Commits for angie

7a92e3aa307573ab74f5f17cba55934b9a18ab15 Thu Apr 6 11:13:22 2023 -0700

Corrections to XBB.1.2, XBB.2.3 and XBB.2.3.2: mask bases that aren't essential to the lineage definition. Order of mutations changed quite a bit for XBB.2.3[.2]. HT @corneliusroemer
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 3, context: html, text, full: html, text

f2aee59866d6bdd224a7183323f72390a861b328 Sat Apr 22 18:17:02 2023 -0700

Auto-download new GenBase sequences from China National Center for Bioinformation.
- src/hg/utils/otto/sarscov2phylo/getCncb.sh - lines changed 131, context: html, text, full: html, text

8ec3c55d2932bb09df06ae9bd9be0b0dd37c2ea9 Sat Apr 22 18:21:48 2023 -0700

Overhaul detection of duplicates in previous day's protobuf vs. today's ID-mapping, and get latest sequence names from metadata, by first converting previous day's names to accessions only. Add in detection of new CNCB sequences.
- src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh - lines changed 225, context: html, text, full: html, text

2df325b2cfee5a71d16157bf3aaa62c3e6734ec3 Sat Apr 22 18:23:06 2023 -0700

Guard against truncated download file which can happen despite successful return from datasets command.
- src/hg/utils/otto/sarscov2phylo/getNcbi.sh - lines changed 8, context: html, text, full: html, text

d2edb9c3250f1d05950235c55998d9e00a450016 Sat Apr 22 18:24:17 2023 -0700

New lineages and a few missed pango-maskings (C193T to C193N) from earlier.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 35, context: html, text, full: html, text

d091ea9bacb0841f1aa4b17b5f1e8a5219b43929 Sat Apr 22 18:25:31 2023 -0700

Get new sequences from CNCB.
- src/hg/utils/otto/sarscov2phylo/updatePublic.sh - lines changed 5, context: html, text, full: html, text

fa9ed9b7c17b901dd736a36049879099d23badd2 Sat Apr 22 18:26:59 2023 -0700

Strip out more fluff from sequence names.
- src/hg/utils/otto/sarscov2phylo/util.sh - lines changed 5, context: html, text, full: html, text