de2cb47114dbcf3ae57ac372bb2cab0263a3e9c5 chmalee Thu Oct 14 15:46:17 2021 -0700 Restoring pre-emptive removal of detailsTabUrls setting, which fixes crispr, snp153 and gnomad tracks, refs #28335 diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra index e7b8f3c..2a3a571 100644 --- src/hg/makeDb/trackDb/human/trackDb.ra +++ src/hg/makeDb/trackDb/human/trackDb.ra @@ -1594,31 +1594,31 @@ defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp151OrthoPt5Pa2Rm8 chimpDb panTro5 orangDb ponAbe2 macaqueDb rheMac8 hapmapPhase III codingAnnotations snp151CodingDbSnp, #track dbSnp152 #shortLabel All dbSNP (152) #longLabel Short Genetic Variants from dbSNP release 152 #bigDataUrl /gbdb/$D/snp/dbSnp152.bb -#detailsUrls _dataOffset=/gbdb/hgFixed/dbSnp/dbSnp152Details.tab.gz +#detailsTabUrls _dataOffset=/gbdb/hgFixed/dbSnp/dbSnp152Details.tab.gz #group varRep #visibility hide #url https://www.ncbi.nlm.nih.gov/snp/$$ #urlLabel dbSNP: #type bigDbSnp #freqSourceOrder 1000Genomes,GnomAD_exomes,TOPMED,GnomAD,ExAC,GoESP,ALSPAC,TWINSUK,Estonian #maxWindowToDraw 1000000 #classFilterValues snv,mnv,ins,del,delins,identity #classFilterType multipleListOr #ucscNotesFilterValues |(nothing noted),classMismatch|Variant class/type is inconsistent with allele sizes,clinvar|Present in ClinVar,clusterError|Overlaps a variant with the same type/class and position,commonAll|MAF >= 1% in all projects that report frequencies,commonSome|MAF >= 1% in at least one project that reports frequencies,delMismatch|Deleted sequence mismatches genomic reference sequence,diffMajor|Different projects report different major alleles,multiMap|Variant is placed in more than one genomic position,overlapDiffClass|Variant overlaps other variant(s) of different type/class,overlapSameClass|Variant overlaps other variant(s) of same type/class but different position,refIsMinor|Genomic reference allele is minor allele in at least one project that reports frequencies,refIsRare|Genomic reference allele frequency is <1% in at least one project,refIsSingleton|Genomic reference frequency is 0 in all projects reporting frequencies,revStrand|Variant maps to opposite strand relative to dbSNP's preferred top-level placement #ucscNotesFilterType multipleListOr #maxFuncImpactFilterValues 0|(not annotated),0865|frameshift,1587|stop_gained,1574|splice_acceptor_variant,1575|splice_donor_variant,1821|inframe_insertion,1583|missense_variant,1590|terminator_codon_variant,1819|synonymous_variant,1580|coding_sequence_variant,1623|5_prime_UTR_variant,1624|3_prime_UTR_variant,1619|nc_transcript_variant,2153|genic_upstream_transcript_variant,1986|upstream_transcript_variant,2152|genic_downstream_transcript_variant,1987|downstream_transcript_variant,1627|intron_variant #maxFuncImpactFilterType multipleListOr #priority 6.8 #release alpha @@ -1629,31 +1629,31 @@ 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 dense type bigDbSnp - detailsUrls _dataOffset=/gbdb/hgFixed/dbSnp/dbSnp153Details.tab.gz + 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,\ commonSome|MAF >= 1% in at least one project that reports frequencies,\ diffMajor|Different projects report different major alleles,\