Commits for angie

89d5c7e854fc4f5360852a5cb0657e20f962ae6a Thu Jan 22 15:22:07 2026 -0800

Some shortening of paths where auto-collapsing didn't work, some new lineages, and tweaks to QC.6 and XFG.4.1.5 because they were assigned to single sequences instead of the appropriate branches.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 76, context: html, text, full: html, text

de6c27b63c74c93c069030f93a2817b93bf71b8e Tue Mar 10 15:49:39 2026 -0700

Update lorax track iframeUrl to point to new lorax.ucsc.edu server
- src/hg/makeDb/trackDb/human/hg38/tgpArchive.ra - lines changed 1, context: html, text, full: html, text

9ed022cb1f0b16bc57c95a629a0abd4243e750cc Tue Mar 10 15:51:25 2026 -0700

New lineages, small corrections to RD.1.1.1 and PQ.25.2, new label for split lineage.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 12, context: html, text, full: html, text

2c7413be1d0412785eb7238454dacefc57de05bc Tue Mar 10 15:53:08 2026 -0700

Mask reversions caused by dropout in BA.3.2
- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml - lines changed 8, context: html, text, full: html, text

3397b75245fd2bfc21439e1568b1eac855739cd3 Tue Mar 10 15:54:38 2026 -0700

Adding several more sequences by request
- src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv - lines changed 12, context: html, text, full: html, text

7931c9562bb9808463e9b3ede322b0d415986de3 Wed Mar 11 10:37:13 2026 -0700

Made galGal6ToGCF_016699485.2.chainBridge.over.chain.gz for MLQ #37185
- src/hg/makeDb/doc/galGal6/lastzRuns.txt - lines changed 28, context: html, text, full: html, text

cbffb0dd48c0c9621532fd6d129845128c743655 Fri Mar 13 11:04:18 2026 -0700

Made hg19ToHg38.chainBridge.over.chain.gz for MLQ #37156
- src/hg/makeDb/doc/hg19.txt - lines changed 28, context: html, text, full: html, text