Commits for max

v438_preview to v438_preview2 (2022-09-26 to 2022-10-03) v438

ecc936e1b2c4bf8fbd37e1dc6bbc616b947c369e Tue Sep 27 07:29:58 2022 -0700

• fixing small typo in spUniprot track, no redmine, just saw this
  • src/hg/makeDb/trackDb/ebola/eboVir3/spUniprot.html - lines changed 2, context: html, text, full: html, text

80def04a3a6e24537a0669ecc0d61b189457bd62 Thu Sep 29 05:29:54 2022 -0700

• adding UK Biobank depletion rank score track, refs #30070
  • src/hg/makeDb/doc/hg38/ukbDepletion.txt - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/constraintSuper.html - lines changed 41, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/constraintSuper.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/ukbDepletion.ra - lines changed 18, context: html, text, full: html, text

baa7c0f9f1c8d08da187dc9ce180e448d802bd39 Thu Sep 29 05:32:10 2022 -0700

• cleaning up UK Biobank depletion rank score trackdb, and removing HMC pennant icon, refs #30070
  • src/hg/makeDb/trackDb/human/hmc.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/ukbDepletion.ra - lines changed 8, context: html, text, full: html, text

30121498c6fa71d6fe94a21d48c63130dd370572 Thu Sep 29 06:39:51 2022 -0700

• last author suggests to add deCODE to uk biobank score, refs #30070
  • src/hg/makeDb/trackDb/human/ukbDepletion.ra - lines changed 2, context: html, text, full: html, text

914384264d6d019d05db34ceec0e0ce8ddc9d8e3 Fri Sep 30 02:09:13 2022 -0700

• fixing monkeyprimer primer 102 manually, arg, refs #30010
  • src/hg/makeDb/doc/mpxvRivers/pcrAmplicon.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/mpxvRivers/pcrAmplicon.html - lines changed 2, context: html, text, full: html, text

bf8c83cb36f5e791e4c0fc9eeefe715cc06b1c80 Fri Sep 30 02:42:13 2022 -0700

• adding recombination track to SARS-CoV-2, refs #30074
  • src/hg/makeDb/doc/wuhCor1/recomb.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/recomb.html - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 9, context: html, text, full: html, text

09caafffbfa1ca9b04f613b6db5223aede591180 Fri Sep 30 02:51:14 2022 -0700

• trying to move to bottom of browser image, refs #30074
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 19, context: html, text, full: html, text

c92f7b90d84743f704b29b131f7bf4e33aefb2f5 Fri Sep 30 02:53:36 2022 -0700

• making recomb in wuCor1 a bit smaller, refs #30074
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 1, context: html, text, full: html, text

f3b0f36ba4671a8315afc12ec2eacf5e4c6b75c3 Fri Sep 30 03:13:20 2022 -0700

• adding monkeypox transcriptomic stage track, refs #30074
  • src/hg/makeDb/autoSql/viralzone.as - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/mpxvRivers/viralzoneGenes.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/mpxvRivers/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/mpxvRivers/viralzone.html - lines changed 70, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/mpxvRivers/viralzone.ra - lines changed 18, context: html, text, full: html, text

37720f2ddc791da76c5f08fd33bc0a81dba783cb Fri Sep 30 06:10:49 2022 -0700

• adding doWiggle to tagTypes, no idea how that was missing... apparently we have no single track that uses it, no redmine
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text

633b963290422cb3bbfbe3c7970f1e960473292e Fri Sep 30 08:31:55 2022 -0700

• small changes to the monkeypox browser trackDb, no redmine
  • src/hg/makeDb/trackDb/virus/mpxvRivers/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/mpxvRivers/viralzone.ra - lines changed 8, context: html, text, full: html, text

f94190412d16ea558ace1ec9ea175db39aaa104b Fri Sep 30 08:40:43 2022 -0700

• panelApp otto job, refs #25568
  • src/hg/makeDb/trackDb/human/hg19/panelAppTracks.html - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/panelAppTracks.html - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/panelApp.html - lines changed 43, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/panelApp/cnv.as - lines changed 37, context: html, text, full: html, text
  • src/hg/utils/otto/panelApp/cnv.py - lines changed 200, context: html, text, full: html, text
  • src/hg/utils/otto/panelApp/genes.as - lines changed 41, context: html, text, full: html, text
  • src/hg/utils/otto/panelApp/genes.py - lines changed 425, context: html, text, full: html, text
  • src/hg/utils/otto/panelApp/makefile - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/otto/panelApp/tandRep.as - lines changed 44, context: html, text, full: html, text
  • src/hg/utils/otto/panelApp/tandRep.py - lines changed 223, context: html, text, full: html, text
  • src/hg/utils/otto/panelApp/test.py - lines changed 447, context: html, text, full: html, text
  • src/hg/utils/otto/panelApp/updatePanelApp - lines changed 91, context: html, text, full: html, text

c4e4f05177a63a6d7a4e42c87c54d676f2d54b73 Fri Sep 30 08:41:25 2022 -0700

• removing test file committed by mistake, no redmine
  • src/hg/utils/otto/panelApp/test.py - lines changed 447, context: html, text, full: html, text

b699b06e04864f35702fbb42cbd20fdf9e67420c Fri Sep 30 08:42:24 2022 -0700

• panelApp trackDb file, refs #25568
  • src/hg/makeDb/trackDb/human/panelApp.ra - lines changed 52, context: html, text, full: html, text

88d86eb7a11bad9d37c6908d3ab5e5c2e1fc1273 Mon Oct 3 03:39:03 2022 -0700

• updating panelApp otto, refs #25568
  • src/hg/utils/otto/panelApp/genes.py - lines changed 52, context: html, text, full: html, text

6f12bc42ce58df255b9bb28320ab29b0956b12c2 Mon Oct 3 04:24:27 2022 -0700

• adding publications field to panelapp, refs #25568
  • src/hg/makeDb/trackDb/human/panelApp.ra - lines changed 1, context: html, text, full: html, text