File Changes for lrnassar
switch to commits view, user indexv502_preview to v502_preview2 (2026-07-27 to 2026-08-04) v502
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- src/hg/htdocs/allTipsRaw.html
- lines changed 39, context: html, text, full: html, text
37fb40ea02f93e45a97d04567fc6c8d6990cfba3 Mon Aug 3 16:30:26 2026 -0700
Add 22 new "Did you know?" tips and correct outdated content in the existing 25. refs #37976
New tips cover features released since the tip rotation launched (exon search in the
position box, Duplicate track, the Visible Tracks group, track container settings,
amino acid mouseovers, Change Track Color) along with long-standing features that had
no tip (custom tracks, interactive tutorials, External Tools, In-Silico PCR, BLAT all
genomes, Table Browser batch queries and intersections, Data Access sections,
next/previous item arrows, the Reverse button, GenArk and public hubs, gene details
pages, hide all and Reset All User Settings, mailing lists, the poster gallery,
View then Chromosomes, and alternate chromosome names).
Corrections to the existing tips: the Download menu item is "Download Current Track
Data" under Downloads, not "Download track data in view" under Download; /list/schema
returns a track's field schema rather than trackDb stanzas; the rotation runs weekdays,
not daily; the Hub Upload quota is 10 GB; there are now seven Recommended Track Sets;
the View menu item is "In Other Genomes (Convert)"; the Configure page label is "Text
size"; and several menu paths, button labels, and container terms were out of date.
All feature claims were verified against the v501 CGIs on genome.ucsc.edu rather than
the source tree, since master is ahead of what the public can use. Adds 10 screenshots
displayed at 2x pixel density to match the sharpness of the existing tip images.
- lines changed 4, context: html, text, full: html, text
4d078885529f20b1eb60a0dbb7931ae76793a5ea Tue Aug 4 09:24:38 2026 -0700
Fix stale alt text and copy problems in the tip rotation per CR feedback. refs #37976
The image alt text on the "Download Current Track Data" tip still carried the old
incorrect label, "Download track data in view", so the correction in the previous
commit only reached the visible text and left the wrong wording in the accessibility
layer. Also replaced the internal "RTS" abbreviation in the Recommended Track Sets
alt text with the full name.
Other copy fixes: the Track Collection Builder tip called the result a "container"
in one sentence and a "collection" in the next, so both now say collection to match
the tool name; a "which" clause in the multi-region tip attached the exon view
keyboard shortcut to "exon sequencing data" rather than to the view itself; and the
Recommended Track Sets tip listed six of the seven sets, so exon relevance was added.
- src/hg/htdocs/goldenPath/help/publicHubGuidelines.html
- lines changed 10, context: html, text, full: html, text
34aec9e1cf9e55e0f674234e490eaa596472081a Thu Jul 30 18:06:05 2026 -0700
Adding unique track labels as a public hub requirement. refs #37922
Every track needs a shortLabel and longLabel that distinguish it from the other
tracks in the hub. This was already how we reviewed public hub submissions, but it
was not written down anywhere on the guidelines page, which previously only carried
the shortLabel length recommendation.
Notes that a metadata table on a composite configuration page does not satisfy this,
since those values are not displayed anywhere outside that page. Came up on the
Sci-ModoM submission, where 161 subtracks shared 8 shortLabels and 33 longLabels.
- src/hg/htdocs/goldenPath/help/trackDb/changes.html
- lines changed 10, context: html, text, full: html, text
ca4b6d0d29c6d29b43df588a4635b556acc84f7f Fri Jul 31 16:59:51 2026 -0700
Fix maxCheckboxes spelling in trackDb docs, which listed it as maxCheckBoxes.
Setting names are case sensitive and the browser reads the lowercase form, so
hubs copying the documented spelling silently got the default. Also adds
level-new tags to the faceted composite settings metaDataUrl, primaryKey,
maxCheckboxes and dataTypes so hubCheck -checkSettings recognizes them instead
of reporting them as unknown. refs #37965
- src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
- lines changed 3, context: html, text, full: html, text
ca4b6d0d29c6d29b43df588a4635b556acc84f7f Fri Jul 31 16:59:51 2026 -0700
Fix maxCheckboxes spelling in trackDb docs, which listed it as maxCheckBoxes.
Setting names are case sensitive and the browser reads the lowercase form, so
hubs copying the documented spelling silently got the default. Also adds
level-new tags to the faceted composite settings metaDataUrl, primaryKey,
maxCheckboxes and dataTypes so hubCheck -checkSettings recognizes them instead
of reporting them as unknown. refs #37965
- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
- lines changed 6, context: html, text, full: html, text
ca4b6d0d29c6d29b43df588a4635b556acc84f7f Fri Jul 31 16:59:51 2026 -0700
Fix maxCheckboxes spelling in trackDb docs, which listed it as maxCheckBoxes.
Setting names are case sensitive and the browser reads the lowercase form, so
hubs copying the documented spelling silently got the default. Also adds
level-new tags to the faceted composite settings metaDataUrl, primaryKey,
maxCheckboxes and dataTypes so hubCheck -checkSettings recognizes them instead
of reporting them as unknown. refs #37965
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
- lines changed 2, context: html, text, full: html, text
ca4b6d0d29c6d29b43df588a4635b556acc84f7f Fri Jul 31 16:59:51 2026 -0700
Fix maxCheckboxes spelling in trackDb docs, which listed it as maxCheckBoxes.
Setting names are case sensitive and the browser reads the lowercase form, so
hubs copying the documented spelling silently got the default. Also adds
level-new tags to the faceted composite settings metaDataUrl, primaryKey,
maxCheckboxes and dataTypes so hubCheck -checkSettings recognizes them instead
of reporting them as unknown. refs #37965
- src/hg/htdocs/images/containerApplyTip.png
- lines changed 0, context: html, text, full: html, text
37fb40ea02f93e45a97d04567fc6c8d6990cfba3 Mon Aug 3 16:30:26 2026 -0700
Add 22 new "Did you know?" tips and correct outdated content in the existing 25. refs #37976
New tips cover features released since the tip rotation launched (exon search in the
position box, Duplicate track, the Visible Tracks group, track container settings,
amino acid mouseovers, Change Track Color) along with long-standing features that had
no tip (custom tracks, interactive tutorials, External Tools, In-Silico PCR, BLAT all
genomes, Table Browser batch queries and intersections, Data Access sections,
next/previous item arrows, the Reverse button, GenArk and public hubs, gene details
pages, hide all and Reset All User Settings, mailing lists, the poster gallery,
View then Chromosomes, and alternate chromosome names).
Corrections to the existing tips: the Download menu item is "Download Current Track
Data" under Downloads, not "Download track data in view" under Download; /list/schema
returns a track's field schema rather than trackDb stanzas; the rotation runs weekdays,
not daily; the Hub Upload quota is 10 GB; there are now seven Recommended Track Sets;
the View menu item is "In Other Genomes (Convert)"; the Configure page label is "Text
size"; and several menu paths, button labels, and container terms were out of date.
All feature claims were verified against the v501 CGIs on genome.ucsc.edu rather than
the source tree, since master is ahead of what the public can use. Adds 10 screenshots
displayed at 2x pixel density to match the sharpness of the existing tip images.
- src/hg/htdocs/images/duplicateTrackTip.png
- lines changed 0, context: html, text, full: html, text
37fb40ea02f93e45a97d04567fc6c8d6990cfba3 Mon Aug 3 16:30:26 2026 -0700
Add 22 new "Did you know?" tips and correct outdated content in the existing 25. refs #37976
New tips cover features released since the tip rotation launched (exon search in the
position box, Duplicate track, the Visible Tracks group, track container settings,
amino acid mouseovers, Change Track Color) along with long-standing features that had
no tip (custom tracks, interactive tutorials, External Tools, In-Silico PCR, BLAT all
genomes, Table Browser batch queries and intersections, Data Access sections,
next/previous item arrows, the Reverse button, GenArk and public hubs, gene details
pages, hide all and Reset All User Settings, mailing lists, the poster gallery,
View then Chromosomes, and alternate chromosome names).
Corrections to the existing tips: the Download menu item is "Download Current Track
Data" under Downloads, not "Download track data in view" under Download; /list/schema
returns a track's field schema rather than trackDb stanzas; the rotation runs weekdays,
not daily; the Hub Upload quota is 10 GB; there are now seven Recommended Track Sets;
the View menu item is "In Other Genomes (Convert)"; the Configure page label is "Text
size"; and several menu paths, button labels, and container terms were out of date.
All feature claims were verified against the v501 CGIs on genome.ucsc.edu rather than
the source tree, since master is ahead of what the public can use. Adds 10 screenshots
displayed at 2x pixel density to match the sharpness of the existing tip images.
- src/hg/htdocs/images/exonSearchTip.png
- lines changed 0, context: html, text, full: html, text
37fb40ea02f93e45a97d04567fc6c8d6990cfba3 Mon Aug 3 16:30:26 2026 -0700
Add 22 new "Did you know?" tips and correct outdated content in the existing 25. refs #37976
New tips cover features released since the tip rotation launched (exon search in the
position box, Duplicate track, the Visible Tracks group, track container settings,
amino acid mouseovers, Change Track Color) along with long-standing features that had
no tip (custom tracks, interactive tutorials, External Tools, In-Silico PCR, BLAT all
genomes, Table Browser batch queries and intersections, Data Access sections,
next/previous item arrows, the Reverse button, GenArk and public hubs, gene details
pages, hide all and Reset All User Settings, mailing lists, the poster gallery,
View then Chromosomes, and alternate chromosome names).
Corrections to the existing tips: the Download menu item is "Download Current Track
Data" under Downloads, not "Download track data in view" under Download; /list/schema
returns a track's field schema rather than trackDb stanzas; the rotation runs weekdays,
not daily; the Hub Upload quota is 10 GB; there are now seven Recommended Track Sets;
the View menu item is "In Other Genomes (Convert)"; the Configure page label is "Text
size"; and several menu paths, button labels, and container terms were out of date.
All feature claims were verified against the v501 CGIs on genome.ucsc.edu rather than
the source tree, since master is ahead of what the public can use. Adds 10 screenshots
displayed at 2x pixel density to match the sharpness of the existing tip images.
- src/hg/htdocs/images/externalToolsTip.png
- lines changed 0, context: html, text, full: html, text
37fb40ea02f93e45a97d04567fc6c8d6990cfba3 Mon Aug 3 16:30:26 2026 -0700
Add 22 new "Did you know?" tips and correct outdated content in the existing 25. refs #37976
New tips cover features released since the tip rotation launched (exon search in the
position box, Duplicate track, the Visible Tracks group, track container settings,
amino acid mouseovers, Change Track Color) along with long-standing features that had
no tip (custom tracks, interactive tutorials, External Tools, In-Silico PCR, BLAT all
genomes, Table Browser batch queries and intersections, Data Access sections,
next/previous item arrows, the Reverse button, GenArk and public hubs, gene details
pages, hide all and Reset All User Settings, mailing lists, the poster gallery,
View then Chromosomes, and alternate chromosome names).
Corrections to the existing tips: the Download menu item is "Download Current Track
Data" under Downloads, not "Download track data in view" under Download; /list/schema
returns a track's field schema rather than trackDb stanzas; the rotation runs weekdays,
not daily; the Hub Upload quota is 10 GB; there are now seven Recommended Track Sets;
the View menu item is "In Other Genomes (Convert)"; the Configure page label is "Text
size"; and several menu paths, button labels, and container terms were out of date.
All feature claims were verified against the v501 CGIs on genome.ucsc.edu rather than
the source tree, since master is ahead of what the public can use. Adds 10 screenshots
displayed at 2x pixel density to match the sharpness of the existing tip images.
- src/hg/htdocs/images/posterGalleryTip.png
- lines changed 0, context: html, text, full: html, text
37fb40ea02f93e45a97d04567fc6c8d6990cfba3 Mon Aug 3 16:30:26 2026 -0700
Add 22 new "Did you know?" tips and correct outdated content in the existing 25. refs #37976
New tips cover features released since the tip rotation launched (exon search in the
position box, Duplicate track, the Visible Tracks group, track container settings,
amino acid mouseovers, Change Track Color) along with long-standing features that had
no tip (custom tracks, interactive tutorials, External Tools, In-Silico PCR, BLAT all
genomes, Table Browser batch queries and intersections, Data Access sections,
next/previous item arrows, the Reverse button, GenArk and public hubs, gene details
pages, hide all and Reset All User Settings, mailing lists, the poster gallery,
View then Chromosomes, and alternate chromosome names).
Corrections to the existing tips: the Download menu item is "Download Current Track
Data" under Downloads, not "Download track data in view" under Download; /list/schema
returns a track's field schema rather than trackDb stanzas; the rotation runs weekdays,
not daily; the Hub Upload quota is 10 GB; there are now seven Recommended Track Sets;
the View menu item is "In Other Genomes (Convert)"; the Configure page label is "Text
size"; and several menu paths, button labels, and container terms were out of date.
All feature claims were verified against the v501 CGIs on genome.ucsc.edu rather than
the source tree, since master is ahead of what the public can use. Adds 10 screenshots
displayed at 2x pixel density to match the sharpness of the existing tip images.
- src/hg/htdocs/images/reverseButtonTip.png
- lines changed 0, context: html, text, full: html, text
37fb40ea02f93e45a97d04567fc6c8d6990cfba3 Mon Aug 3 16:30:26 2026 -0700
Add 22 new "Did you know?" tips and correct outdated content in the existing 25. refs #37976
New tips cover features released since the tip rotation launched (exon search in the
position box, Duplicate track, the Visible Tracks group, track container settings,
amino acid mouseovers, Change Track Color) along with long-standing features that had
no tip (custom tracks, interactive tutorials, External Tools, In-Silico PCR, BLAT all
genomes, Table Browser batch queries and intersections, Data Access sections,
next/previous item arrows, the Reverse button, GenArk and public hubs, gene details
pages, hide all and Reset All User Settings, mailing lists, the poster gallery,
View then Chromosomes, and alternate chromosome names).
Corrections to the existing tips: the Download menu item is "Download Current Track
Data" under Downloads, not "Download track data in view" under Download; /list/schema
returns a track's field schema rather than trackDb stanzas; the rotation runs weekdays,
not daily; the Hub Upload quota is 10 GB; there are now seven Recommended Track Sets;
the View menu item is "In Other Genomes (Convert)"; the Configure page label is "Text
size"; and several menu paths, button labels, and container terms were out of date.
All feature claims were verified against the v501 CGIs on genome.ucsc.edu rather than
the source tree, since master is ahead of what the public can use. Adds 10 screenshots
displayed at 2x pixel density to match the sharpness of the existing tip images.
- src/hg/htdocs/images/trackColorTip.png
- lines changed 0, context: html, text, full: html, text
37fb40ea02f93e45a97d04567fc6c8d6990cfba3 Mon Aug 3 16:30:26 2026 -0700
Add 22 new "Did you know?" tips and correct outdated content in the existing 25. refs #37976
New tips cover features released since the tip rotation launched (exon search in the
position box, Duplicate track, the Visible Tracks group, track container settings,
amino acid mouseovers, Change Track Color) along with long-standing features that had
no tip (custom tracks, interactive tutorials, External Tools, In-Silico PCR, BLAT all
genomes, Table Browser batch queries and intersections, Data Access sections,
next/previous item arrows, the Reverse button, GenArk and public hubs, gene details
pages, hide all and Reset All User Settings, mailing lists, the poster gallery,
View then Chromosomes, and alternate chromosome names).
Corrections to the existing tips: the Download menu item is "Download Current Track
Data" under Downloads, not "Download track data in view" under Download; /list/schema
returns a track's field schema rather than trackDb stanzas; the rotation runs weekdays,
not daily; the Hub Upload quota is 10 GB; there are now seven Recommended Track Sets;
the View menu item is "In Other Genomes (Convert)"; the Configure page label is "Text
size"; and several menu paths, button labels, and container terms were out of date.
All feature claims were verified against the v501 CGIs on genome.ucsc.edu rather than
the source tree, since master is ahead of what the public can use. Adds 10 screenshots
displayed at 2x pixel density to match the sharpness of the existing tip images.
- src/hg/htdocs/images/tutorialsTip.png
- lines changed 0, context: html, text, full: html, text
37fb40ea02f93e45a97d04567fc6c8d6990cfba3 Mon Aug 3 16:30:26 2026 -0700
Add 22 new "Did you know?" tips and correct outdated content in the existing 25. refs #37976
New tips cover features released since the tip rotation launched (exon search in the
position box, Duplicate track, the Visible Tracks group, track container settings,
amino acid mouseovers, Change Track Color) along with long-standing features that had
no tip (custom tracks, interactive tutorials, External Tools, In-Silico PCR, BLAT all
genomes, Table Browser batch queries and intersections, Data Access sections,
next/previous item arrows, the Reverse button, GenArk and public hubs, gene details
pages, hide all and Reset All User Settings, mailing lists, the poster gallery,
View then Chromosomes, and alternate chromosome names).
Corrections to the existing tips: the Download menu item is "Download Current Track
Data" under Downloads, not "Download track data in view" under Download; /list/schema
returns a track's field schema rather than trackDb stanzas; the rotation runs weekdays,
not daily; the Hub Upload quota is 10 GB; there are now seven Recommended Track Sets;
the View menu item is "In Other Genomes (Convert)"; the Configure page label is "Text
size"; and several menu paths, button labels, and container terms were out of date.
All feature claims were verified against the v501 CGIs on genome.ucsc.edu rather than
the source tree, since master is ahead of what the public can use. Adds 10 screenshots
displayed at 2x pixel density to match the sharpness of the existing tip images.
- src/hg/htdocs/images/viewChromosomesTip.png
- lines changed 0, context: html, text, full: html, text
37fb40ea02f93e45a97d04567fc6c8d6990cfba3 Mon Aug 3 16:30:26 2026 -0700
Add 22 new "Did you know?" tips and correct outdated content in the existing 25. refs #37976
New tips cover features released since the tip rotation launched (exon search in the
position box, Duplicate track, the Visible Tracks group, track container settings,
amino acid mouseovers, Change Track Color) along with long-standing features that had
no tip (custom tracks, interactive tutorials, External Tools, In-Silico PCR, BLAT all
genomes, Table Browser batch queries and intersections, Data Access sections,
next/previous item arrows, the Reverse button, GenArk and public hubs, gene details
pages, hide all and Reset All User Settings, mailing lists, the poster gallery,
View then Chromosomes, and alternate chromosome names).
Corrections to the existing tips: the Download menu item is "Download Current Track
Data" under Downloads, not "Download track data in view" under Download; /list/schema
returns a track's field schema rather than trackDb stanzas; the rotation runs weekdays,
not daily; the Hub Upload quota is 10 GB; there are now seven Recommended Track Sets;
the View menu item is "In Other Genomes (Convert)"; the Configure page label is "Text
size"; and several menu paths, button labels, and container terms were out of date.
All feature claims were verified against the v501 CGIs on genome.ucsc.edu rather than
the source tree, since master is ahead of what the public can use. Adds 10 screenshots
displayed at 2x pixel density to match the sharpness of the existing tip images.
- src/hg/htdocs/images/visibleTracksTip.png
- lines changed 0, context: html, text, full: html, text
37fb40ea02f93e45a97d04567fc6c8d6990cfba3 Mon Aug 3 16:30:26 2026 -0700
Add 22 new "Did you know?" tips and correct outdated content in the existing 25. refs #37976
New tips cover features released since the tip rotation launched (exon search in the
position box, Duplicate track, the Visible Tracks group, track container settings,
amino acid mouseovers, Change Track Color) along with long-standing features that had
no tip (custom tracks, interactive tutorials, External Tools, In-Silico PCR, BLAT all
genomes, Table Browser batch queries and intersections, Data Access sections,
next/previous item arrows, the Reverse button, GenArk and public hubs, gene details
pages, hide all and Reset All User Settings, mailing lists, the poster gallery,
View then Chromosomes, and alternate chromosome names).
Corrections to the existing tips: the Download menu item is "Download Current Track
Data" under Downloads, not "Download track data in view" under Download; /list/schema
returns a track's field schema rather than trackDb stanzas; the rotation runs weekdays,
not daily; the Hub Upload quota is 10 GB; there are now seven Recommended Track Sets;
the View menu item is "In Other Genomes (Convert)"; the Configure page label is "Text
size"; and several menu paths, button labels, and container terms were out of date.
All feature claims were verified against the v501 CGIs on genome.ucsc.edu rather than
the source tree, since master is ahead of what the public can use. Adds 10 screenshots
displayed at 2x pixel density to match the sharpness of the existing tip images.
- src/hg/htdocs/indexMeetings.html
- lines changed 13, context: html, text, full: html, text
9d7f7e0328fdcf061fb7fa523dc74a8e7c5d6499 Fri Jul 31 20:24:45 2026 -0700
Remove past VALT and McKusick meetings from indexMeetings page and rebalance columns. No RM.
- src/hg/makeDb/doc/Cardiomyopathy.txt
- lines changed 35, context: html, text, full: html, text
614ca430db1c23f496ccc5655d27b469e1c53443 Fri Jul 31 16:38:30 2026 -0700
Apply Cardiomyopathy VCEP feedback: BP7 splice-only, drop PS4 tracks, evidence-first Variant Evidence Summary. refs #37446
Per the CM VCEP's answers to the interpretation questions:
- BP7: remove the conservation (phyloP) requirement and set the SpliceAI cutoff
to < 0.1, per Walker 2023 (PMID 37352859).
- PS4: remove the Walsh 2017 gene-level OR and Atlas EF display tracks (the VCEP
computes PS4 from current cohorts). Scripts and data are retained in the tree;
the tracks are dropped from the hub trackDb.
- Rename the former provisional/computable-codes track to "Variant Evidence
Summary" and switch its mouseover to an evidence-first layout: each item leads
with the data and is tagged with the ACMG criterion it would support; no overall
classification is computed.
- Confirmed and reflected in the docs: EvRepo is the PS1/PM5 reference (Q1); the
PM4 last-exon / within-50-nt rule (Q2); CardioBoost stays informational (Q6);
the PM1 codon ranges are HCM-only (Q8); no functional-score dataset is currently
VCEP-approved (Q4).
- src/hg/makeDb/doc/hg38/popEve.txt
- lines changed 12, context: html, text, full: html, text
e9a2b5a28cb4e3970977c76d84649bdd339a8423 Thu Jul 30 17:00:51 2026 -0700
Address popEVE code-review feedback (v502). refs #37950 refs #37791
- popEve.ra dataVersion now names the score source (March per-transcript release) and the
July VCF as the coordinate/strand source, rather than only the VCF date.
- vcfToPopEveHeatmap.py: when the CSV wildtype disagrees with the genomic wildtype, skip the
position and keep the correct sparse data instead of attaching CSV scores computed for a
different residue; skip CSV rows with a nan/empty popEVE; add a posSparse counter for
positions with genomic coordinates but no CSV row. All three are 0 on the current data, so
the bigBed output is unchanged (verified byte-identical), but they make the converter fail
safe for future per-transcript releases.
- Add the build drivers runBuild.sh and runBuildDense.sh to the tree (the anchor computation
previously lived only in the hive build directory), and add a makedoc forward-pointer so
the intermediate sparse section is not mistaken for the final dense build.
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPProvisionalClass.py
- lines changed 114, context: html, text, full: html, text
614ca430db1c23f496ccc5655d27b469e1c53443 Fri Jul 31 16:38:30 2026 -0700
Apply Cardiomyopathy VCEP feedback: BP7 splice-only, drop PS4 tracks, evidence-first Variant Evidence Summary. refs #37446
Per the CM VCEP's answers to the interpretation questions:
- BP7: remove the conservation (phyloP) requirement and set the SpliceAI cutoff
to < 0.1, per Walker 2023 (PMID 37352859).
- PS4: remove the Walsh 2017 gene-level OR and Atlas EF display tracks (the VCEP
computes PS4 from current cohorts). Scripts and data are retained in the tree;
the tracks are dropped from the hub trackDb.
- Rename the former provisional/computable-codes track to "Variant Evidence
Summary" and switch its mouseover to an evidence-first layout: each item leads
with the data and is tagged with the ACMG criterion it would support; no overall
classification is computed.
- Confirmed and reflected in the docs: EvRepo is the PS1/PM5 reference (Q1); the
PM4 last-exon / within-50-nt rule (Q2); CardioBoost stays informational (Q6);
the PM1 codon ranges are HCM-only (Q8); no functional-score dataset is currently
VCEP-approved (Q4).
- src/hg/makeDb/scripts/popEve/runBuild.sh
- lines changed 72, context: html, text, full: html, text
e9a2b5a28cb4e3970977c76d84649bdd339a8423 Thu Jul 30 17:00:51 2026 -0700
Address popEVE code-review feedback (v502). refs #37950 refs #37791
- popEve.ra dataVersion now names the score source (March per-transcript release) and the
July VCF as the coordinate/strand source, rather than only the VCF date.
- vcfToPopEveHeatmap.py: when the CSV wildtype disagrees with the genomic wildtype, skip the
position and keep the correct sparse data instead of attaching CSV scores computed for a
different residue; skip CSV rows with a nan/empty popEVE; add a posSparse counter for
positions with genomic coordinates but no CSV row. All three are 0 on the current data, so
the bigBed output is unchanged (verified byte-identical), but they make the converter fail
safe for future per-transcript releases.
- Add the build drivers runBuild.sh and runBuildDense.sh to the tree (the anchor computation
previously lived only in the hive build directory), and add a makedoc forward-pointer so
the intermediate sparse section is not mistaken for the final dense build.
- src/hg/makeDb/scripts/popEve/runBuildDense.sh
- lines changed 44, context: html, text, full: html, text
e9a2b5a28cb4e3970977c76d84649bdd339a8423 Thu Jul 30 17:00:51 2026 -0700
Address popEVE code-review feedback (v502). refs #37950 refs #37791
- popEve.ra dataVersion now names the score source (March per-transcript release) and the
July VCF as the coordinate/strand source, rather than only the VCF date.
- vcfToPopEveHeatmap.py: when the CSV wildtype disagrees with the genomic wildtype, skip the
position and keep the correct sparse data instead of attaching CSV scores computed for a
different residue; skip CSV rows with a nan/empty popEVE; add a posSparse counter for
positions with genomic coordinates but no CSV row. All three are 0 on the current data, so
the bigBed output is unchanged (verified byte-identical), but they make the converter fail
safe for future per-transcript releases.
- Add the build drivers runBuild.sh and runBuildDense.sh to the tree (the anchor computation
previously lived only in the hive build directory), and add a makedoc forward-pointer so
the intermediate sparse section is not mistaken for the final dense build.
- src/hg/makeDb/scripts/popEve/vcfToPopEveHeatmap.py
- lines changed 16, context: html, text, full: html, text
e9a2b5a28cb4e3970977c76d84649bdd339a8423 Thu Jul 30 17:00:51 2026 -0700
Address popEVE code-review feedback (v502). refs #37950 refs #37791
- popEve.ra dataVersion now names the score source (March per-transcript release) and the
July VCF as the coordinate/strand source, rather than only the VCF date.
- vcfToPopEveHeatmap.py: when the CSV wildtype disagrees with the genomic wildtype, skip the
position and keep the correct sparse data instead of attaching CSV scores computed for a
different residue; skip CSV rows with a nan/empty popEVE; add a posSparse counter for
positions with genomic coordinates but no CSV row. All three are 0 on the current data, so
the bigBed output is unchanged (verified byte-identical), but they make the converter fail
safe for future per-transcript releases.
- Add the build drivers runBuild.sh and runBuildDense.sh to the tree (the anchor computation
previously lived only in the hive build directory), and add a makedoc forward-pointer so
the intermediate sparse section is not mistaken for the final dense build.
- src/hg/makeDb/trackDb/human/alphaMissense.html
- lines changed 1, context: html, text, full: html, text
9711cb56111546aeed1be4b2c0ba1738080c848c Tue Jul 28 17:31:52 2026 -0700
Fix "basepair" wording and Methods punctuation on the Deleteriousness Predictions description pages per QA feedback. refs #37510
Changes "basepair" to "base" in the shared zoom-in instructions on clinPred,
revel, alphaMissense, caddSuper, and caddSuper1_7, and normalizes
predictionScoresSuper from "base pair" to "base" so the container is consistent.
Removes an awkward comma in the source-repository sentence on clinPred and revel.
Switches the hgdownload links on the clinPred page to https to match the other
links on that page.
- src/hg/makeDb/trackDb/human/caddSuper.html
- lines changed 2, context: html, text, full: html, text
9711cb56111546aeed1be4b2c0ba1738080c848c Tue Jul 28 17:31:52 2026 -0700
Fix "basepair" wording and Methods punctuation on the Deleteriousness Predictions description pages per QA feedback. refs #37510
Changes "basepair" to "base" in the shared zoom-in instructions on clinPred,
revel, alphaMissense, caddSuper, and caddSuper1_7, and normalizes
predictionScoresSuper from "base pair" to "base" so the container is consistent.
Removes an awkward comma in the source-repository sentence on clinPred and revel.
Switches the hgdownload links on the clinPred page to https to match the other
links on that page.
- src/hg/makeDb/trackDb/human/caddSuper1_7.html
- lines changed 2, context: html, text, full: html, text
9711cb56111546aeed1be4b2c0ba1738080c848c Tue Jul 28 17:31:52 2026 -0700
Fix "basepair" wording and Methods punctuation on the Deleteriousness Predictions description pages per QA feedback. refs #37510
Changes "basepair" to "base" in the shared zoom-in instructions on clinPred,
revel, alphaMissense, caddSuper, and caddSuper1_7, and normalizes
predictionScoresSuper from "base pair" to "base" so the container is consistent.
Removes an awkward comma in the source-repository sentence on clinPred and revel.
Switches the hgdownload links on the clinPred page to https to match the other
links on that page.
- src/hg/makeDb/trackDb/human/clinPred.html
- lines changed 5, context: html, text, full: html, text
9711cb56111546aeed1be4b2c0ba1738080c848c Tue Jul 28 17:31:52 2026 -0700
Fix "basepair" wording and Methods punctuation on the Deleteriousness Predictions description pages per QA feedback. refs #37510
Changes "basepair" to "base" in the shared zoom-in instructions on clinPred,
revel, alphaMissense, caddSuper, and caddSuper1_7, and normalizes
predictionScoresSuper from "base pair" to "base" so the container is consistent.
Removes an awkward comma in the source-repository sentence on clinPred and revel.
Switches the hgdownload links on the clinPred page to https to match the other
links on that page.
- src/hg/makeDb/trackDb/human/popEve.ra
- lines changed 1, context: html, text, full: html, text
e9a2b5a28cb4e3970977c76d84649bdd339a8423 Thu Jul 30 17:00:51 2026 -0700
Address popEVE code-review feedback (v502). refs #37950 refs #37791
- popEve.ra dataVersion now names the score source (March per-transcript release) and the
July VCF as the coordinate/strand source, rather than only the VCF date.
- vcfToPopEveHeatmap.py: when the CSV wildtype disagrees with the genomic wildtype, skip the
position and keep the correct sparse data instead of attaching CSV scores computed for a
different residue; skip CSV rows with a nan/empty popEVE; add a posSparse counter for
positions with genomic coordinates but no CSV row. All three are 0 on the current data, so
the bigBed output is unchanged (verified byte-identical), but they make the converter fail
safe for future per-transcript releases.
- Add the build drivers runBuild.sh and runBuildDense.sh to the tree (the anchor computation
previously lived only in the hive build directory), and add a makedoc forward-pointer so
the intermediate sparse section is not mistaken for the final dense build.
- src/hg/makeDb/trackDb/human/predictionScoresSuper.html
- lines changed 1, context: html, text, full: html, text
9711cb56111546aeed1be4b2c0ba1738080c848c Tue Jul 28 17:31:52 2026 -0700
Fix "basepair" wording and Methods punctuation on the Deleteriousness Predictions description pages per QA feedback. refs #37510
Changes "basepair" to "base" in the shared zoom-in instructions on clinPred,
revel, alphaMissense, caddSuper, and caddSuper1_7, and normalizes
predictionScoresSuper from "base pair" to "base" so the container is consistent.
Removes an awkward comma in the source-repository sentence on clinPred and revel.
Switches the hgdownload links on the clinPred page to https to match the other
links on that page.
- src/hg/makeDb/trackDb/human/revel.html
- lines changed 2, context: html, text, full: html, text
9711cb56111546aeed1be4b2c0ba1738080c848c Tue Jul 28 17:31:52 2026 -0700
Fix "basepair" wording and Methods punctuation on the Deleteriousness Predictions description pages per QA feedback. refs #37510
Changes "basepair" to "base" in the shared zoom-in instructions on clinPred,
revel, alphaMissense, caddSuper, and caddSuper1_7, and normalizes
predictionScoresSuper from "base pair" to "base" so the container is consistent.
Removes an awkward comma in the source-repository sentence on clinPred and revel.
Switches the hgdownload links on the clinPred page to https to match the other
links on that page.
- src/hg/utils/otto/otto.crontab
- lines changed 5, context: html, text, full: html, text
0bcea84e83ceef4cccba34202e1792e8ad05d980 Fri Jul 31 18:09:53 2026 -0700
Adding monthly otto notifier that compares our VCEP hub spec versions against the ClinGen CSpec registry. refs #37795
New script src/hg/utils/otto/vcepVersions/checkVcepVersions.py scrapes the
published version from each VCEP hub description page on hgdownload (ENIGMA
BRCA1/BRCA2 and InSiGHT Lynch syndrome) and compares it to the current released
version in the ClinGen CSpec registry, which embeds its specification list as
inline JSON on the affiliation page. Silent when the versions agree, prints a
report when a hub is behind or when the check itself fails.
Only released specs for the genes a hub actually displays are compared, since
an affiliation can carry specs for more genes than we show, on their own
schedule. InSiGHT 50099 for instance also holds APC and MUTYH.
Also adds the monthly crontab entry, mailing otto-group.
- src/hg/utils/otto/vcepVersions/checkVcepVersions.py
- lines changed 155, context: html, text, full: html, text
0bcea84e83ceef4cccba34202e1792e8ad05d980 Fri Jul 31 18:09:53 2026 -0700
Adding monthly otto notifier that compares our VCEP hub spec versions against the ClinGen CSpec registry. refs #37795
New script src/hg/utils/otto/vcepVersions/checkVcepVersions.py scrapes the
published version from each VCEP hub description page on hgdownload (ENIGMA
BRCA1/BRCA2 and InSiGHT Lynch syndrome) and compares it to the current released
version in the ClinGen CSpec registry, which embeds its specification list as
inline JSON on the affiliation page. Silent when the versions agree, prints a
report when a hub is behind or when the check itself fails.
Only released specs for the genes a hub actually displays are compared, since
an affiliation can carry specs for more genes than we show, on their own
schedule. InSiGHT 50099 for instance also holds APC and MUTYH.
Also adds the monthly crontab entry, mailing otto-group.
- src/utils/qa/trackCountsParse
- lines changed 291, context: html, text, full: html, text
06270582e562da3029320d8be4d527091d012602 Fri Jul 31 20:03:55 2026 -0700
Fix and speed up trackCountsParse, the seldom-used track usage report. refs #37975
The script did not run at all, it aborted with a NameError before doing any work,
so last year's report was produced by hand-editing a debug line. Also fixes -c and
-n, which arrived from argparse as strings and raised TypeError, and -h, which
aborted on an unescaped percent sign in a help string.
Replaces the per-track tdbQuery calls with a single bulk tdbQuery dump, taking a six
month run from hours down to a few minutes. The parent chain walk is now a loop
rather than three fixed hops. The hub and custom track filter matches the start of
the track name field instead of anywhere on the line, so real tracks such as
dbVar_conflict_pathogenic are no longer silently dropped, and it uses awk rather
than grep because grep -P failed to drop some rows in a 650k line report.
averageTrackCount now averages every month searched rather than only the months in
which a track fell under the cutoff. Adds averageSummedCount, monthsBelowCutoff and
the per month cutoffs to the output, labels names with no trackDb entry as
notInTrackDb, and adds -a/--asOfDate so an earlier window can be reproduced. Cached
count files carry a v2 in the name so the previous filtering is not reused silently.
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