aa3bab94fb50013ebdf152f761359925fc88b674
mspeir
  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>

diff --git src/hg/utils/otto/g2p/g2p.as src/hg/utils/otto/g2p/g2p.as
index 5c1f3427489..9ca538e9f83 100644
--- src/hg/utils/otto/g2p/g2p.as
+++ src/hg/utils/otto/g2p/g2p.as
@@ -1,35 +1,35 @@
 table g2p
 "All panels in the Gene2Phenotype (G2P) database - BED 9+20"
 (
     string chrom;        "Reference sequence chromosome or scaffold"
     uint   chromStart;    "Start position of feature on chromosome"
     uint   chromEnd;      "End position of feature on chromosome"
     string name;          "Gene symbol"
     uint   score;         "Score"
     char[1] strand;       "+ or - for strand"
     uint   thickStart;    "Coding region start"
     uint   thickEnd;      "Coding region end"
-    uint   itemRGB;       "Color based on confidence (R,G,B values)"
+    uint   itemRgb;       "Color based on confidence (R,G,B values)"
 
     # ----- 20 additional custom fields -----
     string g2p_id;                           "G2P ID"
     string   gene_mim;                         "Gene MIM ID"
     string   hgnc_id;                          "HGNC ID"
     string previous_gene_symbols;            "List of previous gene symbols"
     lstring disease_name;                     "Disease name"
     string disease_mim;                      "Disease MIM ID"
     string disease_MONDO;                    "MONDO ID"
     string allelic_requirement;              "Number of alleles affected to cause the relevant disease"
     string cross_cutting_modifier;           "Optional cross-cutting modifiers giving extra info"
     string confidence;                       "Likelihood that the gene-disease association is true"
     string variant_consequence;              "SO terms for the variant consequence"
     lstring variant_types;                    "SO terms for variant types"
     string molecular_mechanism;              "Molecular mechanism"
     string molecular_mechanism_categorisation; "Categorisation of the molecular mechanism"
     lstring molecular_mechanism_evidence;     "Evidence to determine the disease mechanism"
     lstring phenotypes;                       "Human phenotype ontology IDs"
     lstring publications;                     "Pubmed IDs"
     string panel;                            "Disease grouping or defined clinical category"
     lstring comments;                         "Comments added by online curators"
     string date_of_last_review;              "Date of last review"
 )