e408d52de2f812c4dc407b1865c97c45090dcf16 chmalee Mon Oct 11 16:40:46 2021 -0700 Renaming the trackDb settings extraDetailsTable and extraTableFields to the more descriptive and more accurate detailsStaticTable and detailsDynamicTable. Also rename detailsTabUrls to detailsUrls, luckily that setting has not been documented yet, so a simple rename is possible diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra index 2a3a571..e7b8f3c 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 -#detailsTabUrls _dataOffset=/gbdb/hgFixed/dbSnp/dbSnp152Details.tab.gz +#detailsUrls _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 - detailsTabUrls _dataOffset=/gbdb/hgFixed/dbSnp/dbSnp153Details.tab.gz + detailsUrls _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,\