Commits for angie

48f4046340295c6795f5bd4491fdbfec1a2c8527 Tue Mar 21 11:40:36 2023 -0700

New lineages and some corrections: * BA.2_dropout had 21762 and 21846 twice, oops * BS.1.2 was defined too narrowly, should not have required C29642T * BF.7.6 was defined too narrowly, should not have required A2692T and C15540T * CK.2.1.1 needed G2393N (order-shuffling) * XAW apparently got a bunch of new sequences after cleanup and needed quite a few new Ns * XBC needed C22329T (early sequences had Ns and needed to be removed and re-added to impute)
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 12, context: html, text, full: html, text

f559b66a0d86b81dd0e1254a198132462f45874c Thu Mar 23 13:25:14 2023 -0700

Another slew of new lineages.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 70, context: html, text, full: html, text

613458edda9014ed673838956868f75a9913cf96 Thu Mar 23 13:27:13 2023 -0700

Omicron persists past 2022, assume it's here for the decade.
- src/hg/utils/otto/sarscov2phylo/findDropoutContam.pl - lines changed 1, context: html, text, full: html, text

a5a4f89c3230564550036f73c9821617d3ab4bac Thu Mar 23 13:28:16 2023 -0700

No idea why I was skipping the first 3 lines of includeRecombinants.tsv rather than just the header line.
- src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh - lines changed 1, context: html, text, full: html, text

61b8f5004b8c9249e46f1b87fe9d34c369b97450 Thu Mar 23 13:30:50 2023 -0700

Adding some sequences for older proposed recombinants that would be removed from the tree by a harsher application of filters otherwise.
- src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv - lines changed 10, context: html, text, full: html, text

2d342c85706fa108decc142314c97c0a0564280b Thu Mar 23 20:10:22 2023 -0700

Fixing a few typos I spotted in code review. refs #30826
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/problematic.html - lines changed 1, context: html, text, full: html, text

cd2c57b40633f481b204fdd59b7e1ca212ecd04d Thu Mar 23 20:11:44 2023 -0700

Updating the very outdated Nextstrain Clade subtrack stanzas.
- src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - lines changed 436, context: html, text, full: html, text