Commits for angie

v465_preview to v465_preview2 (2024-04-29 to 2024-05-06) v465

7e6a7ad1f3194e32d9af0a87aff074aa01a859d3 Mon Apr 22 14:16:28 2024 -0700

• Added more sites by request, including new branch GE.1.2.1.
  • src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml - lines changed 10, context: html, text, full: html, text

705420e703b067fbcad43ab67ed3e131552e7ac8 Wed Apr 24 14:23:03 2024 -0700

• Pathogen drop-down choices can now be groups of references/trees, for example 'Dengue (types 1 - 4)' instead of a separate choice for each type. Instead of config.ra, each group has an organism.ra and subdirectories named after reference accessions that contain reference.ra files. nextclade sort is used to match the user's uploaded sequences against available references for the selected pathogen. SARS-CoV-2, M. tuberculosis and hMPXV still have only one reference and still use config.ra, but RSV, Dengue and Influenza will become groups. Presentation is still kinda rough, just a loop on the original results output. The server commands part needs testing and will not work yet for groups (currently used only for SARS-CoV-2).
  • src/hg/hgPhyloPlace/hgPhyloPlace.c - lines changed 168, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 563, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlace.h - lines changed 45, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlaceMain.c - lines changed 10, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/runUsher.c - lines changed 51, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 8, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/vcfFromFasta.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/writeCustomTracks.c - lines changed 4, context: html, text, full: html, text

da3772f3615ae3aa407af6aa2215a1b2ff480183 Mon Apr 29 13:40:41 2024 -0700

• If configured, use nextclade to align sequences (better for more diverged viruses like influenza). Also fix some buttons that the last change broke.
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 19, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlace.h - lines changed 4, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/vcfFromFasta.c - lines changed 376, context: html, text, full: html, text

834653e22227fcea282e12a48910bb73068b34df Mon Apr 29 15:33:06 2024 -0700

• Don't depend on having a PSL alignment for the results table, precompute the same values whether aligning with gf/blat or nextclade.
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 19, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlace.h - lines changed 4, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/vcfFromFasta.c - lines changed 20, context: html, text, full: html, text

eed992e6dfb41dffe0102882d47300c904aaf1de Mon Apr 29 19:17:50 2024 -0700

• When multiple reference sequences are matched, sort them alphabetically by description.
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 91, context: html, text, full: html, text

e2d2b97265d31fb70bbc473306eac28305d94a0e Tue Apr 30 08:30:48 2024 -0700

• New lineages -- up to pango-designation release v1.27.
  • src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 74, context: html, text, full: html, text

09ba8a42df0be5b65518715f8f499e4ac965a4ef Tue Apr 30 11:10:37 2024 -0700

• When multiple references are matched, make navigation links at the top of the results page.
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 18, context: html, text, full: html, text