Commits for lrnassar

v468_base to v469_preview (2024-07-15 to 2024-07-22) v469

f5049df8ae200c8c0056bc88dfc41696d03f95f0 Mon Jul 15 13:22:55 2024 -0700

• Removing the gi domain since it isn't under our control as asked by Erich.
  • src/utils/qa/checkHTTPS - lines changed 1, context: html, text, full: html, text

a99ca8e7ccf4b4eedd8de9c343690e85e6e1d26b Tue Jul 16 13:03:29 2024 -0700

• Sqashing old pennantIcons.
  • src/hg/makeDb/trackDb/human/abSplice.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/bayesDel.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/predictionScoresSuper.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.public.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gnomad.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/jaspar.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/jaspar.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/jaspar.ra - lines changed 2, context: html, text, full: html, text

a26e6bfa1bc310a809138e7c39bdcf5ea29a79ef Tue Jul 16 17:13:07 2024 -0700

• Nesting OMIM into a single superTrack, refs #25682
  • src/hg/makeDb/trackDb/human/omim.alpha.ra - lines changed 83, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/omim.ra - lines changed 73, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/omimContainer.html - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 77, context: html, text, full: html, text

c0ddfaebb3c2a75261a4400ab688340d51ce425e Wed Jul 17 15:41:57 2024 -0700

• Tweaking maxItems to a value that works reasonably well without turning the track off due to vertical limit. Refs #33767
  • src/hg/makeDb/trackDb/human/hg19/reMap.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/reMap.ra - lines changed 1, context: html, text, full: html, text

b30321dea90350bcc8f184f9d40f3b5f41411433 Wed Jul 17 16:05:37 2024 -0700

• Raising maxItems back to 10k after Braney's new change #34127 that allows for bigger track heights, refs #33767
  • src/hg/makeDb/trackDb/human/hg19/reMap.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/reMap.ra - lines changed 2, context: html, text, full: html, text

7732bcfe0414219fc9642b42118aa2632dd59ab8 Wed Jul 17 16:54:16 2024 -0700

• Revert "remove include refSeqComposite.ra from higher level definitions refs #34008" This reverts commit 55cdc0578ebe3463380c79c1913c8386e80856f9.
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/trackDb.ra - lines changed 12, context: html, text, full: html, text

cfda5d697701c33ce782310b6343ad3469791620 Wed Jul 17 17:08:36 2024 -0700

• Doing some refSeq surgery to fix mm9 issue on #34008. Essentially it was OK to have human include at that level - which allowed for an override at the species level. The reason for these overrides is Terrence asked us to make ncbiRefSeq (refseq all) the default on all organisms other than human and mouse. Having the addition at the hg38/hg19 level would mean duplicating the entire trackDb stanza in ncbiRefseqComposite.ra. For mouse, however, mm9 was having a conflict with the addition at the mouse level. So I moved mm10 and mm39 to have a new file at the mouse level and removed the mouse include. Refs #34008
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/refSeqComposite.mm10.mm39.ra - lines changed 206, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/trackDb.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/refSeqComposite.ra - lines changed 1, context: html, text, full: html, text

505da6cd60ae9dc005b085a2e713ccbf4e7e808a Thu Jul 18 09:31:36 2024 -0700

• Adding a dbSNP search example to the query page. Refs #34128
  • src/hg/htdocs/goldenPath/help/query.html - lines changed 3, context: html, text, full: html, text

5606e66bdcb63689fd37f9b653088a0551f2e239 Fri Jul 19 16:03:14 2024 -0700

• Adding a link to MANE desc page to let people know we have an archive with the previous versions, refs #27524
  • src/hg/makeDb/trackDb/human/hg38/mane.html - lines changed 4, context: html, text, full: html, text

41c63e4b0795abf47b9fcbaf7554da7f50741ad5 Fri Jul 19 16:29:55 2024 -0700

• Sprucing up the cite.html page with general improvements and organization, refs #31996
  • src/hg/htdocs/cite.html - lines changed 49, context: html, text, full: html, text

772e9b6cbf1a55065db077535c2b9a8cb2dc42bf Fri Jul 19 16:44:51 2024 -0700

• Clarifying search text, the rsID results in multiple hits and the rsID is a location and not a variant, refs #34128
  • src/hg/htdocs/goldenPath/help/query.html - lines changed 1, context: html, text, full: html, text

1a59b509cebd53b0e7f2d322fd0fb46586f53840 Fri Jul 19 18:38:05 2024 -0700

• Restructuring some of the menus based on feedback, refs #33509
  • src/hg/htdocs/goldenPath/newsarch.html - lines changed 4, context: html, text, full: html, text
  • src/hg/htdocs/inc/gbFooterHardcoded.html - lines changed 8, context: html, text, full: html, text
  • src/hg/htdocs/inc/gbPageStartHardcoded.html - lines changed 14, context: html, text, full: html, text
  • src/hg/htdocs/inc/gbsFooter.html - lines changed 7, context: html, text, full: html, text
  • src/hg/htdocs/inc/globalNavBar.inc - lines changed 14, context: html, text, full: html, text
  • src/hg/htdocs/util.html - lines changed 11, context: html, text, full: html, text