Changelog

Clinical-Genomics-Lund/jasentool: Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

minority-report subcommand — computes minority base frequency distribution from a pre-computed samtools mpileup file (.mpileup or .mpileup.gz), with optional blacklist filtering
create-blacklist subcommand — runs mpileup and minority base distribution across a set of BAM files, then aggregates per-position frequencies to produce a minority variant blacklist TSV
--plasmidfinder flag in create-yaml — emits PlasmidFinder result path under the plasmidfinder key
--plasmidfinder-genome-hits flag in create-yaml — emits the path to the PlasmidFinder Hit_in_genome_seq.fsa under the plasmidfinder_genome_hits key
--plasmidfinder-plasmid-seqs flag in create-yaml — emits the path to the PlasmidFinder Plasmid_seqs.fsa under the plasmidfinder_plasmid_seqs key
--shigatyper flag in create-yaml — emits ShigaTyper result path under the shigatyper key (#47)
--samtools-stats and --samtools-bedcov flags in create-yaml — mutually exclusive with --postalnqc

Added plot.py for all plotting functions
Added plotting of n_missing_loci barplot
post-align-qc subcommand — computes post-alignment QC metrics from a BAM file
count-reads subcommand — counts reads from FASTQ file(s), outputs JSON
Added readthedocs
Added pytesting
Added Dockerfile
Added download-ncbi subcommand — downloads genome FASTA and GFF from NCBI Datasets v2 API
Added download-bigsdb subcommand — downloads cgMLST scheme alleles from PubMLST / BIGSdb Pasteur via OAuth1
Added concatenate-files subcommand — merges multiple YAML files (e.g. versions.yml) into one output YAML
Added create-yaml subcommand — creates a YAML input file for Bonsai upload from sample metadata and analysis result paths
Added GA workflows for publishing to dockerhub and pypi
Added pytest for download-ncbi subcommand
Added conda environment.yml for installation
Added annotate-delly subcommand — annotates Delly structural-variant VCFs with gene symbols and locus tags from a tabix-indexed BED file
Added pytests for post-align-qc and count-reads subcommands using simulated S. aureus fixture data
Added S. aureus simulated FASTQ and BAM fixtures (saureus_sim_R1.fastq.gz, saureus_sim_R2.fastq.gz, saureus_test_1.bam) for testing

Changed cronjob to use environmental variables
Changed default --remote_hostname
missing → identify-missing
convert → transform-file-format
fix → reformat-csv
converge → converge-catalogues
All subcommand argument names changed from underscore style (--db_name) to hyphen style (--db-name)
Removed insert subcommand
Change sambamba for pysam
Removed picard hs metrics and --reference arg
download_ncbi.py → ncbi.py (class DownloadNcbi → NCBI), download_bigsdb.py → bigsdb.py (class DownloadBigsdb → BIGSdb) — renamed to match module naming convention
Removed download-krakendb subcommand; Kraken2 DB building is now documented as a Singularity workflow in docs/usage.md
Utils.download_and_save_file upgraded with exponential-backoff retry logic (max_retries parameter); Utils.unzip now returns bool and handles corrupt archives
count-reads: now reads in binary chunks and counts newlines instead of iterating line-by-line in text mode to reduce overhead
annotate-delly: VCF and TabixFile handles now explicitly closed; writer wrapped in try/finally; tabix index existence validated before opening BED file