pangolin v1.1.14

Updates in this release:

• Now by default pangolin only uses the safe lineages versions in the lineages release. This translates to only using lineages that are > 95% recall rate. With the -p or --include-putative flags, all lineages including those with potentially less certainty are included. We believe this will be a useful feature. Putative lineages are indicated with a p before their designation. E.g. B.1.1.p15 lies with certainty within the lineage B.1.1. Putative lineages fit the criteria required for lineage designation, but potentially due to homoplasies, sequencing errors or resolution of the global tree (>27,000 tips now), have not got recall values suitable for lineage assignment. The rationale will be if more data continues to support these lineages, the p will be removed and they will become part of the default lineage groups.
• Developments towards SNP based classification, not integrated into the master pipeline though.