Commits for max
switch to files view, user index
v499_base to v500_preview (2026-06-01 to 2026-06-08) v500
Show details
55e909c0e98fb50a5cd761f1ce2cb52f9089f5f4 Tue Jun 2 03:05:59 2026 -0700
- [Claude] ncOrfs: add 5ULTRA uORFs subtrack (MANE Select, 22,567 features)
Adds fiveUltraUorfs, a new subtrack under the ncOrfs supertrack showing
22,567 ATG-initiated uORFs in MANE Select transcripts from the 5ULTRA
pipeline (Chaldebas et al., Am J Hum Genet 2026, PMID 41881026).
Features are colored by uORF type (Okabe-Ito palette), have exon/intron
structure projected from MANE via addIntrons.py, and carry gene, rank,
and Kozak strength as extra bigBed fields. ncOrfs.html summary table
updated to include the new track.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
refs #37580
- src/hg/makeDb/doc/hg38/ncOrfs.txt - lines changed 62, context: html, text, full: html, text
- src/hg/makeDb/scripts/ncOrfs/fiveUltraUorfs.as - lines changed 21, context: html, text, full: html, text
- src/hg/makeDb/scripts/ncOrfs/maneUorfsToBed.py - lines changed 39, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/fiveUltraUorfs.html - lines changed 150, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/ncOrfs.html - lines changed 23, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/ncOrfs.ra - lines changed 28, context: html, text, full: html, text
038bd0cd3f7c84ee984905608dfdd27d02cc61ec Tue Jun 2 05:19:51 2026 -0700
- [Claude] lrSv1kLin: add 1000 Genomes linear long-read SV subtrack (1,218 samples, hg38+hs1)
Two native VCFs from the Eichler lab (GRCh38 and CHM13/T2T-CHM13v2), merged
with Truvari v5.2.0 and annotated with population-level AFs (EUR, AMR, EAS,
AFR, SAS). Track is alpha-only; not added to lrSvAll -- data not yet published.
hg38: 587,779 SVs; hs1: 614,522 SVs.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
, refs #36258
- src/hg/makeDb/doc/hg38/lrSv.txt - lines changed 39, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSv1kLin1218.as - lines changed 26, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSv1kLin1218VcfToBed.py - lines changed 131, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 84, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/lrSv1kLin.html - lines changed 1, context: html, text, full: html, text
5dc1d6e658ab009f27314e192340275a6bb70237 Tue Jun 2 16:20:48 2026 -0700
- Add colorFields trackDb setting for bigBed/bigGenePred color scheme switching
Adds a new trackDb statement `colorFields` that renders a "Color by:" dropdown
in the track controls page, letting users switch among multiple pre-computed
color schemes stored as extra bigBed fields containing R,G,B strings.
The `default="label"` key renames the standard itemRgb option in the dropdown.
Other entries name extra bigBed fields whose R,G,B values override itemRgb when
selected. When a non-default scheme is active, a "(Coloring by: label)" suffix
appears in the track long label.
Changes:
- hui.c/hui.h: new colorFieldsCfgUi() rendered inside bedScoreCfgUi() for bigBed
- bigBedTrack.c: colorFieldIdx lookup + per-item filterColor override + longLabel suffix
- tagTypes.tab: register colorFields for bigBed and bigGenePred
- trackDbLibrary.shtml, trackDbDoc.html, trackDbHub.v3.html, changes.html: documentation
refs #26253
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- src/hg/hgTracks/bigBedTrack.c - lines changed 28, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/trackDb/changes.html - lines changed 12, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 7, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html - lines changed 7, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 39, context: html, text, full: html, text
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
640ebced50314d2662db498562167e0d21980f78 Tue Jun 2 16:36:43 2026 -0700
- gencNcOrfs: add peptide evidence fields from TransCODE/PeptideAtlas (PMID:42092140)
Extends the GENCODE Phase I ncORF bigGenePred (Ribo-seq_ORFs.kozak.peptides.bb,
44 fields) with 14 peptide evidence fields joined from five supplementary tables
in Mudge et al. 2025. Introduces the "peptidein" concept — ncORFs confidently
detected by mass spectrometry but lacking functional annotation for protein status.
Data covers 2,150 of 7,264 Phase I ORFs; the remaining 5,114 carry default empty
values. Three color schemes are available via the colorFields dropdown:
- Kozak strength (default, pre-existing field 9 colors)
- Evidence type: gold=peptidein, blue=HLA only, green=non-HLA only, purple=both
- HLA class: blue=class I, crimson=class II, purple=both
New filters: isPeptidein, hlaClass, hlaFinalTier, hlaHppCategory, riboseqQuality.
Phase II shortLabels: "GENCODE Phase II ncORFs Prim/Compr".
Phase I kozakTE filterLimits set to -1:1.5 so ORFs with unavailable context are accessible.
Build: peptideSupport/addPeptideEvidence.py
AutoSql: Ribo-seq_ORFs.kozak.peptides.as
BigBed: /gbdb/hg38/ncOrfs/gencNcOrf/Ribo-seq_ORFs.kozak.peptides.bb
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- src/hg/makeDb/doc/hg38/ncOrfs.txt - lines changed 59, context: html, text, full: html, text
- src/hg/makeDb/scripts/ncOrfs/colorByKozak.py - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/gencNcOrfs.html - lines changed 205, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/ncOrfs.ra - lines changed 17, context: html, text, full: html, text
30c1c7161e91d449bf748f1453fe408ffef5b50f Wed Jun 3 05:22:33 2026 -0700
- fixes after AI review, no redmine
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
- src/hg/makeDb/scripts/ncOrfs/fiveUltraUorfs.as - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/gencNcOrfs.html - lines changed 2, context: html, text, full: html, text
6af4f6e10518d33db653c55dadab86b3ed4617ec Wed Jun 3 05:39:35 2026 -0700
- hubApi/blat: fix duplicate itemsReturned, missing target strand, weak default penalty
Three QA issues from Gerardo on #36315:
- writeJsonOutput() emitted "itemsReturned" twice -- apiFinishOutput()
already prints it from the global -- so drop the explicit jsonWriteNumber().
- Protein and translated queries came back with single-char strand because
gfOutput only writes the target-strand character when reportTargetStrand
is set; hgBlat sets it for translated queries, the API path didn't. Set
it when bt.isTx so pslLoad sees the full two-char strand.
- blatDelayFractionDefault was 0.3 -- QA's 40-request burst only added
~2.4s. Bumped to 3.0 for ~24s under the same burst; still tunable in
hg.conf via hubApi.blatDelayFraction=.
refs #36315
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
dfe4ce8ecd6ca71b2bc90b98b4f4ac73fad0c9eb Wed Jun 3 06:47:31 2026 -0700
- EVE track QA fixes: longLabel sentence case, dataVersion, relatedTracks cross-links
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- src/hg/makeDb/trackDb/human/eve.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/relatedTracks.ra - lines changed 10, context: html, text, full: html, text
b7b279e5f1240419fb3a408fff5c82a998a36e76 Wed Jun 3 08:17:09 2026 -0700
- EVE track QA fixes: fix .as field descriptions, clarify protein count in HTML
- thickStart/thickEnd .as descriptions corrected (whole protein span, not start/stop codon)
- reserved .as description corrected (always 0, not itemRgb)
- HTML Methods section: explain that 2,951 of 3,219 proteins have released VCF scores
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- src/hg/makeDb/scripts/eve/eve_heatmap.as - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/eve.html - lines changed 4, context: html, text, full: html, text
64a3f9e7813e823cf724ea188c3928a911578286 Thu Jun 4 00:32:22 2026 -0700
- varFreqs: replace All Databases Combined with two phenotype-split tracks
Replace the single varFreqsAll combined track (and drop the varFreqsDisease
track) with two matched tracks for visual case-vs-background comparison:
varFreqsAffected - variants seen in the affected/case arms of disease
cohorts (SFARI SPARK WES/WGS ASD probands, SCHEMA cases,
GREGoR affected, GA4K); ~130,000 individuals
varFreqsBackground - population reference cohorts + the unaffected/control
arms of disease cohorts ("all other variants");
~1.5 million individuals
A variant seen in both groups appears in both tracks. Genotyping-array cohorts
stay out of both (varFreqsArray unchanged).
vcfToBigBed.py gains --split-affected to emit both tracks in one pass; it reads
phenotype tags (affected/unaffected/unknown) from populations.tsv and
is_disease/disease_role from databases.tsv, and derives the length-filter
ranges from the observed data. TOPMed reclassified as a population cohort.
SPARK WGS display name changed to SFARI SPARK WGS for consistency with the
standalone subtracks. Fixed the trackDb mouseOver $-substitution prefix
collision by wrapping fields in ${}. New description pages for both tracks.
refs #36642
- src/hg/makeDb/doc/hg38/varFreqs.txt - lines changed 62, context: html, text, full: html, text
- src/hg/makeDb/scripts/varFreqs/databases.tsv - lines changed 35, context: html, text, full: html, text
- src/hg/makeDb/scripts/varFreqs/populations.tsv - lines changed 13, context: html, text, full: html, text
- src/hg/makeDb/scripts/varFreqs/vcfToBigBed.py - lines changed 347, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/varFreqs.html - lines changed 25, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 445, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/varFreqsAffected.html - lines changed 134, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/varFreqsAll.html - lines changed 244, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/varFreqsBackground.html - lines changed 121, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/varFreqsDisease.html - lines changed 198, context: html, text, full: html, text
a729e1ee610d17d3dcb36a45437f1709e5699558 Fri Jun 5 02:18:09 2026 -0700
- varFreqs: fix collection page leftovers from the combined-track redesign
Update the SNV Frequencies collection description page for the two-track
(Affected / Background) layout: correct the combined-track count to three,
rewrite the Methods paragraph that still described building the old single
"All Databases" track (now describes the phenotype split via
vcfToBigBed.py --split-affected), and set the Affected/Background sample-count
cells in the dataset table to ~130k and ~1.5M.
refs #36642
- src/hg/makeDb/trackDb/human/varFreqs.html - lines changed 14, context: html, text, full: html, text
f93b8662afd701763c24634879d05dc08b3178de Fri Jun 5 02:24:16 2026 -0700
- Add exon search: jump to GENE exon N from position box
I'm comitting this thinking that the way that we implement searches
leads to duplication of code that doesn't look great to me. While this
feature looks good, the code duplication across C/JS should probably
get reduced with a different approach to the "quick jump" way of the
page. We have currently three ways to quick jump, I think:
- chr:start-end
- rsxxxxx
- gene symbol + autosuggest pick
- HGVS?
They are recognized by both the javascript and the C code with regexes.
I think all of these should be probably be only implemented in the C
code. The JS only sends the current string to the C code and then
gets back if this can be autocompleted and to which position and what
to show in the autosuggest area. For example if you type
"SOD1<space>e" the C code could send back "Continue typing to jump to
exon" and once you're at "SOD1<space>exon 5" the C code sends back
"Hit enter to jump to chrX:123123-123213". This would work with any
type of identifier and the code would stay in the C code, not more
duplication and it would be much clearer to the user what is recognized
in the search box.
Users can now type "TP53 exon 5" or "TP53:e.5[+/-offset]" in the
genome browser position/search box to navigate directly to that exon.
The ":e.N" notation follows the VICC Gene Fusion Specification.
An optional intronic offset (":e.5+2") lands N bases past the exon
boundary, useful for splice site inspection.
C (hgFind.c): findGeneExon() resolves the query against the SQL
genePred tables listed in the hg.conf "geneTracks" key (default:
mane, ncbiRefSeqSelect, knownGene, ncbiRefSeq, ncbiRefSeqHistorical).
bigGenePred tracks (e.g. mane) are supported via bigBedOpenExtraIndex.
Uses the existing exonToPos() function for strand-aware exon lookup.
fixSinglePos() is called so hgp->singlePos is populated for callers.
hgApi.c: new cmd=geneExonToPos returns {"pos":"chrom:start-end"} JSON
so JS can navigate in place without a full page redirect to hgSearch.
Direct URL links (hgTracks?position=GENE+exon+N) also work because
findGeneExon() is hooked into hgPositionsFind().
JS: autocomplete.js injects a local "Jump to exon N" suggestion as
soon as the exon pattern is detected, or a hint item when the query
is still partial ("GENE ex"). Selecting either navigates via hgApi.
hgTracks.js routes the two new autocomplete item types to the hgApi
call. utils.js adds the two regexes (geneExonExp, geneExonCoordExp).
query.html: documents both syntaxes; the :e.N notation links to the
VICC Gene Fusion Specification at fusions.cancervariants.org.
- src/hg/htdocs/goldenPath/help/query.html - lines changed 30, context: html, text, full: html, text
- src/hg/js/autocomplete.js - lines changed 56, context: html, text, full: html, text
9b842af51fa1fa6ebe403f397ce52fc4448b9807 Fri Jun 5 03:32:12 2026 -0700
- docs
- src/hg/htdocs/goldenPath/help/query.html - lines changed 4, context: html, text, full: html, text
6f429cb567c6a0245bb1f8b98c68071739562f1b Mon Jun 8 05:49:53 2026 -0700
- query.html: fix serial comma and quote style in exon search docs
no redmine
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
- src/hg/htdocs/goldenPath/help/query.html - lines changed 1, context: html, text, full: html, text
switch to files view, user index