File Changes for angie

v421_base to v422_preview (2021-09-27 to 2021-10-04) v422

• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 163, context: html, text, full: html, text
    a6e1074250a8fdd5e952ab3ad7bd91705aa56222 Thu Sep 30 09:55:40 2021 -0700
    UI changes suggested by Mary Goldman: reorder elements, simplify, bigger fonts for headers.
• src/hg/utils/faToVcf/faToVcf.c
  • lines changed 71, context: html, text, full: html, text
    37ec02a06719324a9c6cb2b167893b9b0559fbdd Thu Sep 30 09:34:43 2021 -0700
    Added -windowSize and -minAmbigInWindow options to mask bases with too many Ns/ambigs/gaps within +-windowSize bases. Idea taken from Nicola De Maio and Rob Lanfear's mask_seq.py script in sarscov2phylo.
• src/hg/utils/otto/nextstrainNcov/doUpdate.sh
  • lines changed 1, context: html, text, full: html, text
    334b92a7d3c7c61af8ea9facbc7ec1c2442025fa Thu Sep 30 09:59:38 2021 -0700
    Update Nextstrain JSON URL.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 15, context: html, text, full: html, text
    7cef6a7083abdbdfb242575ccb0dcb7a73c42197 Thu Sep 30 09:58:01 2021 -0700
    New script usherClusterRun.sh for running usher on ku, merging & optimizing results instead of single hgwdev job.
• src/hg/utils/otto/sarscov2phylo/updatePublic.sh
  • lines changed 1, context: html, text, full: html, text
    d99de4326bbf1ad8e9461d8072622dd68597d277 Thu Sep 30 09:57:14 2021 -0700
    Invoke updateCombinedTree.sh with new arg for explicitly setting date.
• src/hg/utils/otto/sarscov2phylo/usherClusterRun.sh
  • lines changed 98, context: html, text, full: html, text
    7cef6a7083abdbdfb242575ccb0dcb7a73c42197 Thu Sep 30 09:58:01 2021 -0700
    New script usherClusterRun.sh for running usher on ku, merging & optimizing results instead of single hgwdev job.