a64bc5a6cfe9756104a86f633b0f0a01772c4b83
lrnassar
  Wed Oct 6 16:55:59 2021 -0700
Updating a few things on otto. For the most part these are changes to the wrapper emails, which had not been updated in git, and the big changes are were done by engineers directly to the hive copy without updating the tree version. The big updates for clinvar were Max, and decipher was Braney I believe. To clarify, these now updated versions are the ones that have been running daily/weekly, so all of it has been in action already.

diff --git src/hg/utils/otto/clinvar/clinvar.as src/hg/utils/otto/clinvar/clinvar.as
index 58aee42..17da1a4 100644
--- src/hg/utils/otto/clinvar/clinvar.as
+++ src/hg/utils/otto/clinvar/clinvar.as
@@ -1,45 +1,45 @@
 table clinVarBed
 "Browser extensible data (12 fields) plus information about a ClinVar entry. _clinSignCode has these possible values: BN=benign, LB=likely benign, CF=conflicting, PG=pathogenic, LP=likely pathogenic, UC=uncertain, OT=other"
     (
     string chrom;        "Chromosome (or contig, scaffold, etc.)"
     uint   chromStart;   "Start position in chromosome"
     uint   chromEnd;     "End position in chromosome"
     string name;         "Name of item"
     uint   score;      "Score from 0-1000"
     char[1] strand;    "+ or -"
     uint thickStart;   "Start of where display should be thick (start codon)"
     uint thickEnd;     "End of where display should be thick (stop codon)"
     uint reserved;     "Used as itemRgb as of 2004-11-22"
     int blockCount;    "Number of blocks"
     int[blockCount] blockSizes; "Comma separated list of block sizes"
     int[blockCount] chromStarts; "Start positions relative to chromStart"
     lstring origName;         "Link to ClinVar with Variant ID"
     string clinSign;         "Clinical significance"
     string reviewStatus;   "Review Status"
     string type;         "Type of Variant"
     string geneId;         "Gene Symbol"
     string molConseq;         "Molecular Consequence"
     string snpId;         "dbSNP ID"
     string nsvId;         "dbVar ID"
     lstring rcvAcc;         "ClinVar Allele Submission"
     string testedInGtr;         "Genetic Testing Registry"
     lstring phenotypeList;         "Phenotypes"
     lstring phenotype;         "Phenotype identifiers"
     string origin;         "Allele origin"
     string assembly;         "Genome assembly"
     string cytogenetic;         "Cytogenetic status"
-    lstring hgvsCod;         "Nucleotide HGVS"
-    lstring hgvsProt;         "Protein HGVS"
+    lstring _jsonHgvsTable;         "HGVS names"
+    lstring _hgvsProt;         "Protein HGVS"
     string numSubmit;         "Number of submitters"
     string lastEval;         "Last evaluation"
     string guidelines;         "Guidelines"
     lstring otherIds;         "Other identifiers e.g. OMIM IDs, etc."
     lstring _mouseOver;        "Mouse over text"
     string _clinSignCode;        "Clinical Significance"
     string _originCode;        "Allele Origin Code"
     string _allTypeCode;        "Variation Type"
     uint _varLen;            "Variant Length in base pairs"
     uint _starCount;         "Number of stars"
     int _variantId;           "ClinVar variant ID"
     string _dbVarSsvId;           "dbVar SSV ID"
     )