4654fecc7b9d5d905365bd72fee9d3fa4cb6724f
chmalee
  Thu Jan 13 12:38:46 2022 -0800
Staging updates to clingen tracks: slightly rework the otto job after changes to the clinGen website, get out links on description pages correct, refs #28453

diff --git src/hg/utils/otto/clinGen/clinGenCnv.as src/hg/utils/otto/clinGen/clinGenCnv.as
new file mode 100644
index 0000000..b7406f6
--- /dev/null
+++ src/hg/utils/otto/clinGen/clinGenCnv.as
@@ -0,0 +1,30 @@
+table clinGenCnv
+"CNVs from NCBI Clinical Genome Resource"
+    (
+    string chrom;      "Reference sequence chromosome or scaffold"
+    uint   chromStart; "Start position in chromosome"
+    uint   chromEnd;   "End position in chromosome"
+    string name;       "Short 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"
+    uint size;         "Size of variant"
+    string alias; "Item Alias"
+    string variantRegion; "Variant Region"
+    string startRange; "Start Range"
+    string endRange; "End Range"
+    string copyNumber; "Copy Number"
+    string variantType; "Variant Type"
+    string omimId; "OMIM ID(s)"
+    string clinGenId; "ClinGen ID(s)"
+    string phenotype; "Phenotype"
+    string phenotypeId; "Phenotype ID(s)"
+    lstring pubMed; "PubMed ID(s)"
+    string clinicalInterpretation; "Clinical Interpretation"
+    string clinicalSource; "Clinical Source"
+    string sampleName; "Sample Name"
+    string samplesetName; "Sampleset Name"
+    lstring _mouseOver; "mouseOver string"
+    )