v0.3.1

0.3.1 (2024-09-19)

Bug Fixes

• propagate user metadata (eabb78a)

v0.3.0

0.3.0 (2024-09-12)

Features

• add detection of snpCLs (2d075d7)

Bug Fixes

• add counts to lineage scoring (d28718d)
• dont use contig number in consensus fasta header (514d806)
• fix run_pipeline.sh (e6dbab7)
• fix run_pipeline.sh (523a157)
• generalize binding paths when using container (5d5991a)
• introduce vcf entries with ref call if needed (56ff964)

Dependencies

• update juno-lib (fbd67e6)

v0.2.1

0.2.1 (2024-07-25)

Bug Fixes

• update cli (0de09d0)
• update cli (57454c3)

Dependencies

• update juno library (97bb7ad)

v0.2.0

0.2.0 (2024-07-05)

Features

• annotate large deletions based on bed file (095a2c7)

Bug Fixes

• dont fail when no deletions are found (83d143f)

v0.1.1

0.1.1 (2024-03-27)

Bug Fixes

• allow multiple ref data rows merge for single variant (8c4167e)
• fix consensus generation (f967cd5)
• force alt regardless of GT (a23a59b)
• merge using python (ec93c14)
• set rules to local (4a5e439)

v0.1.0

0.1.0 (2024-03-18)

Features

• add consensus generation (037d125)
• add manual version checks (1577530)
• add mtb lineage type as prototype (f9f1273)
• add parsing of snpeff to variant table (4cb2cbf)
• add presets (8c5309d)
• add small test dataset based on K1F phage (d4a3bdb)
• add snpeff annotation (a2123fa)
• copy and prepare input files (4d98315)
• include unfiltered variants in tsv output (5832b92)
• produce tb sequence experiment json for database (502fc57)

Bug Fixes

• add data to coll positions bed (9765610)
• add helper scripts for variant annotation (88605d4)
• add rrs and rrl count to output (794a7a9)
• bind db dir in wrapper (df1c0c8)
• correct path to db (2ac4337)
• correct path to resistance list on biogrid (aea4ead)
• count only filtered variants in defined regions (c7aa626)
• first conversion of template to jvt (3b5d02d)
• fix error when no typing needed (152bbc7)
• fix filtering for resistance mutations (7d61cff)
• fix mypy typing error (e8f5118)
• make column names more informative (62ca364)
• python executable name for container (85a8ad2)
• snpeff executable (294eff7)
• snpeff executable name (2b9af66)
• sync conda and sing versions (e82a948)
• treat ref and allele columns as non-VCF compliant (0e6a956)
• typo in default arg (200210b)
• update typing (06482cd)

Dependencies

• add conda envs (5d2bb78)
• add containers (d9d4f5e)
• remove anaconda (ca745ec)
• set correct container (cef23c4)
• sync conda install with containers (f9a8d6b)
• update library version (8c23189)
• upgrade snakemake and juno-lib (cd94fed)
• use smk v7.24 to prevent reinstall with pip (fca70fb)