File Changes for angie

v420_base to v421_preview (2021-09-07 to 2021-09-13) v421

• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 6, context: html, text, full: html, text
    1813d94a8d9108b9709cb48166b4980d0f02d839 Wed Sep 8 12:02:05 2021 -0700
    Add coloring options for Nextstrain clade and Pango lineage assigned by usher (really by matUtils annotate) if metadata includes columns for those.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 4, context: html, text, full: html, text
    1813d94a8d9108b9709cb48166b4980d0f02d839 Wed Sep 8 12:02:05 2021 -0700
    Add coloring options for Nextstrain clade and Pango lineage assigned by usher (really by matUtils annotate) if metadata includes columns for those.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 12, context: html, text, full: html, text
    15b84072ef48791ec41cb031ef351997c3dee4d7 Tue Sep 7 15:15:17 2021 -0700
    Added a new branch label option: back-mutations to reference, to highlight problematic parts of the tree.
  • lines changed 78, context: html, text, full: html, text
    1813d94a8d9108b9709cb48166b4980d0f02d839 Wed Sep 8 12:02:05 2021 -0700
    Add coloring options for Nextstrain clade and Pango lineage assigned by usher (really by matUtils annotate) if metadata includes columns for those.
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
  • lines changed 7, context: html, text, full: html, text
    4efa4aebadc39cb64a256c3489035b00bd2abdc6 Wed Sep 8 12:06:50 2021 -0700
    Remove dependency on reference.fa from aligning new sequences; add tree-annotated Nextstrain clade and Pango lineage to metadata.
• src/hg/utils/otto/sarscov2phylo/fixNcbiFastaNames.pl
  • lines changed 4, context: html, text, full: html, text
    2ae2c57f81bed91b2474771b896de8bc885b6b21 Wed Sep 8 12:04:46 2021 -0700
    Don't prepend country and append year if isolate name (e.g. from BioSample) already includes those.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 29, context: html, text, full: html, text
    4efa4aebadc39cb64a256c3489035b00bd2abdc6 Wed Sep 8 12:06:50 2021 -0700
    Remove dependency on reference.fa from aligning new sequences; add tree-annotated Nextstrain clade and Pango lineage to metadata.
• src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh
  • lines changed 107, context: html, text, full: html, text
    39d3f511f6022a1b86ba79a68b19b3878e50db89 Wed Sep 8 12:07:05 2021 -0700
    New script for generating lineageTree.pb used by pangolin --usher: re-root big tree to lineage A, generate random-representative subtrees, test & pick least discordant tree.