File Changes for angie

v466_preview to v466_preview2 (2024-05-20 to 2024-05-27) v466

• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 2, context: html, text, full: html, text
    1d72deb939d79331f80c9fffc1bef03d3c284186 Tue May 21 13:08:04 2024 -0700
    Updating a couple instances of db-->org that I missed previously.
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 127, context: html, text, full: html, text
    0b186effb2d2b536d2c280ec31bec6e153e6bd7e Tue May 21 13:26:39 2024 -0700
    Add support for uploaded names/IDs for the multi-ref/tree organism.ra case. Add new config option anchorSamples, pass to usher-sampled/matUtils/server if present. anchorSamples is a file with names of sequences that should always be included in the subtree to provide some larger-scale context, e.g. well-known vaccine or reference material strains. Influenza user request.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 3, context: html, text, full: html, text
    0b186effb2d2b536d2c280ec31bec6e153e6bd7e Tue May 21 13:26:39 2024 -0700
    Add support for uploaded names/IDs for the multi-ref/tree organism.ra case. Add new config option anchorSamples, pass to usher-sampled/matUtils/server if present. anchorSamples is a file with names of sequences that should always be included in the subtree to provide some larger-scale context, e.g. well-known vaccine or reference material strains. Influenza user request.
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 32, context: html, text, full: html, text
    0b186effb2d2b536d2c280ec31bec6e153e6bd7e Tue May 21 13:26:39 2024 -0700
    Add support for uploaded names/IDs for the multi-ref/tree organism.ra case. Add new config option anchorSamples, pass to usher-sampled/matUtils/server if present. anchorSamples is a file with names of sequences that should always be included in the subtree to provide some larger-scale context, e.g. well-known vaccine or reference material strains. Influenza user request.
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
  • lines changed 9, context: html, text, full: html, text
    99b4f6868e8f0fad4985f6e94e46908eeb744ffe Tue May 21 13:28:45 2024 -0700
    Adding a few more requested sites.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 21, context: html, text, full: html, text
    ac192b6e6f18b63359e0aa30bf096e6883b85588 Thu May 23 13:51:34 2024 -0700
    More new lineages; JN.1.33 redesignated to JN.1.39.3; correction to XDV path.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 17, context: html, text, full: html, text
    19b943548e4c4987365430f090582cc0061156b9 Tue May 21 13:31:43 2024 -0700
    Generate memory-mapped hash tables for metadata and name lookup.