Commits for angie

v458_preview2 to v458_base (2023-12-04 to 2023-12-11) v458

0114df80d5034a730eeb50f04fca0afe73af3dce Tue Dec 5 13:51:41 2023 -0800

• When db is really a db/hub, use it as db not just refName.
  • src/hg/hgPhyloPlace/phyloPlaceMain.c - lines changed 8, context: html, text, full: html, text

f00ee8d8e407da35c50e5d61815250a49960dabe Tue Dec 5 13:52:12 2023 -0800

• More refinements for displaying RSV results. Still need to make it more config-driven.
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 47, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 8, context: html, text, full: html, text

e196e2966a9c192db0ae18a94623487dc2d73175 Thu Dec 7 13:34:30 2023 -0800

• chmod 775 instead of 755 so group members can update the /cluster/bin/scripts installation.
  • src/utils/newPythonProg/newPythonProg.c - lines changed 1, context: html, text, full: html, text

fe3f52d294f42461f732844e254e8f0caa8990ab Fri Dec 8 08:56:32 2023 -0800

• Adding a NULL check, HT braney in code review #32706
  • src/hg/hgTables/bigBed.c - lines changed 8, context: html, text, full: html, text

ff94dc36ad4584d7ccdeeb545b2b92825735d225 Fri Dec 8 09:55:19 2023 -0800

• If an auspiceMeta.json file is specified in config.ra then use it for organism-specific tree colors & filters. Also use CDS coords when writing genome annotations in Auspice output; not all viral genes are CDS-only.
  • src/hg/hgPhyloPlace/phyloPlace.h - lines changed 2, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 114, context: html, text, full: html, text