File Changes for angie

v458_preview to v458_preview2 (2023-11-27 to 2023-12-04) v458

• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 45, context: html, text, full: html, text
    eeac40956b3dd6611f58aeb847ff5c404d3ce883 Fri Dec 1 09:05:41 2023 -0800
    Support trees whose reference/root is not from a db or hub, but rather a custom .2bit file. This means that the selected pathogen may or may not also be a db/hub, so the selection interacts with the db cart variable but does not always match it. Also, in phyloPlace.c, update RSV metadata column headers (RGCC lineages replace Ramaekers 2020 clades).
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 101, context: html, text, full: html, text
    eeac40956b3dd6611f58aeb847ff5c404d3ce883 Fri Dec 1 09:05:41 2023 -0800
    Support trees whose reference/root is not from a db or hub, but rather a custom .2bit file. This means that the selected pathogen may or may not also be a db/hub, so the selection interacts with the db cart variable but does not always match it. Also, in phyloPlace.c, update RSV metadata column headers (RGCC lineages replace Ramaekers 2020 clades).
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 1, context: html, text, full: html, text
    b0039dec371d7665e25e2e39b0e79d3e33ba50a1 Tue Nov 28 13:54:07 2023 -0800
    Fix amino acid translation to support transcipts that have UTR portions and skip noncoding transcripts.
  • lines changed 2, context: html, text, full: html, text
    eeac40956b3dd6611f58aeb847ff5c404d3ce883 Fri Dec 1 09:05:41 2023 -0800
    Support trees whose reference/root is not from a db or hub, but rather a custom .2bit file. This means that the selected pathogen may or may not also be a db/hub, so the selection interacts with the db cart variable but does not always match it. Also, in phyloPlace.c, update RSV metadata column headers (RGCC lineages replace Ramaekers 2020 clades).
• src/hg/hgPhyloPlace/phyloPlaceMain.c
  • lines changed 1, context: html, text, full: html, text
    eeac40956b3dd6611f58aeb847ff5c404d3ce883 Fri Dec 1 09:05:41 2023 -0800
    Support trees whose reference/root is not from a db or hub, but rather a custom .2bit file. This means that the selected pathogen may or may not also be a db/hub, so the selection interacts with the db cart variable but does not always match it. Also, in phyloPlace.c, update RSV metadata column headers (RGCC lineages replace Ramaekers 2020 clades).
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 18, context: html, text, full: html, text
    b0039dec371d7665e25e2e39b0e79d3e33ba50a1 Tue Nov 28 13:54:07 2023 -0800
    Fix amino acid translation to support transcipts that have UTR portions and skip noncoding transcripts.
  • lines changed 25, context: html, text, full: html, text
    ea80dbd18523cfb2ad1efd1306ac81d7e994f9c4 Fri Dec 1 09:01:56 2023 -0800
    Update RSV metadata for new clade system (RSV Genotyping Consensus Consortium lineages replace Ramaekers 2020 clades).
• src/hg/hgPhyloPlace/writeCustomTracks.c
  • lines changed 32, context: html, text, full: html, text
    eeac40956b3dd6611f58aeb847ff5c404d3ce883 Fri Dec 1 09:05:41 2023 -0800
    Support trees whose reference/root is not from a db or hub, but rather a custom .2bit file. This means that the selected pathogen may or may not also be a db/hub, so the selection interacts with the db cart variable but does not always match it. Also, in phyloPlace.c, update RSV metadata column headers (RGCC lineages replace Ramaekers 2020 clades).
• src/hg/hgTables/bigBed.c
  • lines changed 73, context: html, text, full: html, text
    259c477dd82ab1de43ddcf36f809a3bfe99a54da Mon Nov 27 14:29:32 2023 -0800
    In bigBedGetFilteredBedsOnRegions, use nameIndex when user pastes/uploads identifiers, so we don't time out on large bigBeds like dbSnp. refs #32625
• src/hg/lib/customTrack.c
  • lines changed 5, context: html, text, full: html, text
    ae327c5f42eddb3039d0c1b0182a61419b03c98f Fri Dec 1 09:23:18 2023 -0800
    When there is an error while loading customTracks, don't assume it's an unrecoverable file corruption problem; recently we have seen some out-of-mem and/or pthread_create issues. Don't remove the custom track file because it may be a saved session file shared by multiple sessions and users. Instead, ask the user to send us a session link. refs #32627
  • lines changed 7, context: html, text, full: html, text
    35104810b1eefd07d38383abefe90c24553cc146 Fri Dec 1 09:48:55 2023 -0800
    When loading of existing custom tracks fails, do not attempt to merge new custom tracks because we will lose all existing custom tracks. Leave the settings in the cart for next time. (forgot to include this in previous commit) refs #32627
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
  • lines changed 22, context: html, text, full: html, text
    6db87360227e298279ec6088c5e070f8c42e51b8 Tue Nov 14 17:11:45 2023 -0800
    Masking some additional locations in BA.2 (& onward), BA.2.86 and XCK.
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
  • lines changed 4, context: html, text, full: html, text
    3a74edab38d1a6e928729bc6b4feec3762ee2f40 Tue Nov 14 17:05:26 2023 -0800
    Don't offer uncompressed protobuf for download (only compressed). Also don't offer redundant .nextclade.pangolin version of same file.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
  • lines changed 2, context: html, text, full: html, text
    b80d731cca9f9a4b591fd60b7f6b1309e7a4cdbd Tue Nov 14 17:10:44 2023 -0800
    Added some more IDs by request.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 12, context: html, text, full: html, text
    f3be5b0f7ad0fd1efbef1057ae5ed3799efcf5f7 Tue Nov 14 17:13:41 2023 -0800
    A few new lineages and a couple corrections: BA.2.86.1 no longer requires that last mutation and it has a descendant without it. B.1.637 needed some refinement after tree work.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 8, context: html, text, full: html, text
    129db42d275d159115a7aef3d6377abb5d8e6c60 Tue Nov 14 17:08:20 2023 -0800
    Reduce number of threads for usher-sampled -- Cheng's suggestion after mysterious hang on 2023-10-05. Use new matUtils fix subcommand to get rid of annoying grandparent-reversions.
• src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
  • lines changed 2, context: html, text, full: html, text
    f1b5392d9fb6337cf2e2f9d55484a2950ebb3b37 Tue Nov 14 17:10:21 2023 -0800
    CNCB is now updating daily.