Version 1.1.5

Changes

• Fixed lineages L4 and L4.9 assignment
• Removed redundant sambamba indexing rule

Full Changelog: v1.1.4...v1.1.5

Version 1.1.4

Changes

• Bump wrappers version to v1.23.0
• Replace Picard MarkDuplicates with Sambamba markdup
• Replace Samtools index with Sambamba index
• Add GATK VariantsToTable and LeftAlignAndTrimVariants wrappers

Full Changelog: v1.1.3...v1.1.4

Version 1.1.3

Changed some L2 SNPs:

• L2 497491G>A --> 811753C>T
• L2.1 3309880G>A --> 1135798C>T
• L2.2 (ancient) 4280708G>A --> 1288698G>A
• L2.2.AA2 886115T>C --> 3960979A>C
• L2.2.AA3 1477522C>A --> 197705G>A
• L2.2.M6.1 782634A>G --> 1843620T>C
• L2.2.M4.5 4086G>T --> 2908357G>A
• L2.2.M2 2376135A>G --> 15087C>G

Version 1.1.2

Improvements

• Added snakemake report functionality

Version 1.1.1

Improvements

• Added barcoding by levels functionality

Version 1.0.1

Bug fixes:

• Added numpy.ufunc.reduce to fix incorrect lineage assignment

Improvements

• Added dummy vcf file to facilitate lineage 4 prediction

Version 1.0.0

Initial stable release.