cov-lineages/pangolin v2.4

pangolin v2.4

on GitHub

Release notes

Updates to pangolearn.smk:

• Now only map a single time producing a sam file, resulting in speed ups to pangolin
• gofasta now muiltithreading, additional speedups

Updates to output file:

• Output 'conflict' rather than 'probability' now, this is a measure of conflicts within the decision tree, 0 being equivalent to no conflicts, but not a confidence score.
• Output the pango-designation version number now, which is available from pangoLEARN version 2021-04-28 onwards.

Bug fixes:

• Noted discrepancies between minimap -a and minimap without the -a flag, leading to occasional sequences not accounted for in output csv file. This only occured when minimap2 fails to map very diverged sequences, but this is now being accounted for.
• In --no-temp mode, minimap redirection was causing pangolin to break, now no longer re-direct this output, so appears on screen, but pipeline doesn't break.