Commits for max

v498_base to v499_preview (2026-05-11 to 2026-05-18) v499

ebfaebfd8dd3cdd58fd6f8261ef3fc4f84f9c0c6 Tue May 12 05:48:51 2026 -0700

• tiny change to link name on hgTrackUi page, tested with Andrea Tanzer and she did not understand what "Track Collection" could mean.
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 1, context: html, text, full: html, text

e390536dad43cc58b7f27f31ffc1df699c7dee03 Tue May 12 06:57:32 2026 -0700

• ncOrfs: Kozak strength coloring, codon display, and uORF intron recovery Each ORF in every ncOrfs subtrack now carries three new annotation fields: startCodon, kozakStrength, and kozakTE (Noderer 2014 TE / 100). Features are colored by kozakTE on a 5-bin gradient (blue<0.5, teal, green, orange, red>=0.8), with purple for non-ATG starts and grey for contexts that could not be retrieved. The colors are wired in colorByKozak.py (COLOR_BINS / GREY / PURPLE). thickStart and thickEnd now span the whole ORF and the trackDb stanzas enable baseColorUseCds=given + baseColorDefault=genomicCodons so codon shading is on by default. Filters added for startCodon, kozakStrength, kozakTE on every subtrack. The bed12 GENCODE Phase II tracks (primary / comprehensive) and the metamorf bedORFtable are now converted to bigGenePred so codon display works on them. The OpenProt "kozak" field is renamed to "kozakMotif" in the new .as so the mouseOver's $kozakStrength substitution is not eaten greedily as $kozak + "Strength". utrAnnotUorfs ships as bed9+1 with no exon/intron structure. A new addIntrons.py preprocessor matches each uORF against the other ncORF tracks by exact (chrom, start, end, strand) and copies the block structure of any donor with introns; the contributing database names go in a new intronsSource field (also exposed as a filter). 6,508 of 44,435 uORFs (14.6%) picked up introns, mostly from MetamORF; the rest stay single-block (intronsSource=none). The Noderer 2014 TE table (PMC4299517 / PMID 25170020) is cached in the repo so the build is reproducible without network access. Reference: Noderer WL et al. Quantitative analysis of mammalian translation initiation sites by FACS-seq. Mol Syst Biol. 2014;10:748. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/doc/hg38/ncOrfs.txt - lines changed 267, context: html, text, full: html, text
  • src/hg/makeDb/scripts/ncOrfs/addIntrons.py - lines changed 133, context: html, text, full: html, text
  • src/hg/makeDb/scripts/ncOrfs/colorByKozak.py - lines changed 480, context: html, text, full: html, text
  • src/hg/makeDb/scripts/ncOrfs/gencNcOrf.as - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/scripts/ncOrfs/gencNcOrfPhase2.as - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/scripts/ncOrfs/metamorf.as - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/scripts/ncOrfs/nuorfdb.as - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/scripts/ncOrfs/openprot.as - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/scripts/ncOrfs/run_kozak.sh - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/scripts/ncOrfs/translational_efficiency.txt - lines changed 65536, context: html, text, full: html, text
  • src/hg/makeDb/scripts/ncOrfs/utrAnnotUorfs.as - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/ncOrfs.html - lines changed 216, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/ncOrfs.ra - lines changed 8, context: html, text, full: html, text

e0f6831ec83b8ded192579901d76dfff561d0500 Tue May 12 07:15:28 2026 -0700

• ncOrfs: point subtrack docs at the .kozak.bb files The trackDb stanzas now serve the Kozak-colored .kozak.bb files; update the example bigBedToBed download URLs on the four subtrack doc pages so they match what is actually published. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/trackDb/human/hg38/metamorf.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/nuorfdb.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/openprot.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/utrAnnotUorfs.html - lines changed 1, context: html, text, full: html, text

6771720648a87e9780015cd45f03f4eb24406eb6 Tue May 12 07:24:57 2026 -0700

• ncOrfs: document the Kozak annotation scripts and credit VuTR Add a paragraph to the supertrack html describing the colorByKozak.py / addIntrons.py scripts and the per-track autoSql files, with links to the kent source tree and the makedoc. The Kozak strength logic is a Python port of the routines in the VuTR pipeline (Whiffin lab); credit them. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/trackDb/human/hg38/ncOrfs.html - lines changed 20, context: html, text, full: html, text

0c1e751423b38dd741875d4cdcc6ffb5d4c4a135 Tue May 12 07:51:34 2026 -0700

• mei: add DeepMEI 1000G subtrack on hg38 91,617 MEIs (68,282 Alu, 16,891 L1, 6,444 SVA) called by DeepMEI on the 3,202 high-coverage 1000 Genomes samples. Same 1-bp anchor convention and Okabe-Ito colors as meiHgsvc3. DeepMEI's symbolic ALT carries no inserted sequence or insertion length, so the bigBed schema is a subset of meiHgsvc3 (no svLen, callerCount, validation flags, insertSeq). Also fixes the INS-svLen:carrierCount label format note in meiHgsvc3.html. refs #37524
  • src/hg/makeDb/doc/hg38/mei.txt - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mei/meiDeepmei1kg.as - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mei/meiDeepmei1kgVcfToBed.py - lines changed 160, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/mei.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/mei.ra - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/meiDeepmei1kg.html - lines changed 141, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/meiHgsvc3.html - lines changed 1, context: html, text, full: html, text

c75167799dc7d5939b879e49861653c823a81307 Tue May 12 14:16:46 2026 -0700

• fixing browserSetup.sh issue, reported by andy smith, no redmine
  • src/product/installer/browserSetup.sh - lines changed 2, context: html, text, full: html, text

99db113e49bd1dd42a3040eaed1e61188a117ecf Wed May 13 05:44:18 2026 -0700

• mucins: new locus-specific mucin VNTR/non-VNTR exon track on hs1 (alpha) Adds a new 'Locus-specific' container in the genes group with two bigGenePred subtracks (mucinsVntr, mucinsNonVntr) derived from Plender et al. 2024 supplementary table 2. The .ra and HTML files live under trackDb/human/ so future locus-specific tracks can share them; hs1 picks them up via include ../mucins.ra alpha. refs #37540
  • src/hg/makeDb/doc/hs1/mucins.txt - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mucins/mucinsToBigGenePred.py - lines changed 106, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/locusSpec.html - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/mucins.ra - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/mucinsNonVntr.html - lines changed 96, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/mucinsVntr.html - lines changed 98, context: html, text, full: html, text

9a49afb16653363a70d8e4d205513008b7b08df5 Wed May 13 06:18:42 2026 -0700

• varFreqs: add UK Biobank subtrack from Neale Lab Round 2 imputed-v3 variant manifest (13.7M variants, 361k white British samples). TSV → VCF conversion + CrossMap hg19→hg38, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/doc/hg38/varFreqs.txt - lines changed 47, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/ukbbToVcf.py - lines changed 146, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/ukbb.html - lines changed 118, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.html - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 10, context: html, text, full: html, text

3d9187d264d00ee8e681521bc2c942ee2527d4f1 Wed May 13 07:33:38 2026 -0700

• varFreqs: add WBBC (Westlake BioBank for Chinese) subtrack from the Phase I v20210103 release: 4,480 WGS samples, 78.6M variants, per-region frequencies for the 4 Han Chinese geographic subgroups (North/Central/South/Lingnan). databases.tsv + populations.tsv updated for the next varFreqsAll rebuild. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/doc/hg38/varFreqs.txt - lines changed 42, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/databases.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/populations.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/wbbcFix.py - lines changed 68, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/wbbc.html - lines changed 104, context: html, text, full: html, text

4f8f8773bec66a9e993e9897e0b032c6e97dead8 Fri May 15 10:12:29 2026 -0700

• mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524
  • src/hg/makeDb/doc/hg38/mei.txt - lines changed 173, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/varFreqs.txt - lines changed 60, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mei/meiEul1db.as - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mei/meiEul1dbRef.as - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mei/meiEul1dbRefToBed.py - lines changed 115, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mei/meiEul1dbToBed.py - lines changed 342, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mei/meiHmeid.as - lines changed 41, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mei/meiHmeidVcfToBed.py - lines changed 188, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mei/meiSwegen.as - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mei/meiSwegenVcfToBed.py - lines changed 148, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/mei.ra - lines changed 104, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/meiEul1db.html - lines changed 122, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/meiEul1dbRef.html - lines changed 94, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/meiHmeid.html - lines changed 151, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/meiSwegen.html - lines changed 169, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/swefreq.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 18, context: html, text, full: html, text

99ae46aca64e768875e6cbb2a232a0648bea5344 Fri May 15 10:13:21 2026 -0700

• varFreqs: prefix non-downloadable /gbdb subdirs with "_" so hgdownload rsync skips them; update bigDataUrl paths and Data Access wording on description pages for topmed, allofus, sfariSparkExomes/sfariSparkWgs, and mxbFreq. Combined varFreqsAll.bb moved into _all/. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/doc/hg38/varFreqs.txt - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/allofus.html - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/mxbFreq.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/sfariSparkExomes.html - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/topmed.html - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 14, context: html, text, full: html, text

89491842e0ec6b2250aa6f6dc2c83c294930e6d6 Sun May 17 14:38:40 2026 -0700

• Add ChinaMAP phase 1 variant frequencies subtrack on hg38 ChinaMAP (Cao et al. 2020, Cell Res, PMID 32355288) is a deep-WGS cohort of 10,588 Chinese individuals across 27 provinces and 8 ethnic groups, with 147.4 M autosomal variants (136.7 M SNPs + 10.7 M short indels). The released VCF is already on GRCh38 with chr-prefixed chromosomes and ships AC/AF/AN plus matched 1KGP_* INFO fields, so it is served directly via vcfTabix. The ChinaMAP Limitations on Use prohibit redistribution, so the gbdb directory is _chinamap (hidden from hgdownload) and the trackDb stanza has tableBrowser off. Registered in scripts/varFreqs/databases.tsv so the next varFreqsAll combined rebuild picks it up; filter UI is deliberately not added yet (WBBC/TPMI precedent). , refs #36642
  • src/hg/makeDb/doc/hg38/varFreqs.txt - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/databases.tsv - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chinamap.html - lines changed 105, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 11, context: html, text, full: html, text

0a5389e8b81efa99e932f5e9e2424b27ce1af095 Sun May 17 14:53:57 2026 -0700

• varFreqs: add GenomeIndia subtrack (9,768 WGS, 83 endogamous Indian populations, Bhattacharyya 2025) and wire into databases.tsv for the next varFreqsAll rebuild. TSV->VCF conversion synthesizes AC=round(AF*AN) with AN=19536 since the upstream release only ships AF, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/doc/hg38/varFreqs.txt - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/databases.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/genomeindiaToVcf.py - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/genomeindia.html - lines changed 107, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.html - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 15, context: html, text, full: html, text

50d82c22527518595fcedf3066db5b3dbe011b88 Sun May 17 15:28:05 2026 -0700

• Add Taiwan TPMI row to varFreqs overview table The TPMI subtrack was added a few days ago but never made it into the Available Datasets table on the varFreqs supertrack description page. , refs #36642
  • src/hg/makeDb/trackDb/human/varFreqs.html - lines changed 9, context: html, text, full: html, text

fa5cb52522742a54651d302464cb5deadfa7b7c7 Mon May 18 02:54:46 2026 -0700

• andy smith noticed that on the most recent ubuntu the mysql datadir was moved. Adding code now to auto-detect the datadir location and running the function after every use of MYSQLDIR. Except for OSX, but OSX without brew is not really supported anymore and needs work anyways. No redmine
  • src/product/installer/browserSetup.sh - lines changed 27, context: html, text, full: html, text