v1.6.0

1.6.0 (2022-03-31)

Features

• pharmcat.org website redesign and new content (48cd154)
• website: tweak the website styling and layout (b52b7d6)

Bug Fixes

• add more clarifying info to TestVcfBuilder alt allele mismatch message (63d0dfd)
• fix bundle call for running local jekyll (a1034a7)
• fix CLI arg description for Phenotyper (f31085c)
• fix jekyll front matter on disclaimers page (a2ecb79)
• fix permissions on VCF scripts (3d5cb34), closes #89
• data: update to CPIC 1.16 (5ee8d37)
• datamanager: correctly loading definitions in dataManager when skipping alleles (2687635)
• datamanager: improve error when encounter external service error (93de324)
• docker: make sure scripts are executable (dfc080f), closes #89
• docker: use docker 3.9 to work around numpy incompatibility (44cf6d1)
• namedallelematcher: discard position with AD field (6b717db)
• namedallelematcher: do not discard position if novel ALT allele is found (ba48472)
• namedallelematcher: handle . AD value (2591ae9)
• namedallelematcher: improve AD field handling (only catch reference overlap) (cb152c6)
• namedallelematcher: improve checking for unexpected ALT (f74b309)
• preprocessor: improved way to identify block gVCF (b57a6e2), closes #79
• preprocessor: sort VCF in a way that the non-PGx variants that occur at the PGx positions will appear after the line of the PGx variants (3a2be37), closes #95
• reporter: fix total gene count in report genotypes table (02fd57d)
• reporter: make DrugLinks comparable to sort properly in final output (501db22)
• reporter: update more PharmCATTest tests to new wrapper (89e5354)

Reverts

• update TPMT test for new calling rules (63f4775)