v0.3.0

New features

• freebayes variant calling
• naibr variant calling
• bam filename/RG tag validations
• unit testing (not relevant for end-user)
• --vcf-samples options for impute and phase
• file/vcf sample validations
• STITCH parameter file validations
• genome assembly bgzipping validation/handling
• much more flexible regex for fastq filenames
• STITCH param file column order no longer matters and is not case-sensitive
• new demultiplex module for Generation I (Meier et al., 2022) haplotag beads

Breaking changes

• snp and sv variant calling now split into separate submodules under variants
  • variants --method is now variants snp --method and variants sv --method
• STITCH param file has extra column bxlimit
• the validations listed above will force Harpy to terminate if errors are detected
• folder structure for output of align slightly different

Non-breaking changes

• added Snakemake --nolock and --rerun-incomplete flags to all workflows
• all workflows now provide appropriate exit codes
• snp variant calling now occurs by genomic interval rather than by contig (a lot more parallel, a lot faster)
• EMA aligns all preproc files at once into single alignment file, rather than aligning each individually and merging after
• samtools stats/flagstat reports combined into single report
• phase reports reworked/rewritten

v0.2.0

Added

• naibr variant calling
• BX assessment scripts written in python instead of perl
• BX assessment report
• --quiet (-q) option to shut snakemake up

changed

• --methods instead of --bwa or --leviathan
• version info
• some of the output directory structures
• some deps, but that's a conda build concern

0.1.1

add ema-h binary

0.1.0

Initial release for conda integration