31edfe728ae141f60d9974ab972ef022d6b7b4cd
lrnassar
  Tue Dec 3 14:31:11 2019 -0800
Adjusting dbSNP 153 visibilities to dense/hide now that it's out of development refs #23283

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index 3a8bcb9..a7c28bb 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -1620,31 +1620,31 @@
 compositeTrack on
 shortLabel dbSNP 153
 longLabel Short Genetic Variants from dbSNP release 153
 type bed 3
 group varRep
 visibility pack
 url https://www.ncbi.nlm.nih.gov/snp/$$
 urlLabel dbSNP: 
 subGroup1 view Views variants=Variants errs=Mapping_Errors
 priority 0.8
 
     track dbSnp153ViewVariants
     view variants
     parent dbSnp153Composite
     shortLabel Variants
-    visibility pack
+    visibility dense
     type bigDbSnp
     detailsTabUrls _dataOffset=/gbdb/hgFixed/dbSnp/dbSnp153Details.tab.gz
     freqSourceOrder 1000Genomes,GnomAD_exomes,TOPMED,ExAC,PAGE_STUDY,GnomAD,GoESP,Estonian,ALSPAC,TWINSUK,NorthernSweden,Vietnamese
     classFilterValues snv,mnv,ins,del,delins,identity
     classFilterType multipleListOr
     showCfg on
     ucscNotesFilterValues \
         altIsAmbiguous|Alternate allele contains IUPAC ambiguous base(s),\
         classMismatch|Variant class/type is inconsistent with allele sizes,\
         clinvar|Present in ClinVar,\
         clinvarBenign|ClinVar significance of benign and/or likely benign,\
         clinvarConflicting|ClinVar includes both benign and pathogenic reports,\
         clinvarPathogenic|ClinVar significance of pathogenic and/or likely pathogenic,\
         clusterError|Overlaps a variant with the same type/class and position,\
         commonAll|MAF >= 1% in all projects that report frequencies,\
@@ -1686,62 +1686,62 @@
         1986|upstream_transcript_variant,\
         2152|genic_downstream_transcript_variant,\
         1987|downstream_transcript_variant,\
         1627|intron_variant
     maxFuncImpactFilterType multipleListOr
 
         track dbSnp153Common
         parent dbSnp153ViewVariants on
         subGroups view=variants
         shortLabel Common dbSNP (153)
         longLabel Common (1000 Genomes Phase 3 MAF >= 1%) Short Genetic Variants from dbSNP Release 153
         bigDataUrl /gbdb/$D/snp/dbSnp153Common.bb
         priority 1
 
         track dbSnp153ClinVar
-        parent dbSnp153ViewVariants
+        parent dbSnp153ViewVariants off
         subGroups view=variants
         shortLabel ClinVar dbSNP (153)
         longLabel Short Genetic Variants from dbSNP Release 153 Included in ClinVar
         bigDataUrl /gbdb/$D/snp/dbSnp153ClinVar.bb
         priority 2
 
         track dbSnp153Mult
-        parent dbSnp153ViewVariants
+        parent dbSnp153ViewVariants off
         subGroups view=variants
         shortLabel Mult. dbSNP (153)
         longLabel Short Genetic Variants from dbSNP Release 153 that Map to Multiple Genomic Loci
         bigDataUrl /gbdb/$D/snp/dbSnp153Mult.bb
         priority 3
 
         track dbSnp153
-        parent dbSnp153ViewVariants
+        parent dbSnp153ViewVariants off
         subGroups view=variants
         shortLabel All dbSNP (153)
         longLabel All Short Genetic Variants from dbSNP Release 153
         bigDataUrl /gbdb/$D/snp/dbSnp153.bb
         maxWindowToDraw 1000000
         priority 4
 
     track dbSnp153ViewErrs
     parent dbSnp153Composite
     view errs
     shortLabel Mapping Errors
-    visibility pack
+    visibility dense
 
         track dbSnp153BadCoords
-        parent dbSnp153ViewErrs
+        parent dbSnp153ViewErrs off
         subGroups view=errs
         shortLabel Map Err dbSnp (153)
         longLabel Mappings with Inconsistent Coordinates from dbSNP 153
         bigDataUrl /gbdb/$D/snp/dbSnp153BadCoords.bb
         type bigBed 4
         color 100,100,100
         priority 5
 
 track hgdpGeo
 shortLabel HGDP Allele Freq
 longLabel Human Genome Diversity Project SNP Population Allele Frequencies
 group varRep
 visibility hide
 url http://hgdp.uchicago.edu/cgi-bin/gbrowse/HGDP/?name=$$
 urlLabel HGDP Selection Browser: