Commits for angie

99936258b0be1c69c8017993091ee6c6cb219119 Tue May 9 10:31:45 2023 -0700

Another hundred-odd new lineages and a couple minor corrections.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 145, context: html, text, full: html, text

01ad4bc701089c54f7a738b808eab4f422740b60 Wed May 24 10:52:15 2023 -0700

Added XBB.2.9 -- pango-designation v1.20. Add BA.4_dropout, BA.5_dropout, XBB_dropout to catch more of those in pangolin. Corrected paths to Q.4, BA.5.2.62, XC. Add more Ns to B.1.1.529_dropout since a lot of intermediate nodes went away with cleanup.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 8, context: html, text, full: html, text

52cebd83cd791590bbd74bbae30df228dc4b8244 Wed May 24 10:58:24 2023 -0700

Different representative for XBB - nodes have been shuffled around a bit.
- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml - lines changed 1, context: html, text, full: html, text

4d771afe20833a75ac19216081a730846bb4bb5f Wed May 24 10:59:03 2023 -0700

Run more things in parallel where possible.
- src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh - lines changed 19, context: html, text, full: html, text

3e8756ab36ff31538dfc529aca39f9c8ef720e31 Wed May 24 11:00:45 2023 -0700

More new lineages.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 9, context: html, text, full: html, text

693b252e4597e0d97badea0f19b9836ded21ddae Wed May 24 11:02:16 2023 -0700

Added 23A, 23B.
- src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv - lines changed 2, context: html, text, full: html, text

7106942562801f0a7a7c9dc4c101c9f7e8afc1a8 Fri May 26 15:55:20 2023 -0700

User reported in MLQ #31322 that axtChain gave fewer results for fasta inputs than for 2bit inputs. It turned out to be an almost 20-year-old bug that we never noticed because we always use 2bit: loadFaSeq mimiced the strand-change detection logic in loadIfNewSeq but ignored the fact that loadIfNewSeq gets a fresh new sequence on the + strand every time the name changes, and only compares to the previous value of strand when the sequence name has not changed. Instead of unsuccessfully mimicing that code, just let the caller reverse-complement the sequence when strand is - and then restore it to + strand after use.
- src/hg/mouseStuff/axtChain/axtChain.c - lines changed 30, context: html, text, full: html, text