File Changes for angie

v418_preview to v418_preview2 (2021-07-12 to 2021-07-19) v418

• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 3, context: html, text, full: html, text
    f97456f7cdd92737b1c2ac14a0147b0c6a30c9e1 Mon Jul 12 16:30:53 2021 -0700
    Update single-subtree button label to indicate it's a subsampled global tree.
  • lines changed 93, context: html, text, full: html, text
    3fd9e9e8d0a977ee255486e60c785aef5689cc39 Tue Jul 13 09:42:47 2021 -0700
    Add summary table for results from pasted/uploaded IDs, to show lineages & subtree numbers, requested by Russ.
  • lines changed 58, context: html, text, full: html, text
    0e66591e44d669ef83fa016069b1ceb283c01800 Thu Jul 15 12:40:43 2021 -0700
    Support more flexible ID search: accessions without dot-versions and isolate names. When loading FASTA, detect sequence names that are numeric or already in the tree and add a prefix to prevent usher from rejecting the sequences.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 1, context: html, text, full: html, text
    0e66591e44d669ef83fa016069b1ceb283c01800 Thu Jul 15 12:40:43 2021 -0700
    Support more flexible ID search: accessions without dot-versions and isolate names. When loading FASTA, detect sequence names that are numeric or already in the tree and add a prefix to prevent usher from rejecting the sequences.
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 6, context: html, text, full: html, text
    82fa23eab37e677681978a8f4ffed9be2c553f8c Thu Jul 15 12:35:19 2021 -0700
    Detect missing single-subtree output (e.g. when usher rejects all sequences as already in the tree) and provide an error message with info for us to debug instead of crashing.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 12, context: html, text, full: html, text
    49566dc7263cab04bca529355999e4a4e7acfa78 Tue Jul 6 10:19:05 2021 -0700
    Update to latest Nextstrain clade coloring.
• src/hg/hgPhyloPlace/vcfFromFasta.c
  • lines changed 19, context: html, text, full: html, text
    0e66591e44d669ef83fa016069b1ceb283c01800 Thu Jul 15 12:40:43 2021 -0700
    Support more flexible ID search: accessions without dot-versions and isolate names. When loading FASTA, detect sequence names that are numeric or already in the tree and add a prefix to prevent usher from rejecting the sequences.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 8, context: html, text, full: html, text
    ed0c81dda84b8a3c690fba2c78e2662c5cd6940f Mon Jul 12 16:32:14 2021 -0700
    Exclude NCBI metadata for sequences that are not (yet) in fasta.
• src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh
  • lines changed 15, context: html, text, full: html, text
    fd68d9c62b0b68f005804457fd5934d0c10a70c8 Mon Jul 12 16:33:09 2021 -0700
    Add in country from GISAID sequence names (retaining spaces) to metadata.
  • lines changed 3, context: html, text, full: html, text
    77d911dafe3d0fefac4aa3f9e3b5982df129815f Tue Jul 13 09:43:39 2021 -0700
    join -a doesn't include placeholder columns when there is no matching line, so make output columns explicit; otherwise country can end up in clade column.
• src/hg/utils/otto/sarscov2phylo/gisaidNameToCountry.pl
  • lines changed 82, context: html, text, full: html, text
    2463467c57af3dff3d900a94ebed353bb5a749bd Mon Jul 12 16:33:25 2021 -0700
    Get GISAID country name from sequence names, correcting a few known typos and substituting Chinese cities/regions to China.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 13, context: html, text, full: html, text
    ab3504a9bc0e6077a70cdcefc29264833ced8126 Mon Jul 12 16:36:23 2021 -0700
    Add in sub-UK country to match COG-UK sequence names; correct outdated lineage names in lineages.metadata.csv; make alternate lineageToName file, still need to do comparison of using it.
  • lines changed 2, context: html, text, full: html, text
    2ba814d9a2b0df7bdc2cce0bb3e52464288a61bc Tue Jul 13 09:44:37 2021 -0700
    no need to run matUtils extract -u twice.
  • lines changed 73, context: html, text, full: html, text
    873bc700cc4fbedfa5164ba912f7e69adf80b127 Thu Jul 15 12:46:17 2021 -0700
    Use matUtils annotate's new -P/--clade-paths option to assign clades using curated path files instead of -c/--clade-names. It is much faster and allows manual correction of not-quite-right paths inferred by -c. It will also require manual updates (but so did ../lineageToName.newLineages) and will fail if the tree structure changes significantly.