410ca755b501b9c84b618ef8e49b9208cff3d145 max Fri Jan 31 05:40:19 2020 -0800 oops, previous commit was into wrong directory diff --git src/hg/utils/otto/clinvar.as src/hg/utils/otto/clinvar.as deleted file mode 100644 index 4ce0768..0000000 --- src/hg/utils/otto/clinvar.as +++ /dev/null @@ -1,39 +0,0 @@ -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; "ClinVar Variation Report" - string clinSign; "Clinical significance" - string reviewStatus; "Review Status" - string type; "Type of Variant" - string geneId; "Gene Symbol" - 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; "Data origin" - string assembly; "Genome assembly" - string cytogenetic; "Cytogenetic status" - lstring hgvsCod; "Nucleotide HGVS" - 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" - uint _varLen; "Variant Length in base pairs " - )