File Changes for lrnassar

v503_preview to v503_preview2 (2026-08-17 to 2026-08-24) v503

• src/hg/makeDb/doc/enigma.txt
  • lines changed 51, context: html, text, full: html, text
    0a48f8c6284efb6756f1d2ba23694b58c9aa6f47 Tue Aug 18 12:01:13 2026 -0700
    Update ENIGMA BRCA1/BRCA2 hub scripts and data to CSpec v1.2. refs #38130 Rebuilds the BRCAsplicing and BRCAfunctionalAssays tracks from the v1.2 specification tables downloaded from the ClinGen CSpec registry. Adds exportV12Sheets.py (xlsx to text with merged-cell expansion) and convertTable4toFlat.py (converts the v1.2 visual Table 4 layout back to the flat format the track script consumes, including NMD-boundary PTC sub-ranges). Build scripts now write to a versioned dir instead of overwriting the files the public hub serves, and the hgSearch coordinate scraper was fixed for the current page format and made to fail loudly on a missed lookup. Also updates the vcepVersions monitor regex for the corrected BRCA1/BRCA2 wording on the hub description page.
  • lines changed 42, context: html, text, full: html, text
    1478a90404ea80636ae160b7b150fcaa34d80b50 Tue Aug 18 15:14:02 2026 -0700
    Adding Zanti et al 2025 case-control LRs to the ENIGMA BRCA1/BRCA2 PP4/BP5 track. refs #37886 New BRCAmlaZanti.py rebuilds the BRCAmla track with the case-control likelihood ratios from Zanti et al. 2025 (PMID 40413188) replacing the 20-variant iCOGS case-control component from Parsons et al. 2019, which overlaps the Zanti cohorts. Track grows from 4,436 to 13,481 variants per assembly, with new per-cohort columns (BRIDGES, CARRIERS, UK Biobank). Makedoc documents the build and release steps. Approach and combined-LR caveats reviewed with the ENIGMA collaborators on the ticket.
• src/hg/makeDb/doc/mm10.txt
  • lines changed 40, context: html, text, full: html, text
    78988553dd9b460c26f0b9f21f15a1aacfad9dab Fri Aug 21 15:44:40 2026 -0700
    Polish pass on the mouseDevTimecourse tracks after a Playwright QA sweep. refs #37001 Sentence-case the tissue names and the facet column titles, so the barChart facet filter reads "Tissue / Spleen" rather than "tissue / spleen" and the bigWig matrix reads "Spleen". Only the first character is upper-cased. Added sentenceCaseTissues.sh, which does the .facets and .categories files and is idempotent, since the hub still ships lower-case and this has to be replayed after any refetch. The count and color column names are deliberately left lower-case: barChartUi.c requires a field literally named "count" to load the file at all, and facetedTable.c keys its merge logic on "count", "color" and "val". Renaming the faceted columns means trackDb matches, so the stanzas now read barChartFacets Tissue,Timepoint. Set priority on the container children so the default-visible M21 TPM sorts first and the signal composite sorts last. The composite needs an explicit value; without one it inherits the superTrack's 0.6 and floats to the top. Fix the All reads view, which was inert. Every all-reads subtrack shipped parent off, so switching the view to full revealed nothing. The view's own visibility already gates drawing, so the subtrack state should not encode the view as well. The default image is unchanged at 78 unique-reads rep1 tracks, and switching the view to full now yields 156. This also makes the Rep 2 toggle symmetric across the two views. Rename the bigWig subGroup3 display label from Age to Timepoint, matching the barChart facet and the .facets column. The group name stays "age" because dimensions and sortOrder reference it by name. Add relatedTracks cross-links between the mm10 container and Tabula Muris. Not Tabula Muris Senis, which is not on the RR. Description pages: reorder the mm10 subtrack list to match the new display order, "sub tracks" to "subtracks", capitalise the colour legend tissue names, and correct the mm39 Il11ra2 note - the gene appears three times, two of them stacked at one position and sharing a details page, with the third 497 kb away. Makedocs record the casing step, its ordering constraint relative to the reorder and colour steps, and the count/color naming constraint.
• src/hg/makeDb/doc/mm39/mouseDevTimecourse.txt
  • lines changed 14, context: html, text, full: html, text
    78988553dd9b460c26f0b9f21f15a1aacfad9dab Fri Aug 21 15:44:40 2026 -0700
    Polish pass on the mouseDevTimecourse tracks after a Playwright QA sweep. refs #37001 Sentence-case the tissue names and the facet column titles, so the barChart facet filter reads "Tissue / Spleen" rather than "tissue / spleen" and the bigWig matrix reads "Spleen". Only the first character is upper-cased. Added sentenceCaseTissues.sh, which does the .facets and .categories files and is idempotent, since the hub still ships lower-case and this has to be replayed after any refetch. The count and color column names are deliberately left lower-case: barChartUi.c requires a field literally named "count" to load the file at all, and facetedTable.c keys its merge logic on "count", "color" and "val". Renaming the faceted columns means trackDb matches, so the stanzas now read barChartFacets Tissue,Timepoint. Set priority on the container children so the default-visible M21 TPM sorts first and the signal composite sorts last. The composite needs an explicit value; without one it inherits the superTrack's 0.6 and floats to the top. Fix the All reads view, which was inert. Every all-reads subtrack shipped parent off, so switching the view to full revealed nothing. The view's own visibility already gates drawing, so the subtrack state should not encode the view as well. The default image is unchanged at 78 unique-reads rep1 tracks, and switching the view to full now yields 156. This also makes the Rep 2 toggle symmetric across the two views. Rename the bigWig subGroup3 display label from Age to Timepoint, matching the barChart facet and the .facets column. The group name stays "age" because dimensions and sortOrder reference it by name. Add relatedTracks cross-links between the mm10 container and Tabula Muris. Not Tabula Muris Senis, which is not on the RR. Description pages: reorder the mm10 subtrack list to match the new display order, "sub tracks" to "subtracks", capitalise the colour legend tissue names, and correct the mm39 Il11ra2 note - the gene appears three times, two of them stacked at one position and sharing a details page, with the third 497 kb away. Makedocs record the casing step, its ordering constraint relative to the reorder and colour steps, and the count/color naming constraint.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPProvisionalClass.py
  • lines changed 11, context: html, text, full: html, text
    3632060685c8b5ca508635ff45b0c27bf0df0dc1 Fri Aug 21 10:32:48 2026 -0700
    Harden Cardiomyopathy VCEP scripts against silent data-source failures. refs #38139 - cmpVCEPProvisionalClass: a SpliceAI read failure (wrong/renamed bigBed path) now stops the script with a clear error instead of returning an empty dict, which had silently fired BP7 for every synonymous variant with the mouseover showing "no record" as if it were a measurement. Also stop suppressing bigBedToBed's stderr. - cmpVCEPWalsh2019: compare the ClinVar transcript by accession without the version so a ClinVar version bump does not silently drop every matched row for a gene.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPWalsh2019.py
  • lines changed 3, context: html, text, full: html, text
    3632060685c8b5ca508635ff45b0c27bf0df0dc1 Fri Aug 21 10:32:48 2026 -0700
    Harden Cardiomyopathy VCEP scripts against silent data-source failures. refs #38139 - cmpVCEPProvisionalClass: a SpliceAI read failure (wrong/renamed bigBed path) now stops the script with a clear error instead of returning an empty dict, which had silently fired BP7 for every synonymous variant with the mouseover showing "no record" as if it were a measurement. Also stop suppressing bigBedToBed's stderr. - cmpVCEPWalsh2019: compare the ClinVar transcript by accession without the version so a ClinVar version bump does not silently drop every matched row for a gene.
• src/hg/makeDb/scripts/enigma/BRCAfunctionalAssays.py
  • lines changed 23, context: html, text, full: html, text
    0a48f8c6284efb6756f1d2ba23694b58c9aa6f47 Tue Aug 18 12:01:13 2026 -0700
    Update ENIGMA BRCA1/BRCA2 hub scripts and data to CSpec v1.2. refs #38130 Rebuilds the BRCAsplicing and BRCAfunctionalAssays tracks from the v1.2 specification tables downloaded from the ClinGen CSpec registry. Adds exportV12Sheets.py (xlsx to text with merged-cell expansion) and convertTable4toFlat.py (converts the v1.2 visual Table 4 layout back to the flat format the track script consumes, including NMD-boundary PTC sub-ranges). Build scripts now write to a versioned dir instead of overwriting the files the public hub serves, and the hgSearch coordinate scraper was fixed for the current page format and made to fail loudly on a missed lookup. Also updates the vcepVersions monitor regex for the corrected BRCA1/BRCA2 wording on the hub description page.
• src/hg/makeDb/scripts/enigma/BRCAmlaZanti.py
  • lines changed 292, context: html, text, full: html, text
    1478a90404ea80636ae160b7b150fcaa34d80b50 Tue Aug 18 15:14:02 2026 -0700
    Adding Zanti et al 2025 case-control LRs to the ENIGMA BRCA1/BRCA2 PP4/BP5 track. refs #37886 New BRCAmlaZanti.py rebuilds the BRCAmla track with the case-control likelihood ratios from Zanti et al. 2025 (PMID 40413188) replacing the 20-variant iCOGS case-control component from Parsons et al. 2019, which overlaps the Zanti cohorts. Track grows from 4,436 to 13,481 variants per assembly, with new per-cohort columns (BRIDGES, CARRIERS, UK Biobank). Makedoc documents the build and release steps. Approach and combined-LR caveats reviewed with the ENIGMA collaborators on the ticket.
• src/hg/makeDb/scripts/enigma/BRCAsplicing.py
  • lines changed 28, context: html, text, full: html, text
    0a48f8c6284efb6756f1d2ba23694b58c9aa6f47 Tue Aug 18 12:01:13 2026 -0700
    Update ENIGMA BRCA1/BRCA2 hub scripts and data to CSpec v1.2. refs #38130 Rebuilds the BRCAsplicing and BRCAfunctionalAssays tracks from the v1.2 specification tables downloaded from the ClinGen CSpec registry. Adds exportV12Sheets.py (xlsx to text with merged-cell expansion) and convertTable4toFlat.py (converts the v1.2 visual Table 4 layout back to the flat format the track script consumes, including NMD-boundary PTC sub-ranges). Build scripts now write to a versioned dir instead of overwriting the files the public hub serves, and the hgSearch coordinate scraper was fixed for the current page format and made to fail loudly on a missed lookup. Also updates the vcepVersions monitor regex for the corrected BRCA1/BRCA2 wording on the hub description page.
• src/hg/makeDb/scripts/enigma/convertTable4toFlat.py
  • lines changed 128, context: html, text, full: html, text
    0a48f8c6284efb6756f1d2ba23694b58c9aa6f47 Tue Aug 18 12:01:13 2026 -0700
    Update ENIGMA BRCA1/BRCA2 hub scripts and data to CSpec v1.2. refs #38130 Rebuilds the BRCAsplicing and BRCAfunctionalAssays tracks from the v1.2 specification tables downloaded from the ClinGen CSpec registry. Adds exportV12Sheets.py (xlsx to text with merged-cell expansion) and convertTable4toFlat.py (converts the v1.2 visual Table 4 layout back to the flat format the track script consumes, including NMD-boundary PTC sub-ranges). Build scripts now write to a versioned dir instead of overwriting the files the public hub serves, and the hgSearch coordinate scraper was fixed for the current page format and made to fail loudly on a missed lookup. Also updates the vcepVersions monitor regex for the corrected BRCA1/BRCA2 wording on the hub description page.
• src/hg/makeDb/scripts/enigma/exportV12Sheets.py
  • lines changed 68, context: html, text, full: html, text
    0a48f8c6284efb6756f1d2ba23694b58c9aa6f47 Tue Aug 18 12:01:13 2026 -0700
    Update ENIGMA BRCA1/BRCA2 hub scripts and data to CSpec v1.2. refs #38130 Rebuilds the BRCAsplicing and BRCAfunctionalAssays tracks from the v1.2 specification tables downloaded from the ClinGen CSpec registry. Adds exportV12Sheets.py (xlsx to text with merged-cell expansion) and convertTable4toFlat.py (converts the v1.2 visual Table 4 layout back to the flat format the track script consumes, including NMD-boundary PTC sub-ranges). Build scripts now write to a versioned dir instead of overwriting the files the public hub serves, and the hgSearch coordinate scraper was fixed for the current page format and made to fail loudly on a missed lookup. Also updates the vcepVersions monitor regex for the corrected BRCA1/BRCA2 wording on the hub description page.
• src/hg/makeDb/scripts/mouseDevTimecourse/generateBigwigTrackDb.py
  • lines changed 25, context: html, text, full: html, text
    78988553dd9b460c26f0b9f21f15a1aacfad9dab Fri Aug 21 15:44:40 2026 -0700
    Polish pass on the mouseDevTimecourse tracks after a Playwright QA sweep. refs #37001 Sentence-case the tissue names and the facet column titles, so the barChart facet filter reads "Tissue / Spleen" rather than "tissue / spleen" and the bigWig matrix reads "Spleen". Only the first character is upper-cased. Added sentenceCaseTissues.sh, which does the .facets and .categories files and is idempotent, since the hub still ships lower-case and this has to be replayed after any refetch. The count and color column names are deliberately left lower-case: barChartUi.c requires a field literally named "count" to load the file at all, and facetedTable.c keys its merge logic on "count", "color" and "val". Renaming the faceted columns means trackDb matches, so the stanzas now read barChartFacets Tissue,Timepoint. Set priority on the container children so the default-visible M21 TPM sorts first and the signal composite sorts last. The composite needs an explicit value; without one it inherits the superTrack's 0.6 and floats to the top. Fix the All reads view, which was inert. Every all-reads subtrack shipped parent off, so switching the view to full revealed nothing. The view's own visibility already gates drawing, so the subtrack state should not encode the view as well. The default image is unchanged at 78 unique-reads rep1 tracks, and switching the view to full now yields 156. This also makes the Rep 2 toggle symmetric across the two views. Rename the bigWig subGroup3 display label from Age to Timepoint, matching the barChart facet and the .facets column. The group name stays "age" because dimensions and sortOrder reference it by name. Add relatedTracks cross-links between the mm10 container and Tabula Muris. Not Tabula Muris Senis, which is not on the RR. Description pages: reorder the mm10 subtrack list to match the new display order, "sub tracks" to "subtracks", capitalise the colour legend tissue names, and correct the mm39 Il11ra2 note - the gene appears three times, two of them stacked at one position and sharing a details page, with the third 497 kb away. Makedocs record the casing step, its ordering constraint relative to the reorder and colour steps, and the count/color naming constraint.
• src/hg/makeDb/scripts/mouseDevTimecourse/sentenceCaseTissues.sh
  • lines changed 72, context: html, text, full: html, text
    78988553dd9b460c26f0b9f21f15a1aacfad9dab Fri Aug 21 15:44:40 2026 -0700
    Polish pass on the mouseDevTimecourse tracks after a Playwright QA sweep. refs #37001 Sentence-case the tissue names and the facet column titles, so the barChart facet filter reads "Tissue / Spleen" rather than "tissue / spleen" and the bigWig matrix reads "Spleen". Only the first character is upper-cased. Added sentenceCaseTissues.sh, which does the .facets and .categories files and is idempotent, since the hub still ships lower-case and this has to be replayed after any refetch. The count and color column names are deliberately left lower-case: barChartUi.c requires a field literally named "count" to load the file at all, and facetedTable.c keys its merge logic on "count", "color" and "val". Renaming the faceted columns means trackDb matches, so the stanzas now read barChartFacets Tissue,Timepoint. Set priority on the container children so the default-visible M21 TPM sorts first and the signal composite sorts last. The composite needs an explicit value; without one it inherits the superTrack's 0.6 and floats to the top. Fix the All reads view, which was inert. Every all-reads subtrack shipped parent off, so switching the view to full revealed nothing. The view's own visibility already gates drawing, so the subtrack state should not encode the view as well. The default image is unchanged at 78 unique-reads rep1 tracks, and switching the view to full now yields 156. This also makes the Rep 2 toggle symmetric across the two views. Rename the bigWig subGroup3 display label from Age to Timepoint, matching the barChart facet and the .facets column. The group name stays "age" because dimensions and sortOrder reference it by name. Add relatedTracks cross-links between the mm10 container and Tabula Muris. Not Tabula Muris Senis, which is not on the RR. Description pages: reorder the mm10 subtrack list to match the new display order, "sub tracks" to "subtracks", capitalise the colour legend tissue names, and correct the mm39 Il11ra2 note - the gene appears three times, two of them stacked at one position and sharing a details page, with the third 497 kb away. Makedocs record the casing step, its ordering constraint relative to the reorder and colour steps, and the count/color naming constraint.
• src/hg/makeDb/scripts/tp53/tp53AFfrequencies.py
  • lines changed 11, context: html, text, full: html, text
    ad8e7d43125d15461861a22ccb4d99e2b46c88c0 Fri Aug 21 10:46:04 2026 -0700
    Fix TP53 gnomAD PASS filtering and FLOSSIES carrier count, per code review. refs #37399 refs #38139 Two independent correctness fixes from CR #38139: - tp53AFfrequencies.py: skip non-PASS gnomAD records (mostly AC0, i.e. observed in nobody after QC). They were entering the present-set and wrongly counting as present in gnomAD, blocking the absent -> PM2_Supporting rule. 68 missense variants now correctly get PM2, changing 6 provisional classes at the 5/6 and -2/-1 boundaries. gnomAD frequency use is PASS-only regardless. - tp53Flossies.py: count carriers as het + hom by summing the per-population het and hom counts, instead of allele_count - hom_count. In this FLOSSIES export allele_count is already het + hom (not the usual het + 2*hom), so the old formula dropped homozygous carriers (e.g. P72R showed 4031 carriers, not 8372). No BS2 tier changes in the current export; fixes the mouseover count and a latent tier bug for low-count variants with homozygotes.
• src/hg/makeDb/scripts/tp53/tp53Flossies.py
  • lines changed 6, context: html, text, full: html, text
    ad8e7d43125d15461861a22ccb4d99e2b46c88c0 Fri Aug 21 10:46:04 2026 -0700
    Fix TP53 gnomAD PASS filtering and FLOSSIES carrier count, per code review. refs #37399 refs #38139 Two independent correctness fixes from CR #38139: - tp53AFfrequencies.py: skip non-PASS gnomAD records (mostly AC0, i.e. observed in nobody after QC). They were entering the present-set and wrongly counting as present in gnomAD, blocking the absent -> PM2_Supporting rule. 68 missense variants now correctly get PM2, changing 6 provisional classes at the 5/6 and -2/-1 boundaries. gnomAD frequency use is PASS-only regardless. - tp53Flossies.py: count carriers as het + hom by summing the per-population het and hom counts, instead of allele_count - hom_count. In this FLOSSIES export allele_count is already het + hom (not the usual het + 2*hom), so the old formula dropped homozygous carriers (e.g. P72R showed 4031 carriers, not 8372). No BS2 tier changes in the current export; fixes the mouseover count and a latent tier bug for low-count variants with homozygotes.
• src/hg/makeDb/trackDb/mouse/mm10/developmentTimecourseSignalMm10.html
  • lines changed 17, context: html, text, full: html, text
    78988553dd9b460c26f0b9f21f15a1aacfad9dab Fri Aug 21 15:44:40 2026 -0700
    Polish pass on the mouseDevTimecourse tracks after a Playwright QA sweep. refs #37001 Sentence-case the tissue names and the facet column titles, so the barChart facet filter reads "Tissue / Spleen" rather than "tissue / spleen" and the bigWig matrix reads "Spleen". Only the first character is upper-cased. Added sentenceCaseTissues.sh, which does the .facets and .categories files and is idempotent, since the hub still ships lower-case and this has to be replayed after any refetch. The count and color column names are deliberately left lower-case: barChartUi.c requires a field literally named "count" to load the file at all, and facetedTable.c keys its merge logic on "count", "color" and "val". Renaming the faceted columns means trackDb matches, so the stanzas now read barChartFacets Tissue,Timepoint. Set priority on the container children so the default-visible M21 TPM sorts first and the signal composite sorts last. The composite needs an explicit value; without one it inherits the superTrack's 0.6 and floats to the top. Fix the All reads view, which was inert. Every all-reads subtrack shipped parent off, so switching the view to full revealed nothing. The view's own visibility already gates drawing, so the subtrack state should not encode the view as well. The default image is unchanged at 78 unique-reads rep1 tracks, and switching the view to full now yields 156. This also makes the Rep 2 toggle symmetric across the two views. Rename the bigWig subGroup3 display label from Age to Timepoint, matching the barChart facet and the .facets column. The group name stays "age" because dimensions and sortOrder reference it by name. Add relatedTracks cross-links between the mm10 container and Tabula Muris. Not Tabula Muris Senis, which is not on the RR. Description pages: reorder the mm10 subtrack list to match the new display order, "sub tracks" to "subtracks", capitalise the colour legend tissue names, and correct the mm39 Il11ra2 note - the gene appears three times, two of them stacked at one position and sharing a details page, with the third 497 kb away. Makedocs record the casing step, its ordering constraint relative to the reorder and colour steps, and the count/color naming constraint.
• src/hg/makeDb/trackDb/mouse/mm10/developmentTimecourseSignalMm10.ra
  • lines changed 81, context: html, text, full: html, text
    78988553dd9b460c26f0b9f21f15a1aacfad9dab Fri Aug 21 15:44:40 2026 -0700
    Polish pass on the mouseDevTimecourse tracks after a Playwright QA sweep. refs #37001 Sentence-case the tissue names and the facet column titles, so the barChart facet filter reads "Tissue / Spleen" rather than "tissue / spleen" and the bigWig matrix reads "Spleen". Only the first character is upper-cased. Added sentenceCaseTissues.sh, which does the .facets and .categories files and is idempotent, since the hub still ships lower-case and this has to be replayed after any refetch. The count and color column names are deliberately left lower-case: barChartUi.c requires a field literally named "count" to load the file at all, and facetedTable.c keys its merge logic on "count", "color" and "val". Renaming the faceted columns means trackDb matches, so the stanzas now read barChartFacets Tissue,Timepoint. Set priority on the container children so the default-visible M21 TPM sorts first and the signal composite sorts last. The composite needs an explicit value; without one it inherits the superTrack's 0.6 and floats to the top. Fix the All reads view, which was inert. Every all-reads subtrack shipped parent off, so switching the view to full revealed nothing. The view's own visibility already gates drawing, so the subtrack state should not encode the view as well. The default image is unchanged at 78 unique-reads rep1 tracks, and switching the view to full now yields 156. This also makes the Rep 2 toggle symmetric across the two views. Rename the bigWig subGroup3 display label from Age to Timepoint, matching the barChart facet and the .facets column. The group name stays "age" because dimensions and sortOrder reference it by name. Add relatedTracks cross-links between the mm10 container and Tabula Muris. Not Tabula Muris Senis, which is not on the RR. Description pages: reorder the mm10 subtrack list to match the new display order, "sub tracks" to "subtracks", capitalise the colour legend tissue names, and correct the mm39 Il11ra2 note - the gene appears three times, two of them stacked at one position and sharing a details page, with the third 497 kb away. Makedocs record the casing step, its ordering constraint relative to the reorder and colour steps, and the count/color naming constraint.
• src/hg/makeDb/trackDb/mouse/mm10/mouseDevTimecourse.html
  • lines changed 9, context: html, text, full: html, text
    78988553dd9b460c26f0b9f21f15a1aacfad9dab Fri Aug 21 15:44:40 2026 -0700
    Polish pass on the mouseDevTimecourse tracks after a Playwright QA sweep. refs #37001 Sentence-case the tissue names and the facet column titles, so the barChart facet filter reads "Tissue / Spleen" rather than "tissue / spleen" and the bigWig matrix reads "Spleen". Only the first character is upper-cased. Added sentenceCaseTissues.sh, which does the .facets and .categories files and is idempotent, since the hub still ships lower-case and this has to be replayed after any refetch. The count and color column names are deliberately left lower-case: barChartUi.c requires a field literally named "count" to load the file at all, and facetedTable.c keys its merge logic on "count", "color" and "val". Renaming the faceted columns means trackDb matches, so the stanzas now read barChartFacets Tissue,Timepoint. Set priority on the container children so the default-visible M21 TPM sorts first and the signal composite sorts last. The composite needs an explicit value; without one it inherits the superTrack's 0.6 and floats to the top. Fix the All reads view, which was inert. Every all-reads subtrack shipped parent off, so switching the view to full revealed nothing. The view's own visibility already gates drawing, so the subtrack state should not encode the view as well. The default image is unchanged at 78 unique-reads rep1 tracks, and switching the view to full now yields 156. This also makes the Rep 2 toggle symmetric across the two views. Rename the bigWig subGroup3 display label from Age to Timepoint, matching the barChart facet and the .facets column. The group name stays "age" because dimensions and sortOrder reference it by name. Add relatedTracks cross-links between the mm10 container and Tabula Muris. Not Tabula Muris Senis, which is not on the RR. Description pages: reorder the mm10 subtrack list to match the new display order, "sub tracks" to "subtracks", capitalise the colour legend tissue names, and correct the mm39 Il11ra2 note - the gene appears three times, two of them stacked at one position and sharing a details page, with the third 497 kb away. Makedocs record the casing step, its ordering constraint relative to the reorder and colour steps, and the count/color naming constraint.
• src/hg/makeDb/trackDb/mouse/mm10/mouseDevTimecourse.ra
  • lines changed 8, context: html, text, full: html, text
    78988553dd9b460c26f0b9f21f15a1aacfad9dab Fri Aug 21 15:44:40 2026 -0700
    Polish pass on the mouseDevTimecourse tracks after a Playwright QA sweep. refs #37001 Sentence-case the tissue names and the facet column titles, so the barChart facet filter reads "Tissue / Spleen" rather than "tissue / spleen" and the bigWig matrix reads "Spleen". Only the first character is upper-cased. Added sentenceCaseTissues.sh, which does the .facets and .categories files and is idempotent, since the hub still ships lower-case and this has to be replayed after any refetch. The count and color column names are deliberately left lower-case: barChartUi.c requires a field literally named "count" to load the file at all, and facetedTable.c keys its merge logic on "count", "color" and "val". Renaming the faceted columns means trackDb matches, so the stanzas now read barChartFacets Tissue,Timepoint. Set priority on the container children so the default-visible M21 TPM sorts first and the signal composite sorts last. The composite needs an explicit value; without one it inherits the superTrack's 0.6 and floats to the top. Fix the All reads view, which was inert. Every all-reads subtrack shipped parent off, so switching the view to full revealed nothing. The view's own visibility already gates drawing, so the subtrack state should not encode the view as well. The default image is unchanged at 78 unique-reads rep1 tracks, and switching the view to full now yields 156. This also makes the Rep 2 toggle symmetric across the two views. Rename the bigWig subGroup3 display label from Age to Timepoint, matching the barChart facet and the .facets column. The group name stays "age" because dimensions and sortOrder reference it by name. Add relatedTracks cross-links between the mm10 container and Tabula Muris. Not Tabula Muris Senis, which is not on the RR. Description pages: reorder the mm10 subtrack list to match the new display order, "sub tracks" to "subtracks", capitalise the colour legend tissue names, and correct the mm39 Il11ra2 note - the gene appears three times, two of them stacked at one position and sharing a details page, with the third 497 kb away. Makedocs record the casing step, its ordering constraint relative to the reorder and colour steps, and the count/color naming constraint.
• src/hg/makeDb/trackDb/mouse/mm39/developmentTimecourseM21mm39FPKM.html
  • lines changed 13, context: html, text, full: html, text
    78988553dd9b460c26f0b9f21f15a1aacfad9dab Fri Aug 21 15:44:40 2026 -0700
    Polish pass on the mouseDevTimecourse tracks after a Playwright QA sweep. refs #37001 Sentence-case the tissue names and the facet column titles, so the barChart facet filter reads "Tissue / Spleen" rather than "tissue / spleen" and the bigWig matrix reads "Spleen". Only the first character is upper-cased. Added sentenceCaseTissues.sh, which does the .facets and .categories files and is idempotent, since the hub still ships lower-case and this has to be replayed after any refetch. The count and color column names are deliberately left lower-case: barChartUi.c requires a field literally named "count" to load the file at all, and facetedTable.c keys its merge logic on "count", "color" and "val". Renaming the faceted columns means trackDb matches, so the stanzas now read barChartFacets Tissue,Timepoint. Set priority on the container children so the default-visible M21 TPM sorts first and the signal composite sorts last. The composite needs an explicit value; without one it inherits the superTrack's 0.6 and floats to the top. Fix the All reads view, which was inert. Every all-reads subtrack shipped parent off, so switching the view to full revealed nothing. The view's own visibility already gates drawing, so the subtrack state should not encode the view as well. The default image is unchanged at 78 unique-reads rep1 tracks, and switching the view to full now yields 156. This also makes the Rep 2 toggle symmetric across the two views. Rename the bigWig subGroup3 display label from Age to Timepoint, matching the barChart facet and the .facets column. The group name stays "age" because dimensions and sortOrder reference it by name. Add relatedTracks cross-links between the mm10 container and Tabula Muris. Not Tabula Muris Senis, which is not on the RR. Description pages: reorder the mm10 subtrack list to match the new display order, "sub tracks" to "subtracks", capitalise the colour legend tissue names, and correct the mm39 Il11ra2 note - the gene appears three times, two of them stacked at one position and sharing a details page, with the third 497 kb away. Makedocs record the casing step, its ordering constraint relative to the reorder and colour steps, and the count/color naming constraint.
• src/hg/makeDb/trackDb/mouse/mm39/developmentTimecourseM21mm39TPM.html
  • lines changed 15, context: html, text, full: html, text
    78988553dd9b460c26f0b9f21f15a1aacfad9dab Fri Aug 21 15:44:40 2026 -0700
    Polish pass on the mouseDevTimecourse tracks after a Playwright QA sweep. refs #37001 Sentence-case the tissue names and the facet column titles, so the barChart facet filter reads "Tissue / Spleen" rather than "tissue / spleen" and the bigWig matrix reads "Spleen". Only the first character is upper-cased. Added sentenceCaseTissues.sh, which does the .facets and .categories files and is idempotent, since the hub still ships lower-case and this has to be replayed after any refetch. The count and color column names are deliberately left lower-case: barChartUi.c requires a field literally named "count" to load the file at all, and facetedTable.c keys its merge logic on "count", "color" and "val". Renaming the faceted columns means trackDb matches, so the stanzas now read barChartFacets Tissue,Timepoint. Set priority on the container children so the default-visible M21 TPM sorts first and the signal composite sorts last. The composite needs an explicit value; without one it inherits the superTrack's 0.6 and floats to the top. Fix the All reads view, which was inert. Every all-reads subtrack shipped parent off, so switching the view to full revealed nothing. The view's own visibility already gates drawing, so the subtrack state should not encode the view as well. The default image is unchanged at 78 unique-reads rep1 tracks, and switching the view to full now yields 156. This also makes the Rep 2 toggle symmetric across the two views. Rename the bigWig subGroup3 display label from Age to Timepoint, matching the barChart facet and the .facets column. The group name stays "age" because dimensions and sortOrder reference it by name. Add relatedTracks cross-links between the mm10 container and Tabula Muris. Not Tabula Muris Senis, which is not on the RR. Description pages: reorder the mm10 subtrack list to match the new display order, "sub tracks" to "subtracks", capitalise the colour legend tissue names, and correct the mm39 Il11ra2 note - the gene appears three times, two of them stacked at one position and sharing a details page, with the third 497 kb away. Makedocs record the casing step, its ordering constraint relative to the reorder and colour steps, and the count/color naming constraint.
• src/hg/makeDb/trackDb/mouse/mm39/mouseDevTimecourse.html
  • lines changed 13, context: html, text, full: html, text
    78988553dd9b460c26f0b9f21f15a1aacfad9dab Fri Aug 21 15:44:40 2026 -0700
    Polish pass on the mouseDevTimecourse tracks after a Playwright QA sweep. refs #37001 Sentence-case the tissue names and the facet column titles, so the barChart facet filter reads "Tissue / Spleen" rather than "tissue / spleen" and the bigWig matrix reads "Spleen". Only the first character is upper-cased. Added sentenceCaseTissues.sh, which does the .facets and .categories files and is idempotent, since the hub still ships lower-case and this has to be replayed after any refetch. The count and color column names are deliberately left lower-case: barChartUi.c requires a field literally named "count" to load the file at all, and facetedTable.c keys its merge logic on "count", "color" and "val". Renaming the faceted columns means trackDb matches, so the stanzas now read barChartFacets Tissue,Timepoint. Set priority on the container children so the default-visible M21 TPM sorts first and the signal composite sorts last. The composite needs an explicit value; without one it inherits the superTrack's 0.6 and floats to the top. Fix the All reads view, which was inert. Every all-reads subtrack shipped parent off, so switching the view to full revealed nothing. The view's own visibility already gates drawing, so the subtrack state should not encode the view as well. The default image is unchanged at 78 unique-reads rep1 tracks, and switching the view to full now yields 156. This also makes the Rep 2 toggle symmetric across the two views. Rename the bigWig subGroup3 display label from Age to Timepoint, matching the barChart facet and the .facets column. The group name stays "age" because dimensions and sortOrder reference it by name. Add relatedTracks cross-links between the mm10 container and Tabula Muris. Not Tabula Muris Senis, which is not on the RR. Description pages: reorder the mm10 subtrack list to match the new display order, "sub tracks" to "subtracks", capitalise the colour legend tissue names, and correct the mm39 Il11ra2 note - the gene appears three times, two of them stacked at one position and sharing a details page, with the third 497 kb away. Makedocs record the casing step, its ordering constraint relative to the reorder and colour steps, and the count/color naming constraint.
• src/hg/makeDb/trackDb/mouse/mm39/mouseDevTimecourse.ra
  • lines changed 4, context: html, text, full: html, text
    78988553dd9b460c26f0b9f21f15a1aacfad9dab Fri Aug 21 15:44:40 2026 -0700
    Polish pass on the mouseDevTimecourse tracks after a Playwright QA sweep. refs #37001 Sentence-case the tissue names and the facet column titles, so the barChart facet filter reads "Tissue / Spleen" rather than "tissue / spleen" and the bigWig matrix reads "Spleen". Only the first character is upper-cased. Added sentenceCaseTissues.sh, which does the .facets and .categories files and is idempotent, since the hub still ships lower-case and this has to be replayed after any refetch. The count and color column names are deliberately left lower-case: barChartUi.c requires a field literally named "count" to load the file at all, and facetedTable.c keys its merge logic on "count", "color" and "val". Renaming the faceted columns means trackDb matches, so the stanzas now read barChartFacets Tissue,Timepoint. Set priority on the container children so the default-visible M21 TPM sorts first and the signal composite sorts last. The composite needs an explicit value; without one it inherits the superTrack's 0.6 and floats to the top. Fix the All reads view, which was inert. Every all-reads subtrack shipped parent off, so switching the view to full revealed nothing. The view's own visibility already gates drawing, so the subtrack state should not encode the view as well. The default image is unchanged at 78 unique-reads rep1 tracks, and switching the view to full now yields 156. This also makes the Rep 2 toggle symmetric across the two views. Rename the bigWig subGroup3 display label from Age to Timepoint, matching the barChart facet and the .facets column. The group name stays "age" because dimensions and sortOrder reference it by name. Add relatedTracks cross-links between the mm10 container and Tabula Muris. Not Tabula Muris Senis, which is not on the RR. Description pages: reorder the mm10 subtrack list to match the new display order, "sub tracks" to "subtracks", capitalise the colour legend tissue names, and correct the mm39 Il11ra2 note - the gene appears three times, two of them stacked at one position and sharing a details page, with the third 497 kb away. Makedocs record the casing step, its ordering constraint relative to the reorder and colour steps, and the count/color naming constraint.
• src/hg/makeDb/trackDb/mouseDevTimecourseDisplay.shared.html
  • lines changed 17, context: html, text, full: html, text
    78988553dd9b460c26f0b9f21f15a1aacfad9dab Fri Aug 21 15:44:40 2026 -0700
    Polish pass on the mouseDevTimecourse tracks after a Playwright QA sweep. refs #37001 Sentence-case the tissue names and the facet column titles, so the barChart facet filter reads "Tissue / Spleen" rather than "tissue / spleen" and the bigWig matrix reads "Spleen". Only the first character is upper-cased. Added sentenceCaseTissues.sh, which does the .facets and .categories files and is idempotent, since the hub still ships lower-case and this has to be replayed after any refetch. The count and color column names are deliberately left lower-case: barChartUi.c requires a field literally named "count" to load the file at all, and facetedTable.c keys its merge logic on "count", "color" and "val". Renaming the faceted columns means trackDb matches, so the stanzas now read barChartFacets Tissue,Timepoint. Set priority on the container children so the default-visible M21 TPM sorts first and the signal composite sorts last. The composite needs an explicit value; without one it inherits the superTrack's 0.6 and floats to the top. Fix the All reads view, which was inert. Every all-reads subtrack shipped parent off, so switching the view to full revealed nothing. The view's own visibility already gates drawing, so the subtrack state should not encode the view as well. The default image is unchanged at 78 unique-reads rep1 tracks, and switching the view to full now yields 156. This also makes the Rep 2 toggle symmetric across the two views. Rename the bigWig subGroup3 display label from Age to Timepoint, matching the barChart facet and the .facets column. The group name stays "age" because dimensions and sortOrder reference it by name. Add relatedTracks cross-links between the mm10 container and Tabula Muris. Not Tabula Muris Senis, which is not on the RR. Description pages: reorder the mm10 subtrack list to match the new display order, "sub tracks" to "subtracks", capitalise the colour legend tissue names, and correct the mm39 Il11ra2 note - the gene appears three times, two of them stacked at one position and sharing a details page, with the third 497 kb away. Makedocs record the casing step, its ordering constraint relative to the reorder and colour steps, and the count/color naming constraint.
• src/hg/makeDb/trackDb/relatedTracks.ra
  • lines changed 4, context: html, text, full: html, text
    78988553dd9b460c26f0b9f21f15a1aacfad9dab Fri Aug 21 15:44:40 2026 -0700
    Polish pass on the mouseDevTimecourse tracks after a Playwright QA sweep. refs #37001 Sentence-case the tissue names and the facet column titles, so the barChart facet filter reads "Tissue / Spleen" rather than "tissue / spleen" and the bigWig matrix reads "Spleen". Only the first character is upper-cased. Added sentenceCaseTissues.sh, which does the .facets and .categories files and is idempotent, since the hub still ships lower-case and this has to be replayed after any refetch. The count and color column names are deliberately left lower-case: barChartUi.c requires a field literally named "count" to load the file at all, and facetedTable.c keys its merge logic on "count", "color" and "val". Renaming the faceted columns means trackDb matches, so the stanzas now read barChartFacets Tissue,Timepoint. Set priority on the container children so the default-visible M21 TPM sorts first and the signal composite sorts last. The composite needs an explicit value; without one it inherits the superTrack's 0.6 and floats to the top. Fix the All reads view, which was inert. Every all-reads subtrack shipped parent off, so switching the view to full revealed nothing. The view's own visibility already gates drawing, so the subtrack state should not encode the view as well. The default image is unchanged at 78 unique-reads rep1 tracks, and switching the view to full now yields 156. This also makes the Rep 2 toggle symmetric across the two views. Rename the bigWig subGroup3 display label from Age to Timepoint, matching the barChart facet and the .facets column. The group name stays "age" because dimensions and sortOrder reference it by name. Add relatedTracks cross-links between the mm10 container and Tabula Muris. Not Tabula Muris Senis, which is not on the RR. Description pages: reorder the mm10 subtrack list to match the new display order, "sub tracks" to "subtracks", capitalise the colour legend tissue names, and correct the mm39 Il11ra2 note - the gene appears three times, two of them stacked at one position and sharing a details page, with the third 497 kb away. Makedocs record the casing step, its ordering constraint relative to the reorder and colour steps, and the count/color naming constraint.
• src/hg/utils/otto/vcepVersions/checkVcepVersions.py
  • lines changed 1, context: html, text, full: html, text
    0a48f8c6284efb6756f1d2ba23694b58c9aa6f47 Tue Aug 18 12:01:13 2026 -0700
    Update ENIGMA BRCA1/BRCA2 hub scripts and data to CSpec v1.2. refs #38130 Rebuilds the BRCAsplicing and BRCAfunctionalAssays tracks from the v1.2 specification tables downloaded from the ClinGen CSpec registry. Adds exportV12Sheets.py (xlsx to text with merged-cell expansion) and convertTable4toFlat.py (converts the v1.2 visual Table 4 layout back to the flat format the track script consumes, including NMD-boundary PTC sub-ranges). Build scripts now write to a versioned dir instead of overwriting the files the public hub serves, and the hgSearch coordinate scraper was fixed for the current page format and made to fail loudly on a missed lookup. Also updates the vcepVersions monitor regex for the corrected BRCA1/BRCA2 wording on the hub description page.