Commits for lrnassar

v495_base to v496_preview (2026-03-09 to 2026-03-16) v496

785f82c6a4c5443431c8029fee829999c6982864 Mon Mar 9 14:51:18 2026 -0700

• Making the new cCREs track squish as feedback from Zhiping. It looks better since the track just has single coverage and the mouseOvers work in squish mode. Refs #37131
  • src/hg/makeDb/trackDb/human/hg38/encode.cCREs.override.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode.cCREs.override.ra - lines changed 1, context: html, text, full: html, text

98004ba10f89d74192132ac37d9be95ebfdb3d0e Mon Mar 9 16:13:35 2026 -0700

• Adding MLQ automate script to the tree, this runs on a qateam crontab and checks for any updated or new MLQs, accepts pending questions that pass a spam check, and creates/updates redmine tickets. It has been running for months on my personal crontab and is now being migrated to qateam. Refs #36801
  • src/utils/qa/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/mlqAutomate.py - lines changed 1901, context: html, text, full: html, text

30d7f0358fc7d3cec663333e0e9f2a1e0defe909 Mon Mar 9 16:48:55 2026 -0700

• Rolled back the local CDNs for hgdownload since it has some styling issues - some of the downloaded CNDs were missing from that computer. The goal of this was to increase speed on the GB, so for the download server this isn't a big deal. This came up now because I was updating the GenArk name, and this change went out along with it and broke the menus. All good now, refs #37027
  • src/hg/htdocs/inc/gbPageStartHardcoded.html - lines changed 9, context: html, text, full: html, text

b68199a7676fbce5ede8ff948128981183dd1cd4 Mon Mar 9 17:37:03 2026 -0700

• Expanding the script to now also update the new hubPublic field for the hub's email (if possible). Now, when a hub fails, the contact email is printed on hgTracks. Also fixed a small logic bug in the 'if not' loop. Refs #33571
  • src/utils/qa/hubPublicAutoUpdate - lines changed 10, context: html, text, full: html, text

47d5af90d317bffde6f0843beabd2d72c88fbfce Tue Mar 10 08:18:06 2026 -0700

• Adding retry logic around the gmail API call, because it fails periodically (but then works next time it runs). Refs #36801
  • src/utils/qa/mlqAutomate.py - lines changed 2, context: html, text, full: html, text

7155e7f79fb01ff6db8b275ca46eb09f52afe3e2 Tue Mar 10 09:39:41 2026 -0700

• Fixing some typos, no RM.
  • src/hg/hgBlat/hgBlat.c - lines changed 2, context: html, text, full: html, text

48e28c6ab25cc0c901be5531c594868fe28920fb Tue Mar 10 11:14:46 2026 -0700

• Expanding the error message to print out all the possible values, refs #37219
  • src/hg/lib/hui.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c - lines changed 1, context: html, text, full: html, text

d30fb57a294222a2458866d60eae82cc50cf6dde Tue Mar 10 15:15:21 2026 -0700

• Removing meetings that have passed and rearranging them in chronological order, no RM.
  • src/hg/htdocs/indexMeetings.html - lines changed 24, context: html, text, full: html, text

198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700

• Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
  • python/lib/ucscGb/encode/cv.py - lines changed 1, context: html, text, full: html, text
  • python/lib/ucscGb/gbData/ra/raStanza.py - lines changed 1, context: html, text, full: html, text
  • python/lib/ucscGb/qa/tables/trackUtils.py - lines changed 1, context: html, text, full: html, text
  • python/ucsc_virtualenv.py - lines changed 2, context: html, text, full: html, text
  • src/hg/affyTransciptome/maxTranscriptomeExps.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/hgEncodeVocab/hgEncodeVocab.c - lines changed 2, context: html, text, full: html, text
  • src/hg/encode3/importEncode2/encode2Meta/encode2Meta.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgBlat/hgBlat.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hgCoordConv/hgCoordConv.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 5, context: html, text, full: html, text
  • src/hg/hgLiftOver/hgLiftOver.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgSession/hgSession.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.c - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hgTracks/searchTracks.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgUserSuggestion/hgUserSuggestion.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgsqlSwapTables/hgsqlSwapTables.c - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/FAQ/FAQblat.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/FAQ/FAQdownloads.html - lines changed 6, context: html, text, full: html, text
  • src/hg/htdocs/FAQ/FAQformat.html - lines changed 8, context: html, text, full: html, text
  • src/hg/htdocs/FAQ/FAQgenes.html - lines changed 8, context: html, text, full: html, text
  • src/hg/htdocs/FAQ/FAQlicense.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/FAQ/FAQlink.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/FAQ/FAQtracks.html - lines changed 4, context: html, text, full: html, text
  • src/hg/htdocs/assemblySearch.html - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/htdocs/cite.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/covid19.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/credits.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/api.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/barChart.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/bedMethyl.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/bigBed.html - lines changed 5, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/bigChain.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/bigGenePred.html - lines changed 4, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/bigLolly.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/bigMaf.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/bigPsl.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/customTrackText.html - lines changed 4, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hgCodonColoringMrna.html - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/htdocs/goldenPath/help/hgGeneGraph.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hgSessionHelp.html - lines changed 8, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hgTablesHelp.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hgTracksHelp.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html - lines changed 5, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hic.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hubQuickStart.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hubQuickStartGroups.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/interact.html - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/htdocs/goldenPath/help/mirror.html - lines changed 4, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/sessions.html - lines changed 4, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/changes.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/vcf.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/newsarch.html - lines changed 15, context: html, text, full: html, text
  • src/hg/htdocs/inc/gbFooter.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/inc/gbsFooter.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/inc/jWestFooter.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/staff.html - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/htdocs/training/index.html - lines changed 1, context: html, text, full: html, text
  • src/hg/js/react/hgIntegrator/hgIntegrator.jsx - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/baseMaskCommon.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/genomeRangeTreeFile.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/align/gbAlignInstall.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/mdbUpdate/mdbPrint.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/affy.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau6/numtSeq2012.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/beta/cv.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/public/cv.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/gireIntraHost.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/geneid.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chm13/html/GCA_009914755.4_T2T-CHM13v2.0.t2tRepeatMasker.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/clinvar.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/dbSnp153Composite.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/dbSnp155Composite.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/encodeEgaspUpdate.html - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/encodeUncFaire.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/encodeYaleMASPlacRNATars.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/encodeYaleRnaSuper.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/haplotype.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/cnp.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/cnp.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/cnpRedon.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/pgPop.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/pgYri.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/ctgPos.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/ctgPos2.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/gnomad.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/gnomadMpc.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/tfbsConsSites.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSc.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClusteredV3.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/cactus447way.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/cons100way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/cons241way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/encodeCcreCombined.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gnomadPLI.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/rmsk.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/t2tRepeatMasker.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/longReadVariants.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/numtSeq.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/refSeqComposite.html - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/makeDb/trackDb/human/ucsfBrainMethyl.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release4.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/other/centromeres1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pig/susScr2/numtSeq2012.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/mpxvRivers/html/repeatMasker.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/cas13Crispr.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/pbm.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/recomb.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/strains.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/transcriptome.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.ra - lines changed 18, context: html, text, full: html, text
  • src/hg/mouseStuff/chainInfo/chainInfo.c - lines changed 1, context: html, text, full: html, text
  • src/hg/protein/lib/pbUtil.c - lines changed 1, context: html, text, full: html, text
  • src/hg/pslPairs/pslPairs.c - lines changed 1, context: html, text, full: html, text
  • src/hg/randomPlacement/randomPlacement.c - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/fixTrackDb/fixTrackDb.c - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/gtfToGenePred.c - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/positionalTblCheck/positionalTblCheck.c - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslMismatchGapToBed/pslMismatchGapToBed.c - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/tdbQuery/tdbQuery.c - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c - lines changed 1, context: html, text, full: html, text
  • src/hg/zoo/analyze4d/analyze.c - lines changed 1, context: html, text, full: html, text
  • src/inc/meta.h - lines changed 1, context: html, text, full: html, text
  • src/inc/obscure.h - lines changed 1, context: html, text, full: html, text
  • src/inc/twoBit.h - lines changed 1, context: html, text, full: html, text
  • src/lib/cheapcgi.c - lines changed 1, context: html, text, full: html, text
  • src/lib/common.c - lines changed 1, context: html, text, full: html, text
  • src/lib/gemfont.h - lines changed 1, context: html, text, full: html, text
  • src/lib/meta.c - lines changed 1, context: html, text, full: html, text
  • src/lib/obscure.c - lines changed 1, context: html, text, full: html, text
  • src/lib/options.c - lines changed 2, context: html, text, full: html, text
  • src/lib/trix.c - lines changed 2, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 1, context: html, text, full: html, text
  • src/utils/bedGraphToBigWig/bedGraphToBigWig.c - lines changed 1, context: html, text, full: html, text
  • src/utils/bedToBigBed/bedToBigBed.c - lines changed 1, context: html, text, full: html, text
  • src/utils/countChars/countChars.c - lines changed 2, context: html, text, full: html, text
  • src/utils/jimgrep/jimgrep.c - lines changed 2, context: html, text, full: html, text
  • src/utils/methylateGenome/methylateGenome.c - lines changed 2, context: html, text, full: html, text
  • src/utils/tabFmt/tabFmt.c - lines changed 2, context: html, text, full: html, text

08afd09bf225ea50691998f829926e9d71d55b49 Wed Mar 11 19:21:42 2026 -0700

• Fixing small grammatical and consistency errors with the heatmap page and trackDb entry. Also some bigger fixes like a broken anchor. Refs #36176
  • src/hg/htdocs/goldenPath/help/heatmap.html - lines changed 14, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 1, context: html, text, full: html, text

f6989c2ec9dc36e82a71e735d181d4ebecbace42 Fri Mar 13 13:38:58 2026 -0700

• Adding a script for claude redmine communication, it extends on max's redmineDump and allows all RM functionality (make ticket, post, etc.) while also signing posts with a claude signature. No RM.
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/redmineCli - lines changed 650, context: html, text, full: html, text

349e3c4468ffd999aee6b856edc1f9ab697505a1 Fri Mar 13 13:42:46 2026 -0700

• Various improvements to the heatmap.html documentation as described in the ticket, refs #36176
  • src/hg/htdocs/goldenPath/help/heatmap.html - lines changed 115, context: html, text, full: html, text

c17beac2e24b5e0cd8b6e4e828265d5a5df2bbd5 Mon Mar 16 08:54:14 2026 -0700

• Adding new script to perform CRs. It is used in -daily mode to run overnight CRs, or can also be pointed towards specific commits, or towrads all build tickets. Refs #36890
  • src/utils/codeReviewAi.py - lines changed 1637, context: html, text, full: html, text
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text

a8a9567f7b38e02f36edfc58ab733c2cbeefe134 Mon Mar 16 08:55:55 2026 -0700

• Oops, placed the CR script in the wrong section of the makefile with the C utils instead of the standalone scripts. Refs #36890
  • src/utils/makefile - lines changed 2, context: html, text, full: html, text

6570715c5cd53f3c7a71460a6806e13ade21909d Mon Mar 16 09:07:31 2026 -0700

• Removing redmineDump script as it was replaced by redmineCli, refs conversation with Max.
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/redmineDump - lines changed 247, context: html, text, full: html, text

ff25bb5db197e1b8a048154cc9d34dc098ebd434 Mon Mar 16 09:19:20 2026 -0700

• Feedback from AI CR.
  • src/utils/redmineCli - lines changed 6, context: html, text, full: html, text

ec013b7cd85204640ee339dd860b6c819c912bf0 Mon Mar 16 09:31:08 2026 -0700

• More feedback from CR.
  • src/utils/redmineCli - lines changed 13, context: html, text, full: html, text