05e67c59a20a5d00b810a981aef3b00c5bef82e1
max
  Fri Sep 20 06:03:18 2024 -0700
more features to hubtools: search in both parent and subdirs, better docs

diff --git src/hg/makeDb/trackDb/human/clinvar.ra src/hg/makeDb/trackDb/human/clinvar.ra
index 0bc3135..c78351d 100644
--- src/hg/makeDb/trackDb/human/clinvar.ra
+++ src/hg/makeDb/trackDb/human/clinvar.ra
@@ -27,31 +27,31 @@
         filterType._clinSignCode multiple
         filterValues._originCode GERM|germline,SOM|somatic,GERMSOM|germline/somatic,UNK|unknown
         filterType._originCode multiple
         filterLabel._originCode Alelle Origin
         filterValues._allTypeCode SUBST|single nucleotide variant - SUBST,STRUCT|translocation and fusion - STRUCT,LOSS|deletion and copy loss - LOSS,GAIN|duplication and copy gain - GAIN,INS|indel and insertion - INS,INV|inversion - INV,SEQALT|undetermined - SEQALT,SEQLEN|repeat change - SEQLEN
         filterType._allTypeCode multiple
         filter._varLen 0
         skipFields rcvAcc
         filterByRange._varLen on
         filterLimits._varLen 0:49
         filterValues.molConseq genic downstream transcript variant|genic downstream transcript variant,no sequence alteration|no sequence alteration,inframe indel|inframe indel,stop lost|stop lost,genic upstream transcript variant|genic upstream transcript variant,initiatior codon variant|initiatior codon variant,inframe insertion|inframe insertion,inframe deletion|inframe deletion,splice acceptor variant|splice acceptor variant,splice donor variant|splice donor variant,5 prime UTR variant|5 prime UTR variant,nonsense|nonsense,non-coding transcript variant|non-coding transcript variant,3 prime UTR variant|3 prime UTR variant,frameshift variant|frameshift variant,intron variant|intron variant,synonymous variant|synonymous variant,missense variant|missense variant,|unknown,initiator codon variant|initiator codon variant
         mouseOverField _mouseOver
         bigDataUrl /gbdb/$D/bbi/clinvar/clinvarMain.bb
         urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" geneId="https://www.ncbi.nlm.nih.gov/gene/$$" snpId="https://www.ncbi.nlm.nih.gov/snp/$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/"
         noScoreFilter on
-        searchIndex _dbVarSsvId
+        searchIndex _dbVarSsvId,vcvId
         maxWindowCoverage 10000000
 
         track clinvarCnv
         parent clinvar
         shortLabel ClinVar CNVs
         longLabel ClinVar Copy Number Variants >= 50bp
         visibility hide
         type bigBed 12 +
         itemRgb on
         group phenDis
         priority 2
         skipFields rcvAcc
         # note that you cannot change these values. Old carts will contain them. If you must change these, you'll have to rename
         # the field, which will reset the cart variables. Or use the cart rewrite mechanism. You can add more values, though
         filterValues._originCode GERM|germline,SOM|somatic,GERMSOM|germline/somatic,NOVO|de novo,UNK|unknown
@@ -90,17 +90,17 @@
         yAxisLabel.3 3 on 150,150,150 VUS
         yAxisLabel.4 4 on 150,150,150 LP
         yAxisLabel.5 5 on 150,150,150 P
         lollyMaxSize 10
         viewLimits 0:5
         mouseOverField _mouseOver
         urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" geneId="https://www.ncbi.nlm.nih.gov/gene/$$" snpId="https://www.ncbi.nlm.nih.gov/snp/$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/"
 
 searchTable clinvarCnv
 searchType bigBed
 searchDescription ClinVar Copy Number Variants 
 termRegex ^[ne]ssv[0-9]+
 
 searchTable clinvarMain
 searchType bigBed
-searchDescription ClinVar Copy Number Variants
-termRegex ^[ne]ssv[0-9]+
+searchDescription ClinVar Short Nucleotide Variants
+termRegex (^[ne]ssv[0-9]+|vcv[0-9]+.[0-9])