Commits for jnavarr5

v504_base to v505_preview (2026-09-21 to 2026-10-05) v505

983d1e972217fb20781724d2cec9dfaec6fa96af Mon Sep 21 17:48:17 2026 -0700

• Removing the release tags for the cactus mouse strains track, refs #38308
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 1, context: html, text, full: html, text

b6ba7ab70c14692cd2cad15a17fb9b605f0efe1e Fri Sep 25 13:13:09 2026 -0700

• Updating the longLabel to sentence case, refs #38112 #38371
  • src/hg/makeDb/trackDb/human/hg38/episignatures.ra - lines changed 1, context: html, text, full: html, text

70ec78b7ef15cc060932b5b8dd436fd34bcbdaf1 Fri Sep 25 13:31:22 2026 -0700

• Adding a paragraph about a filtering issue that happens when there is a tie in the absolute max value. refs #38112
  • src/hg/makeDb/trackDb/human/hg38/epigenCentral.html - lines changed 7, context: html, text, full: html, text

1aca3edb987bc90a17be6a22efad5446d4e42029 Fri Sep 25 13:44:48 2026 -0700

• Updating the packmode labels to show the episignature instead of the CpG ID. Adding semicolons to the filters so it matches the MethaDory track, refs #38371
  • src/hg/makeDb/trackDb/human/hg38/episignatures.ra - lines changed 3, context: html, text, full: html, text

94ca641d99a7745058c8df8a3c38309898cb5973 Fri Sep 25 13:49:11 2026 -0700

• Updating the script that generates the ra file for EpiCentral so it uses semicolons instead removing the commas outright. refs #38112
  • src/hg/makeDb/scripts/episignatures/epigenCentralToBed.py - lines changed 3, context: html, text, full: html, text

752cb1161a3dc006932fd3ba179c9b2fbe449c8d Fri Sep 25 14:27:43 2026 -0700

• Updating the episignatures makedoc for the semicolon filter labels and adding a recount command for the opposite-direction sites count, refs #38112
  • src/hg/makeDb/doc/hg38/episignatures.txt - lines changed 16, context: html, text, full: html, text

cf3a4c948a0285f6e0ba711688679c904b07e178 Fri Sep 25 14:40:33 2026 -0700

• Adding related tracks for the EpiCentral track, refs #38112
  • src/hg/makeDb/trackDb/relatedTracks.ra - lines changed 4, context: html, text, full: html, text

b0f7c3b8ed633f460990b271070d2c72a4d05ba1 Fri Sep 25 14:55:45 2026 -0700

• Adding GitHub links for the makedoc, scripts, and trackDb to the EpigenCentral page, crediting Max, adding the Turinsky DOI, and using serial commas, refs #38112
  • src/hg/makeDb/trackDb/human/hg38/epigenCentral.html - lines changed 15, context: html, text, full: html, text

b9529a41ea64f905aced9a54e8eb527c4ad490cf Fri Sep 25 14:59:00 2026 -0700

• Adding more missing commas, refs #38112
  • src/hg/makeDb/trackDb/human/hg38/episignatures.html - lines changed 3, context: html, text, full: html, text

10be0991b45bc01981e68f72a660adbbcc999f77 Fri Sep 25 15:53:33 2026 -0700

• Updating the filter paragraph on the track description page. Updating the defaultLabels since searching for a CpG ID would result in not showing that ID, refs #38112
  • src/hg/makeDb/trackDb/human/hg38/epigenCentral.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/episignatures.ra - lines changed 1, context: html, text, full: html, text

f9a684a437d33c33690cf6ffc91faf155d9d5121 Fri Sep 25 15:57:57 2026 -0700

• Staging the Episignatures track on hgwbeta, refs #38112 and #38371
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

b8a77f50143d1cc2a474fe9a56fe7c362183a07f Fri Sep 25 17:35:01 2026 -0700

• Making the shortLabel sentence case. Updating the shortlabel for the subtracks to say 'Predicted' or 'Contributed', refs #35528
  • src/hg/makeDb/outside/proCapNet/proCapNetTrackDb - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra - lines changed 19, context: html, text, full: html, text

717ce54a6012dedd51b0100c643a7a252a16fabb Fri Sep 25 17:46:20 2026 -0700

• Adding windowingFuction maximum to trackDb and the script that generates the trackDb file. refs #35528
  • src/hg/makeDb/outside/proCapNet/proCapNetTrackDb - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra - lines changed 6, context: html, text, full: html, text

f3020b17f2fcd376aca99d97d778c11625c0927f Fri Sep 25 17:49:08 2026 -0700

• Relating different TSS and promoter tracks, refs #35528
  • src/hg/makeDb/trackDb/relatedTracks.ra - lines changed 4, context: html, text, full: html, text

38ccb38771eddfec3230ab3494fb12e11e7cb4ac Fri Sep 25 17:52:32 2026 -0700

• Putting references in alphabetical order. Adding years to citations. Not using the word 'here' and using the actual location/noun. refs #35528
  • src/hg/makeDb/trackDb/human/encode4ProCap.html - lines changed 53, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/proCapNet.html - lines changed 30, context: html, text, full: html, text

fe4c75c272ca27de55c0b42396c47f2b00637a4a Mon Sep 28 16:36:20 2026 -0700

• Linking the encode4ProCap trackDb.ra, saying why PRO-cap and contribution scores are hg38 only on the container page, and limiting the ProCapNet prediction claim to the primary chromosomes, refs #35528
  • src/hg/makeDb/trackDb/human/encode4ProCap.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/proCapNet.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/transcriptionStart.html - lines changed 5, context: html, text, full: html, text

ce7133b45942cf33b8bf074af8b3fd6952381f95 Tue Sep 29 16:50:33 2026 -0700

• Staging the STR track on beta for hg38, hg19, and hs1, refs #38268
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 1, context: html, text, full: html, text

624943dde3397629da2a91d62e83efe7df98d065 Thu Oct 1 16:30:28 2026 -0700

• Pointing the ProCapNet description to the ENCODE Model column of the accession table instead of the removed Experiment column from the bigCompositeUI, refs #35528
  • src/hg/makeDb/trackDb/human/proCapNet.html - lines changed 2, context: html, text, full: html, text

9f6962c173c405e481da17794d67107e7f8e73a9 Fri Oct 2 16:05:31 2026 -0700

• Replacing the subtrack matrix and Sample class filter paragraph on the PRO-cap and ProCapNet description pages with the track collection layout from Mark's change, and noting that ProCapNet minus strand files store negative values, refs #35528
  • src/hg/makeDb/trackDb/human/encode4ProCap.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/proCapNet.html - lines changed 7, context: html, text, full: html, text

3bee9e40921231f206014d66a54c6af7581bd4b7 Fri Oct 2 16:54:40 2026 -0700

• Releasing the ProCapNet tracks, refs #35528
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/trackDb.ra - lines changed 1, context: html, text, full: html, text