Commits for kate

v398_preview to v398_preview2 (2020-04-27 to 2020-05-04) v398

96962227b59e566541cf63670087bbed487a4682 Mon Apr 27 15:37:26 2020 -0700

• Straighten out tables names wrt versioning and add track for GTEx Gene track update to V8 (final). refs #25130
  • src/hg/lib/gtexInfo.c - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/gtex/V8.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.gtex.ra - lines changed 12, context: html, text, full: html, text

832926811b278d5c656957e1565acdde48522def Mon Apr 27 17:59:12 2020 -0700

• Update GTEx gene track click handler and track settings to handle V8 (add Kidney Medulla tissue, support TPM and RPKM). refs #25130
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c - lines changed 9, context: html, text, full: html, text
  • src/hg/hgc/gtexClick.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgc/hgcData/gtexBoxplot.R - lines changed 17, context: html, text, full: html, text
  • src/hg/hgc/hgcData/gtexColorsV8.R - lines changed 119, context: html, text, full: html, text
  • src/hg/inc/gtexInfo.h - lines changed 3, context: html, text, full: html, text
  • src/hg/js/hgGtexTrackSettings.js - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/gtexInfo.c - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/gtexUi.c - lines changed 2, context: html, text, full: html, text

5de72d67529fe096500e1009c53a83afaec25b96 Mon Apr 27 18:26:26 2020 -0700

• Update GTEx Gene track description for V8. refs #25130
  • src/hg/makeDb/trackDb/human/gtexGeneV8.html - lines changed 176, context: html, text, full: html, text

1106b4995dcd8f12c168f50f44c7f724d8c0e901 Tue Apr 28 10:41:25 2020 -0700

• Update fibroblasts label as per GTEx V8 correction. refs #25130
  • src/hg/htdocs/images/gtexBodyMap.svg - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/images/gtexBodyMapPage.svg - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/images/gtexBodyMapSmall.svg - lines changed 1901, context: html, text, full: html, text

f0add51e132dbab425e76cabc6626a31a74f47e9 Tue Apr 28 12:29:40 2020 -0700

• Support TPM in GTEx V8 gene expression. refs #25130
  • src/hg/hgTracks/gtexTracks.c - lines changed 9, context: html, text, full: html, text
  • src/hg/hgc/hgcData/gtexColorsV8.R - lines changed 6, context: html, text, full: html, text

fa261bb6a4e20cb44972593d383589f1e5e4edce Tue Apr 28 12:34:02 2020 -0700

• Redo tissue table, bed file, and related code to slot new kidney medulla tissue in (assign id) in proper alphabetical order. refs #25130
  • src/hg/js/hgGtexTrackSettings.js - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/gtex/V8.txt - lines changed 14, context: html, text, full: html, text

f83fd868fdf1863c36526277c3168b98934b88d2 Tue Apr 28 12:34:38 2020 -0700

• Update GTEx Gene track description for V8. refs #25130
  • src/hg/makeDb/trackDb/human/trackDb.gtex.ra - lines changed 1, context: html, text, full: html, text

55d5984bc5dd9e1d382c811ee9284771925a16b2 Tue Apr 28 12:37:30 2020 -0700

• Assign score field based on tissue medians. refs #25130
  • src/hg/makeDb/doc/hg38/gtex.txt - lines changed 33, context: html, text, full: html, text

a57e43af4d3436c4017a4744b9595b0dcbcf3891 Tue Apr 28 14:06:58 2020 -0700

• Move hideEmptySubtracks control on UI, by request of Ana. refs #23365
  • src/hg/lib/hui.c - lines changed 29, context: html, text, full: html, text

d96751b9e97f16417a020a9f6356432e6d102bc1 Wed Apr 29 10:21:59 2020 -0700

• Correct tissue description, as per GTEx portal page for V8. refs #25130
  • src/hg/makeDb/doc/gtex/V6.txt - lines changed 14, context: html, text, full: html, text

9796c4d65f1f1fcd8eae91e158b68bbf8ee8698f Wed Apr 29 12:01:38 2020 -0700

• Add map box on entire gene graph for click to hgc. refs #25465
  • src/hg/hgTracks/gtexTracks.c - lines changed 8, context: html, text, full: html, text

e99bf5acd96a085eb5581d147209c6f2d5e63556 Wed Apr 29 12:07:09 2020 -0700

• Fixing compile err/warn and simplifying. Not fixing functionality if this is wrong ;-)
  • src/hg/hgTracks/bigBedTrack.c - lines changed 8, context: html, text, full: html, text

5a6e27dc415f2e6595086cbaf7e4027d5c29fcbe Wed Apr 29 12:09:25 2020 -0700

• Fixing merge conflict

bc2f747c9f09b2f50e0a3427e884ec34e936bf07 Wed Apr 29 16:44:24 2020 -0700

• Add question mark with mouseover explanation next to hide empty subtracks checkbox. refs #23365
  • src/hg/lib/hui.c - lines changed 3, context: html, text, full: html, text

a94079e43a772ac582ae64c12c1c66c4897aed09 Thu Apr 30 10:56:36 2020 -0700

• Updated transmission graphic and added two links requested by DavidH. refs #25217
  • src/hg/htdocs/covid19.html - lines changed 16, context: html, text, full: html, text

242d0a9e631b36a90103652c2947df0666843dc5 Thu Apr 30 10:56:55 2020 -0700

• Updated transmission graphic and added two links requested by DavidH. refs #25217
  • src/hg/htdocs/images/covid19-transmission.apr28_2020.nextstrain.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

1a4a1243ebec2eeef6d3dd005c8f6ece5d4b584f Thu Apr 30 12:08:25 2020 -0700

• A few more links from DH. refs #25217
  • src/hg/htdocs/covid19.html - lines changed 26, context: html, text, full: html, text

4da7f36cc07a5babf2a5dfb898f66f58199f1502 Mon May 4 09:12:51 2020 -0700

• Add two more links (NYT) by request of DH. refs #25217
  • src/hg/htdocs/covid19.html - lines changed 18, context: html, text, full: html, text