File Changes for angie

v418_base to v419_preview (2021-07-26 to 2021-08-02) v419

• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 17, context: html, text, full: html, text
    d903a7409978ea81cc0f2e6e34687319f7d9d222 Wed Jul 28 15:50:24 2021 -0700
    When extracting samples from the tree with matUtils, add the new --usher-clades-txt option and create empty placementInfo's to hold the results of parsing clades.txt so we can show clades/lineages according to the tree in the result summary table.
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
  • lines changed 103, context: html, text, full: html, text
    3feec259f20a7cc03affb9fae613492486bdd91a Wed Jul 28 15:41:37 2021 -0700
    Move out the extraction of the public-sequences-only tree from the combined tree into a separate script for ease of manually continuing runs when there's a failure (most often matUtils annotate -P failing due to a changed path in the tree).
• src/hg/utils/otto/sarscov2phylo/gisaidNameToCountry.pl
  • lines changed 2, context: html, text, full: html, text
    632628f9f28b14ca87d07d4baff47822579a5eb1 Wed Jul 28 15:40:58 2021 -0700
    Clean up stripping of trailing \r\n - code review, thx Jonathan.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 79, context: html, text, full: html, text
    3feec259f20a7cc03affb9fae613492486bdd91a Wed Jul 28 15:41:37 2021 -0700
    Move out the extraction of the public-sequences-only tree from the combined tree into a separate script for ease of manually continuing runs when there's a failure (most often matUtils annotate -P failing due to a changed path in the tree).