version error in Dockerfile
• Test files regarding q1, median and q3

Changed

• Workflow that publishes to PyPI and Dockerhub separated into two workflows for testing
• Publish to docker workflow started on completion of PyPI publishing

v0.3.1

[0.3.1]

Added

• Workflow for docker image to be pushed to dockerhub
• Image build file (Dockerfile)
• Add get_db_version and reformat_date_str to utils.py
• Workflow that builds and pushes to both dockerhub and PyPI

Fixed

• Git action versions

Changed

• Move utils.py from prp/parse/phenotype to prp/parse
• Docker/PyPI publishing workflow added workflow_dispatch, removed permissions and changed secret variable names

v0.3.0

[0.3.0]

Added

• Pytest for Mycobacterium tuberculosis

Fixed

• Reordered variant models in ElementTypeResult
• Fixed assignment of TbProfiler variant type

Changed

• Renamed mutations to variants
• Removed prc_dup and dup from postAlnQc output
• Added reference, note fields to PhenotypeInfo
• Mykrobe output parser handles csv format instead of json
• Split generic ResistanceVariant and ResistanceGene to one specified for individual tools
• Include non resistance yeilding variants from tbprofiler

v0.2.0

[0.2.0]

Added

• CLI command for generating QC report for CDM
• Parsing of Virulencefinder STX typing

Fixed

• Bug that prevented parsing of AMRfinder results

Changed

• Resfinder variant describe changed NT instead of codon.
• Antibiotic class is stored with phenotypes.
• Accession nr, gene symbol and AA change is stored for Resfinder variants

v0.1.0

[0.1.0]

Added

• Added PRP application from https://github.com/genomic-medicine-sweden/JASEN
• CHANGELOG reminder github action for PRs
• Test and test files for S.aureus and E.coli
• Pytest github action

Fixed

Changed