962ca87bb38d9d7724188f943cdc7e3d760e90e5
max
  Fri Sep 25 01:44:40 2020 -0700
removing link to color doc after code review, refs #26242

diff --git src/hg/utils/otto/clinvar/clinVarToBed src/hg/utils/otto/clinvar/clinVarToBed
index de72ff2..a23a3c0 100755
--- src/hg/utils/otto/clinvar/clinVarToBed
+++ src/hg/utils/otto/clinvar/clinVarToBed
@@ -32,31 +32,30 @@
 parser.add_option("", "--skipDown", dest="skipDownload", action="store_true", help="Only with --auto: don't download again if it's already there, useful when debugging/developing")
 parser.add_option("", "--maxDiff", dest="maxDiff", action="store", type="float", help="look for last month's download file in current dir and accept this much difference, expressed as a ratio. Can only be used with --auto.")
 (options, args) = parser.parse_args()
 
 if options.debug:
     logging.basicConfig(level=logging.DEBUG)
 else:
     logging.basicConfig(level=logging.INFO)
 
 clinvarExpectHeaders = "#AlleleID	Type	Name	GeneID	GeneSymbol	HGNC_ID	ClinicalSignificance	ClinSigSimple	LastEvaluated	RS# (dbSNP)	nsv/esv (dbVar)	RCVaccession	PhenotypeIDS	PhenotypeList	Origin	OriginSimple	Assembly	ChromosomeAccession	Chromosome	Start	Stop	ReferenceAllele	AlternateAllele	Cytogenetic	ReviewStatus	NumberSubmitters	Guidelines	TestedInGTR	OtherIDs	SubmitterCategories	VariationID	PositionVCF	ReferenceAlleleVCF	AlternateAlleleVCF\n"
 # ==== FUNCTIONs =====
 
 # benign = B, likely benign = LB, conflicting = CF, likely pathogenic= LP, 
 # pathogenic = P, other = OT, uncertain = VUS, RF=risk factor
 # colors were defined by Ana Benet Pages
-# see colortable at https://drive.google.com/file/d/1-iqHrZTwT1wuatNA_A5b6knyqE6JG14f/view?usp=sharing
 cnvColors = {
         "INS" : {
             "OT" : "225,165,0",
             "B" : "250,214,69",
             "LB" : "250,214,69",
             "CF" : "225,165,0",
             "RF" : "225,165,0",
             "VUS" : "225,165,0",
             "LP" : "199,114,3",
             "P" : "199,114,3"
             },
         "LOSS" : {
             "OT" : "255,0,0",
             "B" : "255,98,119",
             "LB" : "255,98,119",