File Changes for angie

v419_base to v420_preview (2021-08-16 to 2021-08-23) v420

• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 10, context: html, text, full: html, text
    54ca6218fe814ea456902835cc107d50dec93f80 Thu Aug 19 17:06:39 2021 -0700
    Instead of complaining when a protobuf has mutations that appear in the problematic sites file, just remove those sites from the set of sites to mask because they were not masked (yet) when the protobuf was created. It's better to be consistent, and not spam the user with warnings caused by the Problematic Sites track being newer than the selected tree.
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 1, context: html, text, full: html, text
    81d541d9b6147b2a699ca84b2f450825fb489802 Mon Aug 16 15:23:18 2021 -0700
    Removing -l (--retain-input-branch-lengths) option from usher because it causes all-0 lengths in subtrees (& wasn't necessary in the first place) -- reported to Russ by user.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 2, context: html, text, full: html, text
    6aef35d07511c6edd9f656fd2d9d0cf95212d3e5 Wed Aug 18 17:13:49 2021 -0700
    Reverse child order in Auspice JSON output so that root of tree usually won't collide with the legend.
• src/hg/makeDb/doc/wuhCor1/phylogenetics.txt
  • lines changed 2, context: html, text, full: html, text
    e1e82df47c6536c27af380103fd0bdcb87fcbe4d Mon Aug 16 15:24:37 2021 -0700
    Updated Problematic Sites track.
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
  • lines changed 54, context: html, text, full: html, text
    95c99e66b78b8b8c4e26bb1ea91a0113d64caf04 Thu Aug 19 11:54:39 2021 -0700
    matUtils annotate -P fails too often because of little changes in the tree that affect which mutations are collapsed into the same code (or not). More sophisticated path-finding logic in matUtils could help with that, but until then, use the previous day's clade assignments as input for matUtils annotate -c for the big tree, and use the big tree's clade assignments as input for -c for the public-only tree.
  • lines changed 13, context: html, text, full: html, text
    60cefbcaddbd1627848c16242aa8145a5186e6a4 Thu Aug 19 20:28:13 2021 -0700
    Use matUtils extract's new option to write protobuf for the awesome Taxodium viewer (cov2tree.org); add it to public downloads.
• src/hg/utils/otto/sarscov2phylo/getCogUk.sh
  • lines changed 20, context: html, text, full: html, text
    3d8092305bf17c5c01713c6ed9b6ba3c289dd8ef Thu Aug 19 11:40:27 2021 -0700
    Add retries for NCBI and COG-UK fetches to get around sporadic network errors.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 1, context: html, text, full: html, text
    acc58669e6546b8705ab44c76add237111279610 Mon Aug 16 15:30:22 2021 -0700
    Use unzip -o (overwrite) so reruns don't get hung up on a prompt.
  • lines changed 20, context: html, text, full: html, text
    3d8092305bf17c5c01713c6ed9b6ba3c289dd8ef Thu Aug 19 11:40:27 2021 -0700
    Add retries for NCBI and COG-UK fetches to get around sporadic network errors.
• src/hg/utils/otto/sarscov2phylo/searchAllSarsCov2BioSample.sh
  • lines changed 1, context: html, text, full: html, text
    67217b614063c0bf07f4b5b69f0705d0125e32b4 Mon Aug 16 15:31:07 2021 -0700
    Wow, 1 million seemed like such a high ceiling once... but GenBank has more than that number of SARS-CoV-2 genomes now\!
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 37, context: html, text, full: html, text
    95c99e66b78b8b8c4e26bb1ea91a0113d64caf04 Thu Aug 19 11:54:39 2021 -0700
    matUtils annotate -P fails too often because of little changes in the tree that affect which mutations are collapsed into the same code (or not). More sophisticated path-finding logic in matUtils could help with that, but until then, use the previous day's clade assignments as input for matUtils annotate -c for the big tree, and use the big tree's clade assignments as input for -c for the public-only tree.
  • lines changed 11, context: html, text, full: html, text
    60cefbcaddbd1627848c16242aa8145a5186e6a4 Thu Aug 19 20:28:13 2021 -0700
    Use matUtils extract's new option to write protobuf for the awesome Taxodium viewer (cov2tree.org); add it to public downloads.