Commits for angie

v409_preview2 to v409_base (2021-01-11 to 2021-01-18) v409

1dc0d205786891dc35074276f3a64ca436b09221 Mon Jan 11 16:36:27 2021 -0800

• As for -detailed, don't print summary at end for -veryDetailed output so it's more pipeline-friendly.
  • src/utils/faSize/faSize.c - lines changed 1, context: html, text, full: html, text

9328f9679316e58caa157cbb591ab022ad4874d9 Tue Jan 12 10:38:13 2021 -0800

• A little more cleanup: regenerate protobufs with updated names.
  • src/hg/makeDb/doc/wuhCor1/phylogenetics.txt - lines changed 19, context: html, text, full: html, text

ed89e722713f45eba35f9a7f08c3ff58c1385bf1 Tue Jan 12 10:39:00 2021 -0800

• Comment tweaks
  • src/hg/utils/otto/sarscov2phylo/publicCredits.sh - lines changed 4, context: html, text, full: html, text

9a1dd73f2df69278e2b5ab8c62d531205ab87845 Tue Jan 12 12:12:46 2021 -0800

• As for wiggle, make bigWig's viewLimits min and max come from the data. (Fun fact: viewLimitsMax is implemented only for composites. It should come from the data anyway).
  • src/hg/lib/wiggleCart.c - lines changed 19, context: html, text, full: html, text

2b17a440f0e380ac166a0df8dc99aa09fef70400 Tue Jan 12 17:24:31 2021 -0800

• Update sarsCov2PhyloPub with release alpha to include only subtracks with all public sequences (omit subset shared w/GISAID). Add sarsCov2PhyloPubParsimony track. refs #26804, #26805
  • src/hg/makeDb/trackDb/virus/wuhCor1/sarsCov2PhyloPubParsimony.html - lines changed 88, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 67, context: html, text, full: html, text

5696c2a99447dd591aef26258f4dbef57e4e5d82 Thu Jan 14 15:39:40 2021 -0800

• Nextstrain added new year-letter clades, and their JSON no longer includes the old clades; update script and subtrack stanzas.
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - lines changed 260, context: html, text, full: html, text
  • src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 36, context: html, text, full: html, text
  • src/hg/utils/otto/nextstrainNcov/nextstrainClade.as - lines changed 1, context: html, text, full: html, text