pathogen-profiler v4.6.0

Changes

• Adding debug statements to barcoding functions
• Allowing user to modify stdeve cutoff for barcode containment
• Adding crude mpileup method to look for barcoding SNPs
• Added script to replace ucsc-fatovcf

pathogen-profiler v4.5.1

Changes

• Update default caller to bcftools or clair3 for nanopore
• Add missing bcftools index command
• Fix for jodyphelan/TBProfiler#402

pathogen-profiler v4.5.0

Changes

• Add strand support extraction from GATK VCFs
• Non-critical bug fixes

pathogen-profiler v4.4.0

Changes

• VCF annotation 3x faster
• Allow pipeline to continue even if delly fails
• Add new variant call class for P. falciparum
• Add db schema version of species db
• Bug fix for VCF variant combination

v4.3.0

What's Changed

• Implement check to see if deletion of tandem repeats can be place outside of gene region
• Add database schema versions to version dictionary
• Implement variant calling classes to allow for future plugins
• Sanity checks to see if sequence names in VCF match database
• Fix bug in coverage qc depth calculation
• Fix for sourmash error

Full Changelog: v4.2.0...v4.3.0

pathogen-profiler v4.2.0

What's Changed

• Added in bwa meme to mappers
• Added option to dump barcoding snps
• Small updates to pydantic models

Dev by @jodyphelan in #44

Full Changelog: v4.1.0...v4.2.0

pathogen-profiler v4.1.0

Changes

• Added barcoding mutations to BarcodeResult type
• Small bug fixes

pathogen-profiler v4.0.0

• Pydantic data models
• Type hints
• Code refactoring

pathogen-profiler v3.1.0

Updates

• Improved hgvs mutation parsing and validation
• Add sourmash sequence similarity searching

pathogen-profiler v3.0.0

Changes

• Stylistic changes (e.g. capitalisation of class names)
• Use of logging for logging
• Hard and soft filtering on variants
• For parallel jobs (e.g. variant calling) now using joblib internally vs gnu parallel
• Using pysam to extract data from VCFs