Commits for angie

v413_preview to v413_preview2 (2021-03-29 to 2021-04-05) v413

9c4b7225d91f5180fcddbecd843b71c4e6503688 Tue Mar 30 10:39:22 2021 -0700

• Add subtree JSON URLs to single-subtree JSON, using Auspice's new url attribute. Allow up to 1000 VCF samples and extend timeout to 15 minutes.
  • src/hg/hgPhyloPlace/hgPhyloPlace.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 22, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlace.h - lines changed 2, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 26, context: html, text, full: html, text

5f3f4e801929d38e98550dc8df784043ff1d8f75 Tue Mar 30 11:55:05 2021 -0700

• Show amino acid back-mutations, not only amino acid differences from reference.
  • src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 12, context: html, text, full: html, text

abdea7a81b3d511adaee6300277721a804f5581f Tue Mar 30 11:57:47 2021 -0700

• Ongoing fixes for odd characters in sequence names and other pipeline tweaks.
  • src/hg/utils/otto/sarscov2phylo/getNcbi.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh - lines changed 19, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/updatePublic.sh - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/util.sh - lines changed 1, context: html, text, full: html, text

cbf33d2dcdd87c41ee8e1afe0ff738c62422bf77 Tue Mar 30 16:01:54 2021 -0700

• Only search for nearest neighbor and neighboring lineage once; then use it in summary table, details output, and now also TSV output. Also set parBase in sncList for TSV output (oops).
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 108, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlace.h - lines changed 3, context: html, text, full: html, text

917b546813930bf7583bdb7e2b34c46c70729942 Tue Mar 30 16:34:10 2021 -0700

• Add option to label branches by only Spike mutations in Nextstrain/Auspice.
  • src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 12, context: html, text, full: html, text

91f8a9abf3dcd3f2209bebbd53c2dc89875cfc37 Wed Mar 31 16:55:15 2021 -0700

• Don't use '.' in track names... triggers bugs in hgTables, hgTracks.js.
  • src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.ra - lines changed 8, context: html, text, full: html, text