pangolin v2.2.2

Release notes

• --threads,-t flag use no longer breaks, it's caught with warning printed that no longer supported.

pangolin v2.2.1

Release notes

• Restoring env name

pangolin v2.2.0

Release notes

• Removing legacy code and options from pangolin install
• Adding custom logger for quiet mode
• Adding coloured print outs
• Removing legacy dependencies and flags

pangolin v2.1.11

Release notes

• Minor release with speed-ups for small numbers from @aunderwo and @bewt85

pangolin v2.1.10

Release notes

• Update to threshold of calling B.1.351:

5 or more defining SNPs
1 or less reference alleles

• Update to threshold of calling B.1.1.7

5 or more defining SNPs
5 or less reference alleles

pangolin v2.1.9

## Release notes

• Raising reference tolerance threshold for B.1.1.7 and B.1.351

pangolin v2.1.8

Release notes

• Explicitly checking for ambiguities over ref alleles in the assignment of B.1.1.7 and B.1.351.
• Now including a --decompress-model flag that can permanently pre-decompress the model prior to running as a time saver.

pangolin v2.1.7

Release notes

• Minor release to include post-hoc curation of lineages P.1 and P.2 (aliases of B.1.1.28.1 and B.1.1.28.2 respectively).
• P.1 requires presence of at 11 or more of the following mutations that occur on the basal branch

aa:orf1ab:S1188L
aa:orf1ab:K1795Q
del:11288:9
aa:S:L18F
aa:S:T20N
aa:S:P26S
aa:S:D138Y
aa:S:R190S
aa:S:K417T
aa:S:E484K
aa:S:N501Y
aa:S:H655Y
aa:S:T1027I
aa:orf3a:G174C
aa:orf8:E92K
aa:N:P80R

• P.2 requires presence of the following amino acid mutations

aa:orf1ab:L3468V
aa:orf1ab:L3930F
aa:S:E484K
aa:S:V1176F
aa:N:A119S

pangolin v2.1.6

Release notes

Updating South African SNP criteria to at least 5 of:

aa:E:P71L
aa:N:T205I
aa:orf1a:K1655N
aa:S:D80A
aa:S:D215G
aa:S:K417N
aa:S:A701V
aa:S:N501Y
aa:S:E484K

pangolin v2.1.4

Release notes

Update to pangolin assignments fixing bug from issue #116