File Changes for lrnassar
switch to commits view, user indexv500_base to v501_preview (2026-06-29 to 2026-07-06) v501
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- src/hg/hgTracks/decorator.c
- lines changed 33, context: html, text, full: html, text
43697ed2271f7819ef6d6f1947c0b404a508539a Wed Jul 1 15:38:24 2026 -0700
Make hgTracks decorators resolve the decoratedItem chrom through chromAlias so decorations link to their items when the decoratedItem field uses an alias (e.g. PanSN or accession names) rather than the native sequence name. refs #37803
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 100, context: html, text, full: html, text
aaead1eeb6e454442e1a6c6dcb6a7c41cf3991d6 Tue Jun 30 16:49:27 2026 -0700
varFreqs: July 1, 2026 release announcement, newsarch + indexNews + pennantIcon. refs #36642
Adds the New SNV Frequencies supertrack release entry to newsarch.html
(anchor #070126) and indexNews.html for the upcoming July 1, 2026 release.
The newsarch entry features rs4986893, the CYP2C19 East Asian founder
stop-gained variant, as the screenshot example. Updates the varFreqs
supertrack pennantIcon to point to the new anchor with hover text
"Released Jul. 1, 2026".
- lines changed 16, context: html, text, full: html, text
30c0e2e97dc0f5391a58a3cc665f55697a3b6152 Tue Jun 30 18:03:44 2026 -0700
varFreqs: newsarch, swap "supertrack" for "container track" and expand credits. refs #36642
Per Max's post-release feedback on the ticket: "supertrack" is jargon
for end users, so all 4 mentions in the SNV Frequencies entry are
swapped to "container track". Credits paragraph expanded to name the
additional investigators and data-access teams who provided source
variant files or helped shape the track (Sarah Tishkoff, Yanan Cao,
Matthew Hobbs, Adam Ameur, Johan Viklund, Ameena Suliman, Julia Sommer,
Cole Shanks, Qudsi Aljabiri). Also fixes "Insoo Jang" spelling to
"Insu Jang" to match his own signature.
- src/hg/htdocs/images/snvFrequenciesNewsarch.png
- lines changed 0, context: html, text, full: html, text
aaead1eeb6e454442e1a6c6dcb6a7c41cf3991d6 Tue Jun 30 16:49:27 2026 -0700
varFreqs: July 1, 2026 release announcement, newsarch + indexNews + pennantIcon. refs #36642
Adds the New SNV Frequencies supertrack release entry to newsarch.html
(anchor #070126) and indexNews.html for the upcoming July 1, 2026 release.
The newsarch entry features rs4986893, the CYP2C19 East Asian founder
stop-gained variant, as the screenshot example. Updates the varFreqs
supertrack pennantIcon to point to the new anchor with hover text
"Released Jul. 1, 2026".
- src/hg/htdocs/indexNews.html
- lines changed 12, context: html, text, full: html, text
aaead1eeb6e454442e1a6c6dcb6a7c41cf3991d6 Tue Jun 30 16:49:27 2026 -0700
varFreqs: July 1, 2026 release announcement, newsarch + indexNews + pennantIcon. refs #36642
Adds the New SNV Frequencies supertrack release entry to newsarch.html
(anchor #070126) and indexNews.html for the upcoming July 1, 2026 release.
The newsarch entry features rs4986893, the CYP2C19 East Asian founder
stop-gained variant, as the screenshot example. Updates the varFreqs
supertrack pennantIcon to point to the new anchor with hover text
"Released Jul. 1, 2026".
- src/hg/makeDb/doc/Cardiomyopathy.txt
- lines changed 502, context: html, text, full: html, text
aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446
Adds the 12 per-track build scripts under
src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies,
REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen
EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain
hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4
per-variant OR, and the NON-FINAL provisional classifier) plus the build
documentation at src/hg/makeDb/doc/Cardiomyopathy.txt.
All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs
(8 genes, affiliation 50002); no thresholds are invented in the build.
- src/hg/makeDb/doc/hg38/popEve.txt
- lines changed 79, context: html, text, full: html, text
b99548fc6477e8f2b46f571248147aab27d5766b Tue Jun 30 17:57:20 2026 -0700
Add popEVE proteome-wide missense deleteriousness track for hg38. refs #37791
New heatmap bigBed track under the Deleteriousness Predictions superTrack, built from
the UKBB-trained popEVE v1.1 GRCh38 VCF. One heatmap entry per protein (columns = amino
acid positions at codon coordinates, rows = 20 amino acids), colored on a global,
cross-gene gradient keyed to the raw popEVE score.
Adds the conversion scripts (extractPopEve.py, vcfToPopEveHeatmap.py, popEve_heatmap.as),
the makedoc, the trackDb stanza and description page, and gates the track alpha via an
include in predictionScoresSuper.ra.
- src/hg/makeDb/doc/hg38/varFreqs.txt
- lines changed 57, context: html, text, full: html, text
5ad55adbb6a5cc72a393700130584aa87fef2c89 Tue Jun 30 06:15:44 2026 -0700
varFreqs: add Top 3 source AFs to mouseOvers; audit excludes SGDP and SVatalog. refs #36642
Adds a Top 3 source AFs ranking to the varFreqsAffected and varFreqsBackground
mouseOvers. Alongside the pooled allele frequency, the mouseOver now lists the
three cohorts/arms with the highest per-source AF, formatted as
"Source (AF), Source (AF), Source (AF)". Disease cohorts with phenotype splits
carry the arm label (SPARK ASD, SCHEMA case, GREGoR unaffected); population
cohorts use the bare key. Per-population sub-ancestries are deliberately
excluded so a high sub-pop AF cannot crowd out actual project-level signals.
vcfToBigBed.py adds a top_n_source_afs helper, collects per-arm AFs into
affected_arm_afs / background_arm_afs, and emits two new fields
topAffectedSources and topBackgroundSources. AS schema field count 163 -> 165.
An AF-distribution sweep across all 28 source cohorts identified SGDP and
SVatalog as encoding allele counts per genotyped individual (small N, AF
defaults near 0.5), making their per-source AF unreliable for the ranking.
Adds a skip_top_ranking column (col 9) to databases.tsv, set to 1 for SGDP
and SVatalog, and gates the per-arm AF append in vcfToBigBed.py on this
flag. Both cohorts still contribute to pooled backgroundAC/AN/AF and still
appear in backgroundSources; they are only suppressed from the Top 3.
Description pages varFreqsAffected.html and varFreqsBackground.html document
the ranking; the latter also documents the SGDP/SVatalog exclusion. Build
documentation in varFreqs.txt is updated.
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAFfrequencies.py
- lines changed 253, context: html, text, full: html, text
aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446
Adds the 12 per-track build scripts under
src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies,
REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen
EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain
hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4
per-variant OR, and the NON-FINAL provisional classifier) plus the build
documentation at src/hg/makeDb/doc/Cardiomyopathy.txt.
All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs
(8 genes, affiliation 50002); no thresholds are invented in the build.
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAnnotate.py
- lines changed 189, context: html, text, full: html, text
aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446
Adds the 12 per-track build scripts under
src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies,
REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen
EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain
hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4
per-variant OR, and the NON-FINAL provisional classifier) plus the build
documentation at src/hg/makeDb/doc/Cardiomyopathy.txt.
All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs
(8 genes, affiliation 50002); no thresholds are invented in the build.
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAtlasEF.py
- lines changed 460, context: html, text, full: html, text
aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446
Adds the 12 per-track build scripts under
src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies,
REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen
EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain
hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4
per-variant OR, and the NON-FINAL provisional classifier) plus the build
documentation at src/hg/makeDb/doc/Cardiomyopathy.txt.
All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs
(8 genes, affiliation 50002); no thresholds are invented in the build.
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPCardioBoost.py
- lines changed 136, context: html, text, full: html, text
aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446
Adds the 12 per-track build scripts under
src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies,
REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen
EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain
hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4
per-variant OR, and the NON-FINAL provisional classifier) plus the build
documentation at src/hg/makeDb/doc/Cardiomyopathy.txt.
All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs
(8 genes, affiliation 50002); no thresholds are invented in the build.
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPClinDomains.py
- lines changed 339, context: html, text, full: html, text
aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446
Adds the 12 per-track build scripts under
src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies,
REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen
EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain
hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4
per-variant OR, and the NON-FINAL provisional classifier) plus the build
documentation at src/hg/makeDb/doc/Cardiomyopathy.txt.
All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs
(8 genes, affiliation 50002); no thresholds are invented in the build.
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPClinVar506161.py
- lines changed 275, context: html, text, full: html, text
aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446
Adds the 12 per-track build scripts under
src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies,
REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen
EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain
hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4
per-variant OR, and the NON-FINAL provisional classifier) plus the build
documentation at src/hg/makeDb/doc/Cardiomyopathy.txt.
All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs
(8 genes, affiliation 50002); no thresholds are invented in the build.
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPEvRepo.py
- lines changed 396, context: html, text, full: html, text
aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446
Adds the 12 per-track build scripts under
src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies,
REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen
EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain
hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4
per-variant OR, and the NON-FINAL provisional classifier) plus the build
documentation at src/hg/makeDb/doc/Cardiomyopathy.txt.
All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs
(8 genes, affiliation 50002); no thresholds are invented in the build.
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPPVS1.py
- lines changed 217, context: html, text, full: html, text
aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446
Adds the 12 per-track build scripts under
src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies,
REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen
EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain
hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4
per-variant OR, and the NON-FINAL provisional classifier) plus the build
documentation at src/hg/makeDb/doc/Cardiomyopathy.txt.
All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs
(8 genes, affiliation 50002); no thresholds are invented in the build.
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPProvisionalClass.py
- lines changed 554, context: html, text, full: html, text
aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446
Adds the 12 per-track build scripts under
src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies,
REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen
EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain
hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4
per-variant OR, and the NON-FINAL provisional classifier) plus the build
documentation at src/hg/makeDb/doc/Cardiomyopathy.txt.
All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs
(8 genes, affiliation 50002); no thresholds are invented in the build.
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPRevel.py
- lines changed 188, context: html, text, full: html, text
aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446
Adds the 12 per-track build scripts under
src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies,
REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen
EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain
hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4
per-variant OR, and the NON-FINAL provisional classifier) plus the build
documentation at src/hg/makeDb/doc/Cardiomyopathy.txt.
All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs
(8 genes, affiliation 50002); no thresholds are invented in the build.
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPWalsh2019.py
- lines changed 354, context: html, text, full: html, text
aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446
Adds the 12 per-track build scripts under
src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies,
REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen
EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain
hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4
per-variant OR, and the NON-FINAL provisional classifier) plus the build
documentation at src/hg/makeDb/doc/Cardiomyopathy.txt.
All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs
(8 genes, affiliation 50002); no thresholds are invented in the build.
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPWalshOR.py
- lines changed 180, context: html, text, full: html, text
aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446
Adds the 12 per-track build scripts under
src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies,
REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen
EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain
hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4
per-variant OR, and the NON-FINAL provisional classifier) plus the build
documentation at src/hg/makeDb/doc/Cardiomyopathy.txt.
All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs
(8 genes, affiliation 50002); no thresholds are invented in the build.
- src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
- lines changed 1, context: html, text, full: html, text
fcb3dd044df301a3c0ea4588e1debf7068b00333 Mon Jun 29 15:43:06 2026 -0700
lrSv: fresh-eyes audit fixes + multi-line HTML mouseOvers on all subtracks. refs #36258
Audit fixes:
- lrSv.html summary table: recompute the per-dataset min/median/max SV-length
columns from current data (length = max(svLen,insLen)); the old values came
from the .ra filter bounds and were off by one in several rows. Fixes the
stale lrSvAll Max (190,088,223 -> 57,207,413, left over from before KimPD was
dropped from the merge) and the APR row's length convention.
- decodeSv.html: align the opening Description to the displayed (deduped) counts
(119,453 / 41,216 DEL) instead of the upstream release counts, noting the
dedup from the 133,886-record release.
- Drop dead svType filter options (CNV/BND/MEI/CTX) that appear in no subtrack,
from the lrSv supertrack filterValues.svType and from lrSvAll (both the
generated lrSvAll.ra and the lrSvMergeAll.py generator).
Reformat the mouseOver of all 16 subtracks to the same multi-line bold-label
HTML style as lrSvAll (Var / SV len / Ins len / per-track fields), using each
track's existing fields.
- src/hg/makeDb/scripts/popEve/extractPopEve.py
- lines changed 99, context: html, text, full: html, text
b99548fc6477e8f2b46f571248147aab27d5766b Tue Jun 30 17:57:20 2026 -0700
Add popEVE proteome-wide missense deleteriousness track for hg38. refs #37791
New heatmap bigBed track under the Deleteriousness Predictions superTrack, built from
the UKBB-trained popEVE v1.1 GRCh38 VCF. One heatmap entry per protein (columns = amino
acid positions at codon coordinates, rows = 20 amino acids), colored on a global,
cross-gene gradient keyed to the raw popEVE score.
Adds the conversion scripts (extractPopEve.py, vcfToPopEveHeatmap.py, popEve_heatmap.as),
the makedoc, the trackDb stanza and description page, and gates the track alpha via an
include in predictionScoresSuper.ra.
- src/hg/makeDb/scripts/popEve/popEve_heatmap.as
- lines changed 24, context: html, text, full: html, text
b99548fc6477e8f2b46f571248147aab27d5766b Tue Jun 30 17:57:20 2026 -0700
Add popEVE proteome-wide missense deleteriousness track for hg38. refs #37791
New heatmap bigBed track under the Deleteriousness Predictions superTrack, built from
the UKBB-trained popEVE v1.1 GRCh38 VCF. One heatmap entry per protein (columns = amino
acid positions at codon coordinates, rows = 20 amino acids), colored on a global,
cross-gene gradient keyed to the raw popEVE score.
Adds the conversion scripts (extractPopEve.py, vcfToPopEveHeatmap.py, popEve_heatmap.as),
the makedoc, the trackDb stanza and description page, and gates the track alpha via an
include in predictionScoresSuper.ra.
- src/hg/makeDb/scripts/popEve/vcfToPopEveHeatmap.py
- lines changed 268, context: html, text, full: html, text
b99548fc6477e8f2b46f571248147aab27d5766b Tue Jun 30 17:57:20 2026 -0700
Add popEVE proteome-wide missense deleteriousness track for hg38. refs #37791
New heatmap bigBed track under the Deleteriousness Predictions superTrack, built from
the UKBB-trained popEVE v1.1 GRCh38 VCF. One heatmap entry per protein (columns = amino
acid positions at codon coordinates, rows = 20 amino acids), colored on a global,
cross-gene gradient keyed to the raw popEVE score.
Adds the conversion scripts (extractPopEve.py, vcfToPopEveHeatmap.py, popEve_heatmap.as),
the makedoc, the trackDb stanza and description page, and gates the track alpha via an
include in predictionScoresSuper.ra.
- src/hg/makeDb/scripts/tad/buildTads3dgb.py
- lines changed 1, context: html, text, full: html, text
5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
Polish TAD description pages and bold the track mouseOvers. refs #21599
Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution
summary table (track / feature / calling method / resolution), placed at the end of
the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra)
to the Methods section; sentence-case the "How to use these tracks" heading.
mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"),
Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate
lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability
("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build
scripts so regenerated stanzas carry the same formatting.
- src/hg/makeDb/scripts/tad/buildTadsEncode.py
- lines changed 2, context: html, text, full: html, text
5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
Polish TAD description pages and bold the track mouseOvers. refs #21599
Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution
summary table (track / feature / calling method / resolution), placed at the end of
the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra)
to the Methods section; sentence-case the "How to use these tracks" heading.
mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"),
Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate
lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability
("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build
scripts so regenerated stanzas carry the same formatting.
- src/hg/makeDb/scripts/varFreqs/databases.tsv
- lines changed 10, context: html, text, full: html, text
5ad55adbb6a5cc72a393700130584aa87fef2c89 Tue Jun 30 06:15:44 2026 -0700
varFreqs: add Top 3 source AFs to mouseOvers; audit excludes SGDP and SVatalog. refs #36642
Adds a Top 3 source AFs ranking to the varFreqsAffected and varFreqsBackground
mouseOvers. Alongside the pooled allele frequency, the mouseOver now lists the
three cohorts/arms with the highest per-source AF, formatted as
"Source (AF), Source (AF), Source (AF)". Disease cohorts with phenotype splits
carry the arm label (SPARK ASD, SCHEMA case, GREGoR unaffected); population
cohorts use the bare key. Per-population sub-ancestries are deliberately
excluded so a high sub-pop AF cannot crowd out actual project-level signals.
vcfToBigBed.py adds a top_n_source_afs helper, collects per-arm AFs into
affected_arm_afs / background_arm_afs, and emits two new fields
topAffectedSources and topBackgroundSources. AS schema field count 163 -> 165.
An AF-distribution sweep across all 28 source cohorts identified SGDP and
SVatalog as encoding allele counts per genotyped individual (small N, AF
defaults near 0.5), making their per-source AF unreliable for the ranking.
Adds a skip_top_ranking column (col 9) to databases.tsv, set to 1 for SGDP
and SVatalog, and gates the per-arm AF append in vcfToBigBed.py on this
flag. Both cohorts still contribute to pooled backgroundAC/AN/AF and still
appear in backgroundSources; they are only suppressed from the Top 3.
Description pages varFreqsAffected.html and varFreqsBackground.html document
the ranking; the latter also documents the SGDP/SVatalog exclusion. Build
documentation in varFreqs.txt is updated.
- src/hg/makeDb/scripts/varFreqs/vcfToBigBed.py
- lines changed 95, context: html, text, full: html, text
5ad55adbb6a5cc72a393700130584aa87fef2c89 Tue Jun 30 06:15:44 2026 -0700
varFreqs: add Top 3 source AFs to mouseOvers; audit excludes SGDP and SVatalog. refs #36642
Adds a Top 3 source AFs ranking to the varFreqsAffected and varFreqsBackground
mouseOvers. Alongside the pooled allele frequency, the mouseOver now lists the
three cohorts/arms with the highest per-source AF, formatted as
"Source (AF), Source (AF), Source (AF)". Disease cohorts with phenotype splits
carry the arm label (SPARK ASD, SCHEMA case, GREGoR unaffected); population
cohorts use the bare key. Per-population sub-ancestries are deliberately
excluded so a high sub-pop AF cannot crowd out actual project-level signals.
vcfToBigBed.py adds a top_n_source_afs helper, collects per-arm AFs into
affected_arm_afs / background_arm_afs, and emits two new fields
topAffectedSources and topBackgroundSources. AS schema field count 163 -> 165.
An AF-distribution sweep across all 28 source cohorts identified SGDP and
SVatalog as encoding allele counts per genotyped individual (small N, AF
defaults near 0.5), making their per-source AF unreliable for the ranking.
Adds a skip_top_ranking column (col 9) to databases.tsv, set to 1 for SGDP
and SVatalog, and gates the per-arm AF append in vcfToBigBed.py on this
flag. Both cohorts still contribute to pooled backgroundAC/AN/AF and still
appear in backgroundSources; they are only suppressed from the Top 3.
Description pages varFreqsAffected.html and varFreqsBackground.html document
the ranking; the latter also documents the SGDP/SVatalog exclusion. Build
documentation in varFreqs.txt is updated.
- src/hg/makeDb/trackDb/human/aou1kSv.html
- lines changed 1, context: html, text, full: html, text
9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258
Per the updated qa-track standard, link the track's UCSC source artifacts on
github.com/ucscGenomeBrowser/kent from every lrSv description page:
- Add the missing links to the lrSv supertrack page and colorsDbSv.
- Backfill the trackDb.ra link (third artifact) across the subtrack pages that
already linked the makedoc + scripts dir.
lrSv1kLin is left as its placeholder (staged, not released).
- src/hg/makeDb/trackDb/human/aprSv.html
- lines changed 1, context: html, text, full: html, text
9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258
Per the updated qa-track standard, link the track's UCSC source artifacts on
github.com/ucscGenomeBrowser/kent from every lrSv description page:
- Add the missing links to the lrSv supertrack page and colorsDbSv.
- Backfill the trackDb.ra link (third artifact) across the subtrack pages that
already linked the makedoc + scripts dir.
lrSv1kLin is left as its placeholder (staged, not released).
- src/hg/makeDb/trackDb/human/chirmade101Sv.html
- lines changed 1, context: html, text, full: html, text
9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258
Per the updated qa-track standard, link the track's UCSC source artifacts on
github.com/ucscGenomeBrowser/kent from every lrSv description page:
- Add the missing links to the lrSv supertrack page and colorsDbSv.
- Backfill the trackDb.ra link (third artifact) across the subtrack pages that
already linked the makedoc + scripts dir.
lrSv1kLin is left as its placeholder (staged, not released).
- src/hg/makeDb/trackDb/human/colorsDbSv.html
- lines changed 8, context: html, text, full: html, text
9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258
Per the updated qa-track standard, link the track's UCSC source artifacts on
github.com/ucscGenomeBrowser/kent from every lrSv description page:
- Add the missing links to the lrSv supertrack page and colorsDbSv.
- Backfill the trackDb.ra link (third artifact) across the subtrack pages that
already linked the makedoc + scripts dir.
lrSv1kLin is left as its placeholder (staged, not released).
- src/hg/makeDb/trackDb/human/cpc1Sv.html
- lines changed 1, context: html, text, full: html, text
9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258
Per the updated qa-track standard, link the track's UCSC source artifacts on
github.com/ucscGenomeBrowser/kent from every lrSv description page:
- Add the missing links to the lrSv supertrack page and colorsDbSv.
- Backfill the trackDb.ra link (third artifact) across the subtrack pages that
already linked the makedoc + scripts dir.
lrSv1kLin is left as its placeholder (staged, not released).
- src/hg/makeDb/trackDb/human/decodeSv.html
- lines changed 1, context: html, text, full: html, text
9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258
Per the updated qa-track standard, link the track's UCSC source artifacts on
github.com/ucscGenomeBrowser/kent from every lrSv description page:
- Add the missing links to the lrSv supertrack page and colorsDbSv.
- Backfill the trackDb.ra link (third artifact) across the subtrack pages that
already linked the makedoc + scripts dir.
lrSv1kLin is left as its placeholder (staged, not released).
- lines changed 4, context: html, text, full: html, text
fcb3dd044df301a3c0ea4588e1debf7068b00333 Mon Jun 29 15:43:06 2026 -0700
lrSv: fresh-eyes audit fixes + multi-line HTML mouseOvers on all subtracks. refs #36258
Audit fixes:
- lrSv.html summary table: recompute the per-dataset min/median/max SV-length
columns from current data (length = max(svLen,insLen)); the old values came
from the .ra filter bounds and were off by one in several rows. Fixes the
stale lrSvAll Max (190,088,223 -> 57,207,413, left over from before KimPD was
dropped from the merge) and the APR row's length convention.
- decodeSv.html: align the opening Description to the displayed (deduped) counts
(119,453 / 41,216 DEL) instead of the upstream release counts, noting the
dedup from the 133,886-record release.
- Drop dead svType filter options (CNV/BND/MEI/CTX) that appear in no subtrack,
from the lrSv supertrack filterValues.svType and from lrSvAll (both the
generated lrSvAll.ra and the lrSvMergeAll.py generator).
Reformat the mouseOver of all 16 subtracks to the same multi-line bold-label
HTML style as lrSvAll (Var / SV len / Ins len / per-track fields), using each
track's existing fields.
- src/hg/makeDb/trackDb/human/ga4kSv.html
- lines changed 1, context: html, text, full: html, text
9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258
Per the updated qa-track standard, link the track's UCSC source artifacts on
github.com/ucscGenomeBrowser/kent from every lrSv description page:
- Add the missing links to the lrSv supertrack page and colorsDbSv.
- Backfill the trackDb.ra link (third artifact) across the subtrack pages that
already linked the makedoc + scripts dir.
lrSv1kLin is left as its placeholder (staged, not released).
- src/hg/makeDb/trackDb/human/gustafsonSv.html
- lines changed 1, context: html, text, full: html, text
9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258
Per the updated qa-track standard, link the track's UCSC source artifacts on
github.com/ucscGenomeBrowser/kent from every lrSv description page:
- Add the missing links to the lrSv supertrack page and colorsDbSv.
- Backfill the trackDb.ra link (third artifact) across the subtrack pages that
already linked the makedoc + scripts dir.
lrSv1kLin is left as its placeholder (staged, not released).
- src/hg/makeDb/trackDb/human/han945Sv.html
- lines changed 1, context: html, text, full: html, text
9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258
Per the updated qa-track standard, link the track's UCSC source artifacts on
github.com/ucscGenomeBrowser/kent from every lrSv description page:
- Add the missing links to the lrSv supertrack page and colorsDbSv.
- Backfill the trackDb.ra link (third artifact) across the subtrack pages that
already linked the makedoc + scripts dir.
lrSv1kLin is left as its placeholder (staged, not released).
- src/hg/makeDb/trackDb/human/hg19/tad.ra
- lines changed 24, context: html, text, full: html, text
5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
Polish TAD description pages and bold the track mouseOvers. refs #21599
Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution
summary table (track / feature / calling method / resolution), placed at the end of
the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra)
to the Methods section; sentence-case the "How to use these tracks" heading.
mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"),
Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate
lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability
("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build
scripts so regenerated stanzas carry the same formatting.
- src/hg/makeDb/trackDb/human/hg19/tads.html
- lines changed 23, context: html, text, full: html, text
5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
Polish TAD description pages and bold the track mouseOvers. refs #21599
Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution
summary table (track / feature / calling method / resolution), placed at the end of
the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra)
to the Methods section; sentence-case the "How to use these tracks" heading.
mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"),
Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate
lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability
("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build
scripts so regenerated stanzas carry the same formatting.
- src/hg/makeDb/trackDb/human/hg38/tad.ra
- lines changed 24, context: html, text, full: html, text
5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
Polish TAD description pages and bold the track mouseOvers. refs #21599
Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution
summary table (track / feature / calling method / resolution), placed at the end of
the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra)
to the Methods section; sentence-case the "How to use these tracks" heading.
mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"),
Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate
lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability
("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build
scripts so regenerated stanzas carry the same formatting.
- src/hg/makeDb/trackDb/human/hg38/tads.html
- lines changed 25, context: html, text, full: html, text
5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
Polish TAD description pages and bold the track mouseOvers. refs #21599
Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution
summary table (track / feature / calling method / resolution), placed at the end of
the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra)
to the Methods section; sentence-case the "How to use these tracks" heading.
mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"),
Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate
lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability
("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build
scripts so regenerated stanzas carry the same formatting.
- src/hg/makeDb/trackDb/human/hg38/tads3dgb.ra
- lines changed 464, context: html, text, full: html, text
5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
Polish TAD description pages and bold the track mouseOvers. refs #21599
Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution
summary table (track / feature / calling method / resolution), placed at the end of
the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra)
to the Methods section; sentence-case the "How to use these tracks" heading.
mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"),
Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate
lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability
("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build
scripts so regenerated stanzas carry the same formatting.
- src/hg/makeDb/trackDb/human/hg38/tadsEncode.ra
- lines changed 117, context: html, text, full: html, text
5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
Polish TAD description pages and bold the track mouseOvers. refs #21599
Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution
summary table (track / feature / calling method / resolution), placed at the end of
the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra)
to the Methods section; sentence-case the "How to use these tracks" heading.
mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"),
Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate
lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability
("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build
scripts so regenerated stanzas carry the same formatting.
- src/hg/makeDb/trackDb/human/hgsvc2Sv.html
- lines changed 1, context: html, text, full: html, text
9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258
Per the updated qa-track standard, link the track's UCSC source artifacts on
github.com/ucscGenomeBrowser/kent from every lrSv description page:
- Add the missing links to the lrSv supertrack page and colorsDbSv.
- Backfill the trackDb.ra link (third artifact) across the subtrack pages that
already linked the makedoc + scripts dir.
lrSv1kLin is left as its placeholder (staged, not released).
- src/hg/makeDb/trackDb/human/hgsvc3Sv.html
- lines changed 1, context: html, text, full: html, text
9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258
Per the updated qa-track standard, link the track's UCSC source artifacts on
github.com/ucscGenomeBrowser/kent from every lrSv description page:
- Add the missing links to the lrSv supertrack page and colorsDbSv.
- Backfill the trackDb.ra link (third artifact) across the subtrack pages that
already linked the makedoc + scripts dir.
lrSv1kLin is left as its placeholder (staged, not released).
- src/hg/makeDb/trackDb/human/hprc2v21Sv.html
- lines changed 2, context: html, text, full: html, text
9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258
Per the updated qa-track standard, link the track's UCSC source artifacts on
github.com/ucscGenomeBrowser/kent from every lrSv description page:
- Add the missing links to the lrSv supertrack page and colorsDbSv.
- Backfill the trackDb.ra link (third artifact) across the subtrack pages that
already linked the makedoc + scripts dir.
lrSv1kLin is left as its placeholder (staged, not released).
- src/hg/makeDb/trackDb/human/lrSv.html
- lines changed 8, context: html, text, full: html, text
9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258
Per the updated qa-track standard, link the track's UCSC source artifacts on
github.com/ucscGenomeBrowser/kent from every lrSv description page:
- Add the missing links to the lrSv supertrack page and colorsDbSv.
- Backfill the trackDb.ra link (third artifact) across the subtrack pages that
already linked the makedoc + scripts dir.
lrSv1kLin is left as its placeholder (staged, not released).
- lines changed 20, context: html, text, full: html, text
fcb3dd044df301a3c0ea4588e1debf7068b00333 Mon Jun 29 15:43:06 2026 -0700
lrSv: fresh-eyes audit fixes + multi-line HTML mouseOvers on all subtracks. refs #36258
Audit fixes:
- lrSv.html summary table: recompute the per-dataset min/median/max SV-length
columns from current data (length = max(svLen,insLen)); the old values came
from the .ra filter bounds and were off by one in several rows. Fixes the
stale lrSvAll Max (190,088,223 -> 57,207,413, left over from before KimPD was
dropped from the merge) and the APR row's length convention.
- decodeSv.html: align the opening Description to the displayed (deduped) counts
(119,453 / 41,216 DEL) instead of the upstream release counts, noting the
dedup from the 133,886-record release.
- Drop dead svType filter options (CNV/BND/MEI/CTX) that appear in no subtrack,
from the lrSv supertrack filterValues.svType and from lrSvAll (both the
generated lrSvAll.ra and the lrSvMergeAll.py generator).
Reformat the mouseOver of all 16 subtracks to the same multi-line bold-label
HTML style as lrSvAll (Var / SV len / Ins len / per-track fields), using each
track's existing fields.
- src/hg/makeDb/trackDb/human/lrSv.ra
- lines changed 17, context: html, text, full: html, text
fcb3dd044df301a3c0ea4588e1debf7068b00333 Mon Jun 29 15:43:06 2026 -0700
lrSv: fresh-eyes audit fixes + multi-line HTML mouseOvers on all subtracks. refs #36258
Audit fixes:
- lrSv.html summary table: recompute the per-dataset min/median/max SV-length
columns from current data (length = max(svLen,insLen)); the old values came
from the .ra filter bounds and were off by one in several rows. Fixes the
stale lrSvAll Max (190,088,223 -> 57,207,413, left over from before KimPD was
dropped from the merge) and the APR row's length convention.
- decodeSv.html: align the opening Description to the displayed (deduped) counts
(119,453 / 41,216 DEL) instead of the upstream release counts, noting the
dedup from the 133,886-record release.
- Drop dead svType filter options (CNV/BND/MEI/CTX) that appear in no subtrack,
from the lrSv supertrack filterValues.svType and from lrSvAll (both the
generated lrSvAll.ra and the lrSvMergeAll.py generator).
Reformat the mouseOver of all 16 subtracks to the same multi-line bold-label
HTML style as lrSvAll (Var / SV len / Ins len / per-track fields), using each
track's existing fields.
- src/hg/makeDb/trackDb/human/lrSv1kgOnt.html
- lines changed 1, context: html, text, full: html, text
9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258
Per the updated qa-track standard, link the track's UCSC source artifacts on
github.com/ucscGenomeBrowser/kent from every lrSv description page:
- Add the missing links to the lrSv supertrack page and colorsDbSv.
- Backfill the trackDb.ra link (third artifact) across the subtrack pages that
already linked the makedoc + scripts dir.
lrSv1kLin is left as its placeholder (staged, not released).
- src/hg/makeDb/trackDb/human/lrSvAll.html
- lines changed 1, context: html, text, full: html, text
9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258
Per the updated qa-track standard, link the track's UCSC source artifacts on
github.com/ucscGenomeBrowser/kent from every lrSv description page:
- Add the missing links to the lrSv supertrack page and colorsDbSv.
- Backfill the trackDb.ra link (third artifact) across the subtrack pages that
already linked the makedoc + scripts dir.
lrSv1kLin is left as its placeholder (staged, not released).
- src/hg/makeDb/trackDb/human/lrSvAll.ra
- lines changed 1, context: html, text, full: html, text
fcb3dd044df301a3c0ea4588e1debf7068b00333 Mon Jun 29 15:43:06 2026 -0700
lrSv: fresh-eyes audit fixes + multi-line HTML mouseOvers on all subtracks. refs #36258
Audit fixes:
- lrSv.html summary table: recompute the per-dataset min/median/max SV-length
columns from current data (length = max(svLen,insLen)); the old values came
from the .ra filter bounds and were off by one in several rows. Fixes the
stale lrSvAll Max (190,088,223 -> 57,207,413, left over from before KimPD was
dropped from the merge) and the APR row's length convention.
- decodeSv.html: align the opening Description to the displayed (deduped) counts
(119,453 / 41,216 DEL) instead of the upstream release counts, noting the
dedup from the 133,886-record release.
- Drop dead svType filter options (CNV/BND/MEI/CTX) that appear in no subtrack,
from the lrSv supertrack filterValues.svType and from lrSvAll (both the
generated lrSvAll.ra and the lrSvMergeAll.py generator).
Reformat the mouseOver of all 16 subtracks to the same multi-line bold-label
HTML style as lrSvAll (Var / SV len / Ins len / per-track fields), using each
track's existing fields.
- src/hg/makeDb/trackDb/human/popEve.html
- lines changed 181, context: html, text, full: html, text
b99548fc6477e8f2b46f571248147aab27d5766b Tue Jun 30 17:57:20 2026 -0700
Add popEVE proteome-wide missense deleteriousness track for hg38. refs #37791
New heatmap bigBed track under the Deleteriousness Predictions superTrack, built from
the UKBB-trained popEVE v1.1 GRCh38 VCF. One heatmap entry per protein (columns = amino
acid positions at codon coordinates, rows = 20 amino acids), colored on a global,
cross-gene gradient keyed to the raw popEVE score.
Adds the conversion scripts (extractPopEve.py, vcfToPopEveHeatmap.py, popEve_heatmap.as),
the makedoc, the trackDb stanza and description page, and gates the track alpha via an
include in predictionScoresSuper.ra.
- src/hg/makeDb/trackDb/human/popEve.ra
- lines changed 13, context: html, text, full: html, text
b99548fc6477e8f2b46f571248147aab27d5766b Tue Jun 30 17:57:20 2026 -0700
Add popEVE proteome-wide missense deleteriousness track for hg38. refs #37791
New heatmap bigBed track under the Deleteriousness Predictions superTrack, built from
the UKBB-trained popEVE v1.1 GRCh38 VCF. One heatmap entry per protein (columns = amino
acid positions at codon coordinates, rows = 20 amino acids), colored on a global,
cross-gene gradient keyed to the raw popEVE score.
Adds the conversion scripts (extractPopEve.py, vcfToPopEveHeatmap.py, popEve_heatmap.as),
the makedoc, the trackDb stanza and description page, and gates the track alpha via an
include in predictionScoresSuper.ra.
- src/hg/makeDb/trackDb/human/predictionScoresSuper.html
- lines changed 43, context: html, text, full: html, text
10c0695c8a4ff88a24ae2f446b4ef705fdbc37d8 Tue Jun 30 17:57:33 2026 -0700
Add popEVE and EVE to the Deleteriousness Predictions page and related tracks. refs #37791
Document EVE and popEVE on the predictionScoresSuper description page, which previously
listed the other member scores but not these two. Also add reciprocal relatedTracks
cross-links between popEVE and EVE, AlphaMissense, PrimateAI-3D, ClinPred, and REVEL.
- src/hg/makeDb/trackDb/human/predictionScoresSuper.ra
- lines changed 1, context: html, text, full: html, text
b99548fc6477e8f2b46f571248147aab27d5766b Tue Jun 30 17:57:20 2026 -0700
Add popEVE proteome-wide missense deleteriousness track for hg38. refs #37791
New heatmap bigBed track under the Deleteriousness Predictions superTrack, built from
the UKBB-trained popEVE v1.1 GRCh38 VCF. One heatmap entry per protein (columns = amino
acid positions at codon coordinates, rows = 20 amino acids), colored on a global,
cross-gene gradient keyed to the raw popEVE score.
Adds the conversion scripts (extractPopEve.py, vcfToPopEveHeatmap.py, popEve_heatmap.as),
the makedoc, the trackDb stanza and description page, and gates the track alpha via an
include in predictionScoresSuper.ra.
- src/hg/makeDb/trackDb/human/tommoJpSv.html
- lines changed 1, context: html, text, full: html, text
9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258
Per the updated qa-track standard, link the track's UCSC source artifacts on
github.com/ucscGenomeBrowser/kent from every lrSv description page:
- Add the missing links to the lrSv supertrack page and colorsDbSv.
- Backfill the trackDb.ra link (third artifact) across the subtrack pages that
already linked the makedoc + scripts dir.
lrSv1kLin is left as its placeholder (staged, not released).
- src/hg/makeDb/trackDb/human/varFreqs.ra
- lines changed 2, context: html, text, full: html, text
5ad55adbb6a5cc72a393700130584aa87fef2c89 Tue Jun 30 06:15:44 2026 -0700
varFreqs: add Top 3 source AFs to mouseOvers; audit excludes SGDP and SVatalog. refs #36642
Adds a Top 3 source AFs ranking to the varFreqsAffected and varFreqsBackground
mouseOvers. Alongside the pooled allele frequency, the mouseOver now lists the
three cohorts/arms with the highest per-source AF, formatted as
"Source (AF), Source (AF), Source (AF)". Disease cohorts with phenotype splits
carry the arm label (SPARK ASD, SCHEMA case, GREGoR unaffected); population
cohorts use the bare key. Per-population sub-ancestries are deliberately
excluded so a high sub-pop AF cannot crowd out actual project-level signals.
vcfToBigBed.py adds a top_n_source_afs helper, collects per-arm AFs into
affected_arm_afs / background_arm_afs, and emits two new fields
topAffectedSources and topBackgroundSources. AS schema field count 163 -> 165.
An AF-distribution sweep across all 28 source cohorts identified SGDP and
SVatalog as encoding allele counts per genotyped individual (small N, AF
defaults near 0.5), making their per-source AF unreliable for the ranking.
Adds a skip_top_ranking column (col 9) to databases.tsv, set to 1 for SGDP
and SVatalog, and gates the per-arm AF append in vcfToBigBed.py on this
flag. Both cohorts still contribute to pooled backgroundAC/AN/AF and still
appear in backgroundSources; they are only suppressed from the Top 3.
Description pages varFreqsAffected.html and varFreqsBackground.html document
the ranking; the latter also documents the SGDP/SVatalog exclusion. Build
documentation in varFreqs.txt is updated.
- lines changed 1, context: html, text, full: html, text
aaead1eeb6e454442e1a6c6dcb6a7c41cf3991d6 Tue Jun 30 16:49:27 2026 -0700
varFreqs: July 1, 2026 release announcement, newsarch + indexNews + pennantIcon. refs #36642
Adds the New SNV Frequencies supertrack release entry to newsarch.html
(anchor #070126) and indexNews.html for the upcoming July 1, 2026 release.
The newsarch entry features rs4986893, the CYP2C19 East Asian founder
stop-gained variant, as the screenshot example. Updates the varFreqs
supertrack pennantIcon to point to the new anchor with hover text
"Released Jul. 1, 2026".
- src/hg/makeDb/trackDb/human/varFreqsAffected.html
- lines changed 15, context: html, text, full: html, text
5ad55adbb6a5cc72a393700130584aa87fef2c89 Tue Jun 30 06:15:44 2026 -0700
varFreqs: add Top 3 source AFs to mouseOvers; audit excludes SGDP and SVatalog. refs #36642
Adds a Top 3 source AFs ranking to the varFreqsAffected and varFreqsBackground
mouseOvers. Alongside the pooled allele frequency, the mouseOver now lists the
three cohorts/arms with the highest per-source AF, formatted as
"Source (AF), Source (AF), Source (AF)". Disease cohorts with phenotype splits
carry the arm label (SPARK ASD, SCHEMA case, GREGoR unaffected); population
cohorts use the bare key. Per-population sub-ancestries are deliberately
excluded so a high sub-pop AF cannot crowd out actual project-level signals.
vcfToBigBed.py adds a top_n_source_afs helper, collects per-arm AFs into
affected_arm_afs / background_arm_afs, and emits two new fields
topAffectedSources and topBackgroundSources. AS schema field count 163 -> 165.
An AF-distribution sweep across all 28 source cohorts identified SGDP and
SVatalog as encoding allele counts per genotyped individual (small N, AF
defaults near 0.5), making their per-source AF unreliable for the ranking.
Adds a skip_top_ranking column (col 9) to databases.tsv, set to 1 for SGDP
and SVatalog, and gates the per-arm AF append in vcfToBigBed.py on this
flag. Both cohorts still contribute to pooled backgroundAC/AN/AF and still
appear in backgroundSources; they are only suppressed from the Top 3.
Description pages varFreqsAffected.html and varFreqsBackground.html document
the ranking; the latter also documents the SGDP/SVatalog exclusion. Build
documentation in varFreqs.txt is updated.
- src/hg/makeDb/trackDb/human/varFreqsBackground.html
- lines changed 29, context: html, text, full: html, text
5ad55adbb6a5cc72a393700130584aa87fef2c89 Tue Jun 30 06:15:44 2026 -0700
varFreqs: add Top 3 source AFs to mouseOvers; audit excludes SGDP and SVatalog. refs #36642
Adds a Top 3 source AFs ranking to the varFreqsAffected and varFreqsBackground
mouseOvers. Alongside the pooled allele frequency, the mouseOver now lists the
three cohorts/arms with the highest per-source AF, formatted as
"Source (AF), Source (AF), Source (AF)". Disease cohorts with phenotype splits
carry the arm label (SPARK ASD, SCHEMA case, GREGoR unaffected); population
cohorts use the bare key. Per-population sub-ancestries are deliberately
excluded so a high sub-pop AF cannot crowd out actual project-level signals.
vcfToBigBed.py adds a top_n_source_afs helper, collects per-arm AFs into
affected_arm_afs / background_arm_afs, and emits two new fields
topAffectedSources and topBackgroundSources. AS schema field count 163 -> 165.
An AF-distribution sweep across all 28 source cohorts identified SGDP and
SVatalog as encoding allele counts per genotyped individual (small N, AF
defaults near 0.5), making their per-source AF unreliable for the ranking.
Adds a skip_top_ranking column (col 9) to databases.tsv, set to 1 for SGDP
and SVatalog, and gates the per-arm AF append in vcfToBigBed.py on this
flag. Both cohorts still contribute to pooled backgroundAC/AN/AF and still
appear in backgroundSources; they are only suppressed from the Top 3.
Description pages varFreqsAffected.html and varFreqsBackground.html document
the ranking; the latter also documents the SGDP/SVatalog exclusion. Build
documentation in varFreqs.txt is updated.
- src/hg/makeDb/trackDb/mouse/mm10/tad.ra
- lines changed 2, context: html, text, full: html, text
5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
Polish TAD description pages and bold the track mouseOvers. refs #21599
Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution
summary table (track / feature / calling method / resolution), placed at the end of
the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra)
to the Methods section; sentence-case the "How to use these tracks" heading.
mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"),
Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate
lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability
("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build
scripts so regenerated stanzas carry the same formatting.
- src/hg/makeDb/trackDb/mouse/mm10/tads.html
- lines changed 22, context: html, text, full: html, text
5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
Polish TAD description pages and bold the track mouseOvers. refs #21599
Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution
summary table (track / feature / calling method / resolution), placed at the end of
the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra)
to the Methods section; sentence-case the "How to use these tracks" heading.
mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"),
Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate
lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability
("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build
scripts so regenerated stanzas carry the same formatting.
- src/hg/makeDb/trackDb/mouse/mm10/tads3dgb.ra
- lines changed 30, context: html, text, full: html, text
5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
Polish TAD description pages and bold the track mouseOvers. refs #21599
Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution
summary table (track / feature / calling method / resolution), placed at the end of
the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra)
to the Methods section; sentence-case the "How to use these tracks" heading.
mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"),
Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate
lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability
("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build
scripts so regenerated stanzas carry the same formatting.
- src/hg/makeDb/trackDb/mouse/mm10/tadsEncode.ra
- lines changed 16, context: html, text, full: html, text
5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
Polish TAD description pages and bold the track mouseOvers. refs #21599
Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution
summary table (track / feature / calling method / resolution), placed at the end of
the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra)
to the Methods section; sentence-case the "How to use these tracks" heading.
mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"),
Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate
lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability
("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build
scripts so regenerated stanzas carry the same formatting.
- src/hg/makeDb/trackDb/mouse/mm39/tad.ra
- lines changed 2, context: html, text, full: html, text
5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
Polish TAD description pages and bold the track mouseOvers. refs #21599
Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution
summary table (track / feature / calling method / resolution), placed at the end of
the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra)
to the Methods section; sentence-case the "How to use these tracks" heading.
mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"),
Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate
lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability
("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build
scripts so regenerated stanzas carry the same formatting.
- src/hg/makeDb/trackDb/mouse/mm39/tads.html
- lines changed 22, context: html, text, full: html, text
5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
Polish TAD description pages and bold the track mouseOvers. refs #21599
Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution
summary table (track / feature / calling method / resolution), placed at the end of
the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra)
to the Methods section; sentence-case the "How to use these tracks" heading.
mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"),
Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate
lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability
("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build
scripts so regenerated stanzas carry the same formatting.
- src/hg/makeDb/trackDb/mouse/mm39/tads3dgb.ra
- lines changed 30, context: html, text, full: html, text
5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
Polish TAD description pages and bold the track mouseOvers. refs #21599
Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution
summary table (track / feature / calling method / resolution), placed at the end of
the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra)
to the Methods section; sentence-case the "How to use these tracks" heading.
mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"),
Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate
lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability
("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build
scripts so regenerated stanzas carry the same formatting.
- src/hg/makeDb/trackDb/mouse/mm39/tadsEncode.ra
- lines changed 16, context: html, text, full: html, text
5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
Polish TAD description pages and bold the track mouseOvers. refs #21599
Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution
summary table (track / feature / calling method / resolution), placed at the end of
the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra)
to the Methods section; sentence-case the "How to use these tracks" heading.
mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"),
Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate
lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability
("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build
scripts so regenerated stanzas carry the same formatting.
- src/hg/makeDb/trackDb/relatedTracks.ra
- lines changed 12, context: html, text, full: html, text
10c0695c8a4ff88a24ae2f446b4ef705fdbc37d8 Tue Jun 30 17:57:33 2026 -0700
Add popEVE and EVE to the Deleteriousness Predictions page and related tracks. refs #37791
Document EVE and popEVE on the predictionScoresSuper description page, which previously
listed the other member scores but not these two. Also add reciprocal relatedTracks
cross-links between popEVE and EVE, AlphaMissense, PrimateAI-3D, ClinPred, and REVEL.
- src/hg/utils/otto/panelApp/doPanelApp.py
- lines changed 15, context: html, text, full: html, text
2dda14f9c5394e1d6fa30f3da69e74b8e8b84413 Tue Jun 30 15:34:05 2026 -0700
Fix panelApp otto crash when reading Ensembl gene locations. The script hardcoded the Ensembl release sub-key (GRch37/82, GRch38/90) when pulling gene coordinates, but PanelApp Australia moved to releases 87/115. Every Australia gene then failed both assembly lookups, leaving the dataframes empty and raising a column-count ValueError. Added an ensemblBuild() helper that selects whichever release key the API returns, and routed all gene/STR coordinate and ensembl_id lookups through it. England (still on 82/90) is unaffected.
No RM, refs otto
- src/utils/qa/errorLogKeywordSearch.py
- lines changed 1, context: html, text, full: html, text
b761e0e7b483d9fbb2832820c138c0baab13a869 Thu Jul 2 17:39:24 2026 -0700
Fix Total out of memory metric in errorLogKeywordSearch.py to count only genuine events. refs #37699
A single needMem OOM failure recurses in the errAbort/warn handler (which itself
allocates), re-emitting the "request size %llu bytes" format string many times per
crash. The old grep "needMem: Out of memory" counted every one of those frames,
inflating the weekly count ~60-175x (e.g. ~1070 reported vs ~18 genuine events for
the week of 20260614). Restrict the match to lines with a numeric request size so
only real allocation failures are counted.
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