File Changes for mspeir

v502_preview2 to v502_base (2026-08-04 to 2026-08-10) v502

• src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/celltype-class.tsv
  • lines changed 119, context: html, text, full: html, text
    83b5ed84ca3b56a4b82c8ab52978a590d4862953 Thu Aug 6 14:24:38 2026 -0700
    singleCellSignalsPeaks: classify every cell type, correct four glia/muscle classes Working through the cell types that had no broad class took the hub from 361 unclassified types across 474 tracks down to zero, and the same crosswalk feeds the native tracks. Most of it was reachable without new curation: the class-map key was not dropping a trailing "cell(s)" the way the cell types themselves do, so entries like "Stromal cell" and "Olfactory ensheathing cell" sat in the table fully classed but unmatched; a " cCREs" suffix and a leading histone mark were being carried into the cell type and splitting the lookup; and the atlases qualify a common type with the tissue it came from ("Fibroblast gastrointestinal", "Smooth muscle colon", "Endothelial cell myocardial"), which the lookup now resolves by falling back to shorter prefixes rather than needing a row per tissue. Those changes live in the hub builder outside this tree. Added here are the 92 rows the above could not reach: Drosophila optic-lobe and mushroom-body neuron types, fly glia, immortalised lines, and PV/PV WT/PV KO/PV TG parvalbumin interneurons. Aggregates and bare cluster identifiers get the explicit Unknown class, so a track reads as "not resolved" rather than being unknown by omission. Also corrected four assignments that were wrong rather than missing. Schwann cells were grouped with astroglia by an earlier decision, but they are peripheral glia, and the table already put olfactory ensheathing cells under Other, so the two disagreed. Enteric glia had the same problem. "Satellite" was read as satellite glia when the data says muscle: its one resolved tissue is muscle, and "Muscle satellite cell" was already classed as Muscle. Bergmann and Muller glia stay under Astrocyte, both being genuine CNS macroglia. A name-versus-class scan over the whole table turned up nothing else. The hg38 .ra changes are the twelve resulting colours plus the priority reshuffle that follows from ranking by class; mm10 has none of these cell types. The description pages gain the reworded Astrocyte and Other legend entries, and the legend now separates each class from its definition with a colon instead of an em dash. refs #37914 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/paper-decodes/hg38_ct_class.tsv
  • lines changed 4, context: html, text, full: html, text
    83b5ed84ca3b56a4b82c8ab52978a590d4862953 Thu Aug 6 14:24:38 2026 -0700
    singleCellSignalsPeaks: classify every cell type, correct four glia/muscle classes Working through the cell types that had no broad class took the hub from 361 unclassified types across 474 tracks down to zero, and the same crosswalk feeds the native tracks. Most of it was reachable without new curation: the class-map key was not dropping a trailing "cell(s)" the way the cell types themselves do, so entries like "Stromal cell" and "Olfactory ensheathing cell" sat in the table fully classed but unmatched; a " cCREs" suffix and a leading histone mark were being carried into the cell type and splitting the lookup; and the atlases qualify a common type with the tissue it came from ("Fibroblast gastrointestinal", "Smooth muscle colon", "Endothelial cell myocardial"), which the lookup now resolves by falling back to shorter prefixes rather than needing a row per tissue. Those changes live in the hub builder outside this tree. Added here are the 92 rows the above could not reach: Drosophila optic-lobe and mushroom-body neuron types, fly glia, immortalised lines, and PV/PV WT/PV KO/PV TG parvalbumin interneurons. Aggregates and bare cluster identifiers get the explicit Unknown class, so a track reads as "not resolved" rather than being unknown by omission. Also corrected four assignments that were wrong rather than missing. Schwann cells were grouped with astroglia by an earlier decision, but they are peripheral glia, and the table already put olfactory ensheathing cells under Other, so the two disagreed. Enteric glia had the same problem. "Satellite" was read as satellite glia when the data says muscle: its one resolved tissue is muscle, and "Muscle satellite cell" was already classed as Muscle. Bergmann and Muller glia stay under Astrocyte, both being genuine CNS macroglia. A name-versus-class scan over the whole table turned up nothing else. The hg38 .ra changes are the twelve resulting colours plus the priority reshuffle that follows from ranking by class; mm10 has none of these cell types. The description pages gain the reworded Astrocyte and Other legend entries, and the legend now separates each class from its definition with a colon instead of an em dash. refs #37914 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py
  • lines changed 36, context: html, text, full: html, text
    54766047e2e79d545162f894d20d631553175d3d Tue Aug 4 15:05:35 2026 -0700
    singleCellSignalsPeaks: cite the SEA-AD resource paper, fail loudly on a hub-format change The Hawrylycz 2024 reference was listed but never cited. It is the SEA-AD resource paper and the source for the two brain regions the SEA-AD tracks cover, so it now appears on that dataset's bullet alongside Gabitto. BrainVar and the Allen basal-ganglia set have no paper to cite, so those bullets stay as they are. makeSingleCellSignalsPeaksRa.py matched the parent line by exact string, so if the hub ever emitted "parent <composite> off" or changed its spacing, every stanza would be skipped and the script would write a header-only .ra and exit 0 -- the next trackDb load would then quietly drop all 925/587 subtracks. It now matches on the parent's first token and refuses to write when nothing matched, or when the subtrack count disagrees with the facet metadata that build_stanzas emits alongside it. Verified: a renamed composite and a truncated stanza file both exit non-zero without writing a file, a "parent <composite> off" line still yields the full 587, and the regenerated .ra files are byte-identical to the previous commit. refs #37914 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 41, context: html, text, full: html, text
    8fc41cc92ad76bdd8fd35671329b47be0b8d29a5 Fri Aug 7 13:27:42 2026 -0700
    singleCellSignalsPeaks: indent the generated .ra, guard the subtrack rename Indenting the hub stanzas broke the "track " match here, so subtracks kept their cellBrowser<Asm>_ names and no longer matched the facet metadata. The counts still passed, so nothing caught it. Now dedents on read, and refuses to write if a subtrack lands outside the track's namespace or a source name is not cellBrowser<Asm>_* (the rename slices at a fixed offset, so an odd name came out mangled but well-formed). Also indents subtracks one step under the composite, matching chainNet/encode3. That produced the whitespace-only .ra change committed separately; this reproduces it exactly. refs #37914 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html
  • lines changed 1, context: html, text, full: html, text
    54766047e2e79d545162f894d20d631553175d3d Tue Aug 4 15:05:35 2026 -0700
    singleCellSignalsPeaks: cite the SEA-AD resource paper, fail loudly on a hub-format change The Hawrylycz 2024 reference was listed but never cited. It is the SEA-AD resource paper and the source for the two brain regions the SEA-AD tracks cover, so it now appears on that dataset's bullet alongside Gabitto. BrainVar and the Allen basal-ganglia set have no paper to cite, so those bullets stay as they are. makeSingleCellSignalsPeaksRa.py matched the parent line by exact string, so if the hub ever emitted "parent <composite> off" or changed its spacing, every stanza would be skipped and the script would write a header-only .ra and exit 0 -- the next trackDb load would then quietly drop all 925/587 subtracks. It now matches on the parent's first token and refuses to write when nothing matched, or when the subtrack count disagrees with the facet metadata that build_stanzas emits alongside it. Verified: a renamed composite and a truncated stanza file both exit non-zero without writing a file, a "parent <composite> off" line still yields the full 587, and the regenerated .ra files are byte-identical to the previous commit. refs #37914 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 23, context: html, text, full: html, text
    83b5ed84ca3b56a4b82c8ab52978a590d4862953 Thu Aug 6 14:24:38 2026 -0700
    singleCellSignalsPeaks: classify every cell type, correct four glia/muscle classes Working through the cell types that had no broad class took the hub from 361 unclassified types across 474 tracks down to zero, and the same crosswalk feeds the native tracks. Most of it was reachable without new curation: the class-map key was not dropping a trailing "cell(s)" the way the cell types themselves do, so entries like "Stromal cell" and "Olfactory ensheathing cell" sat in the table fully classed but unmatched; a " cCREs" suffix and a leading histone mark were being carried into the cell type and splitting the lookup; and the atlases qualify a common type with the tissue it came from ("Fibroblast gastrointestinal", "Smooth muscle colon", "Endothelial cell myocardial"), which the lookup now resolves by falling back to shorter prefixes rather than needing a row per tissue. Those changes live in the hub builder outside this tree. Added here are the 92 rows the above could not reach: Drosophila optic-lobe and mushroom-body neuron types, fly glia, immortalised lines, and PV/PV WT/PV KO/PV TG parvalbumin interneurons. Aggregates and bare cluster identifiers get the explicit Unknown class, so a track reads as "not resolved" rather than being unknown by omission. Also corrected four assignments that were wrong rather than missing. Schwann cells were grouped with astroglia by an earlier decision, but they are peripheral glia, and the table already put olfactory ensheathing cells under Other, so the two disagreed. Enteric glia had the same problem. "Satellite" was read as satellite glia when the data says muscle: its one resolved tissue is muscle, and "Muscle satellite cell" was already classed as Muscle. Bergmann and Muller glia stay under Astrocyte, both being genuine CNS macroglia. A name-versus-class scan over the whole table turned up nothing else. The hg38 .ra changes are the twelve resulting colours plus the priority reshuffle that follows from ranking by class; mm10 has none of these cell types. The description pages gain the reworded Astrocyte and Other legend entries, and the legend now separates each class from its definition with a colon instead of an em dash. refs #37914 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.ra
  • lines changed 68, context: html, text, full: html, text
    83b5ed84ca3b56a4b82c8ab52978a590d4862953 Thu Aug 6 14:24:38 2026 -0700
    singleCellSignalsPeaks: classify every cell type, correct four glia/muscle classes Working through the cell types that had no broad class took the hub from 361 unclassified types across 474 tracks down to zero, and the same crosswalk feeds the native tracks. Most of it was reachable without new curation: the class-map key was not dropping a trailing "cell(s)" the way the cell types themselves do, so entries like "Stromal cell" and "Olfactory ensheathing cell" sat in the table fully classed but unmatched; a " cCREs" suffix and a leading histone mark were being carried into the cell type and splitting the lookup; and the atlases qualify a common type with the tissue it came from ("Fibroblast gastrointestinal", "Smooth muscle colon", "Endothelial cell myocardial"), which the lookup now resolves by falling back to shorter prefixes rather than needing a row per tissue. Those changes live in the hub builder outside this tree. Added here are the 92 rows the above could not reach: Drosophila optic-lobe and mushroom-body neuron types, fly glia, immortalised lines, and PV/PV WT/PV KO/PV TG parvalbumin interneurons. Aggregates and bare cluster identifiers get the explicit Unknown class, so a track reads as "not resolved" rather than being unknown by omission. Also corrected four assignments that were wrong rather than missing. Schwann cells were grouped with astroglia by an earlier decision, but they are peripheral glia, and the table already put olfactory ensheathing cells under Other, so the two disagreed. Enteric glia had the same problem. "Satellite" was read as satellite glia when the data says muscle: its one resolved tissue is muscle, and "Muscle satellite cell" was already classed as Muscle. Bergmann and Muller glia stay under Astrocyte, both being genuine CNS macroglia. A name-versus-class scan over the whole table turned up nothing else. The hg38 .ra changes are the twelve resulting colours plus the priority reshuffle that follows from ranking by class; mm10 has none of these cell types. The description pages gain the reworded Astrocyte and Other legend entries, and the legend now separates each class from its definition with a colon instead of an em dash. refs #37914 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 0, context: html, text, full: html, text
    f90843f04563bb0ab82346f719f2105d5f95a714 Fri Aug 7 13:19:06 2026 -0700
    Changing indentation to match our norms. WHITESPACE-ONLY CHANGE, refs #37914
• src/hg/makeDb/trackDb/human/hs1/hs1PrimateChainNet.html
  • lines changed 1, context: html, text, full: html, text
    69a4cfc0966bc8230504a735ca7f897d5846ed92 Tue Aug 4 14:40:14 2026 -0700
    Tweaks based on automataed CR, no refs
• src/hg/makeDb/trackDb/human/hs1/html/clinVar20220313.html
  • lines changed 1, context: html, text, full: html, text
    69a4cfc0966bc8230504a735ca7f897d5846ed92 Tue Aug 4 14:40:14 2026 -0700
    Tweaks based on automataed CR, no refs
• src/hg/makeDb/trackDb/human/hs1/html/dbSNP155.html
  • lines changed 1, context: html, text, full: html, text
    69a4cfc0966bc8230504a735ca7f897d5846ed92 Tue Aug 4 14:40:14 2026 -0700
    Tweaks based on automataed CR, no refs
• src/hg/makeDb/trackDb/human/hs1/html/gwasSNPs2022-03-08.html
  • lines changed 1, context: html, text, full: html, text
    69a4cfc0966bc8230504a735ca7f897d5846ed92 Tue Aug 4 14:40:14 2026 -0700
    Tweaks based on automataed CR, no refs
• src/hg/makeDb/trackDb/mouse/mm10/singleCellSignalsPeaks.html
  • lines changed 25, context: html, text, full: html, text
    83b5ed84ca3b56a4b82c8ab52978a590d4862953 Thu Aug 6 14:24:38 2026 -0700
    singleCellSignalsPeaks: classify every cell type, correct four glia/muscle classes Working through the cell types that had no broad class took the hub from 361 unclassified types across 474 tracks down to zero, and the same crosswalk feeds the native tracks. Most of it was reachable without new curation: the class-map key was not dropping a trailing "cell(s)" the way the cell types themselves do, so entries like "Stromal cell" and "Olfactory ensheathing cell" sat in the table fully classed but unmatched; a " cCREs" suffix and a leading histone mark were being carried into the cell type and splitting the lookup; and the atlases qualify a common type with the tissue it came from ("Fibroblast gastrointestinal", "Smooth muscle colon", "Endothelial cell myocardial"), which the lookup now resolves by falling back to shorter prefixes rather than needing a row per tissue. Those changes live in the hub builder outside this tree. Added here are the 92 rows the above could not reach: Drosophila optic-lobe and mushroom-body neuron types, fly glia, immortalised lines, and PV/PV WT/PV KO/PV TG parvalbumin interneurons. Aggregates and bare cluster identifiers get the explicit Unknown class, so a track reads as "not resolved" rather than being unknown by omission. Also corrected four assignments that were wrong rather than missing. Schwann cells were grouped with astroglia by an earlier decision, but they are peripheral glia, and the table already put olfactory ensheathing cells under Other, so the two disagreed. Enteric glia had the same problem. "Satellite" was read as satellite glia when the data says muscle: its one resolved tissue is muscle, and "Muscle satellite cell" was already classed as Muscle. Bergmann and Muller glia stay under Astrocyte, both being genuine CNS macroglia. A name-versus-class scan over the whole table turned up nothing else. The hg38 .ra changes are the twelve resulting colours plus the priority reshuffle that follows from ranking by class; mm10 has none of these cell types. The description pages gain the reworded Astrocyte and Other legend entries, and the legend now separates each class from its definition with a colon instead of an em dash. refs #37914 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/singleCellSignalsPeaks.ra
  • lines changed 0, context: html, text, full: html, text
    f90843f04563bb0ab82346f719f2105d5f95a714 Fri Aug 7 13:19:06 2026 -0700
    Changing indentation to match our norms. WHITESPACE-ONLY CHANGE, refs #37914
• src/hg/utils/otto/g2p/doG2p.py
  • lines changed 42, context: html, text, full: html, text
    aa3bab94fb50013ebdf152f761359925fc88b674 Tue Aug 4 14:53:24 2026 -0700
    G2P otto: code-review fixes (logging, mixedCase names, itemRgb) - Log a per-value count when a confidence value is unrecognized and colored black. - Log a per-assembly count of G2P records with no HGNC coordinate match. - Unify function names to mixedCase (confidenceToColor, loadG2p, loadCoordinates, joinAndWrite). - Rename itemRGB to itemRgb in g2p.as for consistency with the rest of the tree. refs #36736 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/utils/otto/g2p/g2p.as
  • lines changed 1, context: html, text, full: html, text
    aa3bab94fb50013ebdf152f761359925fc88b674 Tue Aug 4 14:53:24 2026 -0700
    G2P otto: code-review fixes (logging, mixedCase names, itemRgb) - Log a per-value count when a confidence value is unrecognized and colored black. - Log a per-assembly count of G2P records with no HGNC coordinate match. - Unify function names to mixedCase (confidenceToColor, loadG2p, loadCoordinates, joinAndWrite). - Rename itemRGB to itemRgb in g2p.as for consistency with the rest of the tree. refs #36736 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>