Commits for braney

v483_preview to v483_preview2 (2025-05-26 to 2025-06-02) v483

9cb1efe7ba7f45e80faf3c9a9c6af3833cbae850 Fri May 23 12:27:32 2025 -0700

• add bedMethyl.html skeleton so gitFiles will return it
  • src/hg/htdocs/goldenPath/help/bedMethyl.html - lines changed 92, context: html, text, full: html, text

6ff14cbe503f6d3b20d61308887dc91a692ec507 Wed May 28 09:21:47 2025 -0700

• fix some problems with quickLift reported by QA refs #35609
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 24, context: html, text, full: html, text
  • src/hg/inc/hui.h - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 24, context: html, text, full: html, text

99d93d87504dd96cb48f7730ca1162c2c94ffc82 Wed May 28 09:23:28 2025 -0700

• bedMethyl custom track factory
  • src/hg/lib/customFactory.c - lines changed 138, context: html, text, full: html, text

0edefc9983679d6bbee96ccc100f7d41921def00 Wed May 28 12:25:49 2025 -0700

• working on track visibilities after quickLift
  • src/hg/hgConvert/hgConvert.c - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 77, context: html, text, full: html, text

a885499d72f17dc8e16c629312a9b194aad7fc88 Fri May 30 12:05:41 2025 -0700

• let individual sandboxs opt out of captcha
  • src/hg/lib/cart.c - lines changed 1, context: html, text, full: html, text

b01267e746a100118ca7045113d78b5fa588e685 Fri May 30 17:10:30 2025 -0700

• when a composite has dense tracks the way we deal with center labels the draw routine leaves grek in the track when the decenders of the center label have been drawn even though the center label is not actually drawn, but hidden via CSS. Now in this condition we're drawing slightly smaller fonts for the center labels so they don't exceed the drawing box. refs #29500
  • src/hg/hgTracks/hgTracks.c - lines changed 12, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 3, context: html, text, full: html, text

8165601dddc27978eb4a2fe2654ba81212e30473 Sat May 31 11:46:07 2025 -0700

• hgGene changes for quickLift
  • src/hg/hgGene/hgGene.c - lines changed 45, context: html, text, full: html, text
  • src/hg/hgGene/hgGene.h - lines changed 1, context: html, text, full: html, text
  • src/hg/hgGene/links.c - lines changed 9, context: html, text, full: html, text
  • src/hg/hgGene/pathways.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgGene/sequence.c - lines changed 33, context: html, text, full: html, text

83ccf1c6b15c91b83723894b882f3af1e340882b Sun Jun 1 16:37:23 2025 -0700

• exon frames are in transcription strand order so if it's changed during quickLift we need to flip the order in the genePred
  • src/hg/hgTracks/bigBedTrack.c - lines changed 8, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 10, context: html, text, full: html, text
  • src/hg/inc/genePred.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/genePred.c - lines changed 15, context: html, text, full: html, text