54c56698083e7bd2697e4b261ec232d1642a3157 max Fri Mar 31 02:47:37 2023 -0700 forgot to commit tagTypes change with last commit, refs #30904 diff --git src/hg/makeDb/trackDb/tagTypes.tab src/hg/makeDb/trackDb/tagTypes.tab index 646353e..c2cbaeb 100644 --- src/hg/makeDb/trackDb/tagTypes.tab +++ src/hg/makeDb/trackDb/tagTypes.tab @@ -1,595 +1,596 @@ # tagType - A list of all tags allowed in a trackDb.ra file and what type stanzas they are # allowed in. If you add a new tag to the system you'll need to add it here to get # tdbQuery -check to not complain about it. While you're at it, be sure to add it to # the trackDb/README file too. # # The format of this file is simple. The first word in a line is the tag name. The # subsequent words are types it is allowed in. Wildcards are allowed in the types. # This file was generated initially with src/hg/oneShot/makeTrackDbTypeTags and then # edited lightly by hand. # # Note that type "customTracks" is used to reserve a symbol that can be in a # custom track track line. It is easier if this shares the same symbol space # as trackDb. accession * aggregate bigWig wig bedGraph aliQualRange bam allButtonPair * altColor * alwaysZero wig bedGraph bigWig applyMinQual vcf vcfTabix autoScale * autoTranslate genePred bamColorMode bam bamGrayMode bam bamSkipPrintQualScore bam barChartBars barChart bigBarChart barChartBarMinWidth barChart bigBarChart barChartBarMinPadding barChart bigBarChart barChartColors barChart bigBarChart barChartCategoryUrl barChart bigBarChart barChartFacets barChart bigBarChart barChartMatrixUrl barChart bigBarChart barChartMerge barChart bigBarChart barChartStatsUrl barChart bigBarChart barChartStretchToItem barChart bigBarChart # below for backwards compatibility during QA. barChartDataUrl barChart bigBarChart barChartLimit barChart bigBarChart # barChartLabel barChart bigBarChart barChartMetric barChart bigBarChart barChartMaxSize barChart bigBarChart barChartSizeWindows barChart bigBarChart barChartSampleUrl barChart bigBarChart barChartUnit barChart bigBarChart baseColorDefault * baseColorTickColor bed bigBed bigPsl baseColorUseCds bed psl genePred bigPsl bigGenePred baseColorUseSequence * baseQualRange bam bedFilter bed bedNameLabel bed barChart bigBarChart bigBed bigLolly bedPackDense bed bigBed bigDataUrl customTracks big* bam vcfTabix halSnake gtexTranscExpr hic vcfPhasedTrio bigGeneDataUrl genePred blastRef psl bigPsl boxedCfg * browserLines customTracks canPack * cartVersion * cdnaTable psl bigPsl cdsDrawDefault psl bed genePred bigPsl cdsDrawOptions psl bigPsl cdsEvidence genePred cdsTable psl bigPsl cell bed bedGraph centerLabelsDense * centerLabelsPack * chainColor chain bigChain chainLinearGap netAlign chain bed psl bigPsl bigChain bigMaf chainMinScore netAlign chain bed psl bigPsl bigChain bigMaf chainNormScoreAvailable netAlign bed chain bigChain chimpDb bed chimpMacaqueOrthoTable bed chimpOrangMacOrthoTable bed chip expRatio bed chromosomes * codingAnnoLabel_snp130CodingDbSnp bed codingAnnoLabel_snp131CodingDbSnp bed codingAnnoLabel_snp132CodingDbSnp bed codingAnnoLabel_snp134CodingDbSnp bed codingAnnotations bed colorBy snake collapseEmptySubtracks * hideEmptySubtracks * hideEmptySubtracksLabel * hideEmptySubtracksMultiBedUrl * hideEmptySubtracksSourcesUrl * color * colorByStrand bigBed bed genePred bigGenePred colorChromDefault psl bigPsl compareGenomeLinks bed compositeTrack * configurable * configureByPopup * container * controlledVocabulary * coriellUrlBase bed bigBed darkerLabels * dataUrl customTracks dataVersion * dateSubmitted bedGraph bed dateUnrestricted bed db * dbPrefixUrls bigBed bed bigPsl genePred psl dbPrefixLabels bigBed bed bigPsl genePred psl dbProfile * dbTrackType customTracks detailsUrls big* detailsTabUrls big* defaultGeneTracks bed bigDbSnp defaultLabelFields big* defaultMaf wigMaf defaultMaxWeight bed defaultLinkedTables genePred bigGenePred denseCoverage bigBed densePack bed bigBed dimensionAchecked * dimensionBchecked * dimensionCchecked * dimensionDchecked * dimensionEchecked * dimensionFchecked * dimensionGchecked * dimensionZchecked * dimensions * directUrl * dividers * dragAndDrop * drawMode hic doWiggle bigBed +downloadUrl * endFudge bed ensemblIdUrl genePred ensArchive genePred exonArrows genePred bed broadPeak bigBed exonArrowsDense bed exonNumbers genePred bed broadPeak psl big* expDrawExons expRatio expProbeTable expRatio expScale bed expRatio expStep bed expRatio expTable bed expRatio extTable * externalDb bigGenePred extraDetailsTable bigBed detailsStaticTable bigBed extraTableFields bigBed detailsDynamicTable bigBed fieldCount customTracks filePos * fileSortOrder * filterBy genePred bed factorSource filterComposite * filterTopScorers bed5FloatScoreWithFdr bed5FloatScore firstItemPos customTracks frames wigMaf bigMaf freqSourceOrder bigDbSnp forceFirstCharLowerCase wigMaf ensemblTranscriptIdUrl genePred ensemblGeneIdUrl genePred vegaTranscriptIdUrl genePred vegaGeneIdUrl genePred gClass_2way_consensus_pseudogene genePred gClass_2way_pseudogene genePred gClass_Ambiguous genePred gClass_Artifact bed genePred gClass_Duplicated genePred gClass_Ensembl_RNA genePred gClass_Ensembl_coding genePred gClass_Ensembl_non_coding genePred gClass_Ensembl_processed_pseudogene genePred gClass_Ensembl_pseudogene genePred gClass_Ensembl_unprocessed_pseudogene genePred gClass_Havana_TEC genePred gClass_Havana_coding genePred gClass_Havana_non_coding genePred gClass_Havana_nonsense genePred gClass_Havana_polyA genePred gClass_Havana_processed_pseudogene genePred gClass_Havana_pseudogene genePred gClass_Havana_unprocessed_pseudogene genePred gClass_Known bed genePred gClass_Novel_CDS bed genePred gClass_Novel_Transcript bed genePred gClass_Novel_transcript genePred gClass_Novel_transcript_gencode_conf genePred gClass_Polymorphic bed genePred gClass_Processed genePred gClass_Processed_pseudogene bed genePred gClass_Pseudogene_fragment genePred gClass_Putative bed genePred gClass_Putative_gencode_conf genePred gClass_TEC bed genePred gClass_Undefined genePred gClass_Unprocessed_pseudogene bed genePred gClass_Validated_coding genePred gClass_Validated_processed genePred gClass_Validated_processed_pseudogene genePred gClass_Validated_pseudogene genePred gClass_Validated_unprocessed_pseudogene genePred gClass_main genePred gClass_putative genePred gClass_cDNA_supported genePred gClass_coding genePred gClass_nonCoding genePred gClass_pseudo genePred gClass_problem genePred gainColor bed geneClasses bed genePred geneTrack vcfTabix vcf vcfPhasedTrio genome customTracks graphType bed5FloatScore bedGraph graphTypeDefault wig bigWig gridDefault bed bedGraph wig bigWig group * groupings expRatio hapClusterEnabled vcf vcfTabix hapClusterColorBy vcf vcfTabix hapClusterMethod vcf vcfTabix hapClusterTreeAngle vcf vcfTabix hapClusterHeight vcf vcfTabix hapmapPhase bed hgGene genePred hgsid bed genePred bigBed hicDistanceMin hic hicDistanceMax hic highlightBy genePred highlightColor genePred hoverMetadata wig bigWig html * htmlFile customTracks htmlUrl customTracks idInUrlSql altGraphX genePred chain factorSource bed bigChain idXref genePred psl bigGenePred iframeUrl * iframeOptions * indelDoubleInsert psl bam chain bigBed bigPsl bigChain indelPolyA psl bam bigPsl indelQueryInsert psl bam chain bigBed bigPsl bigChain informant genePred initialPos customTracks inputFieldMetaTables * inputType customTracks interTable encodeFiveC interTableKind encodeFiveC #inputTracks bed factorSource #inputTracksSubgroupSelect bed factorSource inputTracksSubgroupDisplay bed factorSource inputTrackTable bed factorSource inputTableFieldDisplay bed factorSource inputTableFieldUrls factorSource interactDirectional interact bigInteract interactUp interact bigInteract interactMultiRegion interact bigInteract intronGap psl genePred bigPsl bigGenePred irows wigMaf bigMaf isGencode3 genePred bigGenePred isGencode2 genePred bigGenePred isGencode genePred itemAttrTbl genePred itemBigImagePath bed itemClassTbl bed genePred itemClassNameColumn genePred itemClassClassColumn genePred itemCount customTracks itemDetailsHtmlTable genePred psl bed bigPsl itemFirstCharCase wigMafProt wigMaf bigMaf itemImagePath bed itemRgb bedDetail bedGraph bed bedLogR bigBed bigPsl interact bigInteract bigGenePred bigLolly lfPslTable bed linesAt chromGraph linkDataUrl bigChain linkIdInName bed bigBed labelFields big* labelOnFeature bed bigBed labelSeparator bigBed bigPsl bigGenePred logo bigWig lollipopField bigBed bigLolly lollyField bigBed bigLolly lollyMaxSize bigBed bigLolly lollySizeField bigBed bigLolly logoMaf wig longLabel * longlabel genePred longLabelClip * lossColor bed macaqueDb bed mafDot wigMaf mafDotDefault wigMaf mafFile customTracks mafShowSnp wigMaf mafTrack bed mapDispatcher expRatio matrix netAlign bed chain psl bigPsl bigChain bigMaf matrixHeader netAlign bed chain psl bigPsl bigChain bigMaf maxChromName customTracks maxHeightPixels * maxItems * maxLimit * maxScore broadPeak narrowPeak maxWindowToDraw bam big* rmsk joinedRmsk bed narrowPeak broadPeak bedlogR genepred vcf vcfTabix vcfPhasedTrio factorSource maxWindowCoverage * maxWindowToQuery bigWig bed bedlogR metadata * mergeSpannedItems bigBed mgiUrl bed mgiUrlLabel bed minFreq vcf vcfTabix minGrayLevel bed broadPeak narrowPeak bedLogR bigBed minLimit * minMax chromGraph minQual vcf vcfTabix minScore bed broadPeak narrowPeak motifTable factorSource motifPwmTable factorSource bed6FloatScore bigBed motifMapTable factorSource motifMaxWindow factorSource motifDrawDefault factorSource mouseOverField big* mouseOver bigLolly bigBed bigPsl mouseOverFunction bigWig msaTable wig wigMafProt wigMaf multiRegionsBedUrl * ncbiAccXref bed negateValues wigMaf bigWig bedGraph wig nextExonText * nextItemButton * noColorTag bam noInherit * nonBedFieldsLabel bigBed noScoreFilter bedGraph bed bedLogR gvf bedDetail bigBed bigPsl interact bigInteract noParentConfig bed bigBed bigLolly bigWig notNCBI bed noGenomeReason * normalization hic lollyNoStems bigBed bigLolly ococci bed offset customTracks oldToNew genePred onlyVisibility wigMafProt wigMaf bed orangDb bed origAssembly * origTrackLine customTracks otherDb * otherTwoBitUrl * otherDbTable bed otherOrg netAlign chain bigChain otherSpecies halSnake pairEndsByName bam pairedEndUrlFormat bed pairwise wigMaf pairwiseHeight wigMaf parent * patDb expRatio patKey expRatio patTable expRatio pennantIcon * pepTable psl bigPsl pgDbLink bed pgSnp pgPolyphenPredTab bed pgSnp pgSiftPredTab bed pgSnp pred psl bigPsl prevExonText * priority * private bed pslSequence psl bigPsl pslTable bed bigPsl refSeqAnnoVersion genePred release * refUrl bam resolution hic ucscRetroInfo psl bigPsl ucscRetroParentTables * vcfChildSample vcfPhasedTrio vcfParentSamples vcfPhasedTrio vcfUseAltSampleNames vcfPhasedTrio saturationScore hic sGroup_Afrotheria wigMaf bigMaf sGroup_Artiodactyla bigMaf sGroup_Aves wigMaf sGroup_bird wigMaf sGroup_Birds wigMaf sGroup_Brachycera wigMaf sGroup_Bundibugyo_2007 wigMaf sGroup_Caenorhabditis wigMaf sGroup_Carnivore wigMaf bigMaf sGroup_Cetartiodactyla wigMaf bigMaf sGroup_Chiroptera wigMaf bigMaf sGroup_CoV_2019 wigMaf sGroup_CoV wigMaf sGroup_SARS-CoV-2_sequences wigMaf sGroup_Other_CoV_sequences_from_vertebrate_hosts wigMaf sGroup_Chimp wigMaf sGroup_DRC_2007 wigMaf sGroup_Deuterostomia wigMaf sGroup_Dorylaimia wigMaf sGroup_Drosophila wigMaf sGroup_Ebola_2014 wigMaf sGroup_Euarchontoglires wigMaf bigMaf sGroup_fish wigMaf sGroup_Fish wigMaf sGroup_Gabon wigMaf sGroup_Glires wigMaf bigMaf sGroup_hiv wigMafProt wigMaf sGroup_Holometabola wigMaf sGroup_Human wigMaf sGroup_Laurasiatheria wigMaf bigMaf sGroup_Mammal wigMaf sGroup_mammal wigMaf sGroup_Mammals wigMaf bigMaf sGroup_Marburg_1987 wigMaf sGroup_Metatheria bigMaf sGroup_Monotremata bigMaf sGroup_Nematocera wigMaf sGroup_Nematode wigMaf sGroup_Nematodes wigMaf sGroup_Others wigMaf sGroup_Percent99 wigMaf sGroup_Percent98 wigMaf sGroup_Percent97 wigMaf sGroup_Percent96 wigMaf sGroup_Percent95 wigMaf sGroup_Percent94 wigMaf sGroup_Percent93 wigMaf sGroup_Percent92 wigMaf sGroup_Percent91 wigMaf sGroup_Percent90 wigMaf sGroup_Percent88 wigMaf sGroup_placental wigMaf sGroup_Placental wigMaf sGroup_Placental_Mammal wigMaf sGroup_Placental_Mammals wigMaf sGroup_Platyhelminthes wigMaf sGroup_Plectida wigMaf sGroup_Primate wigMaf bigMaf sGroup_Primates wigMaf bigMaf sGroup_primate wigMaf sGroup_Reptiles wigMaf sGroup_Reston_1989-90 wigMaf sGroup_Rhabditina wigMaf sGroup_Rodents wigMaf bigMaf sGroup_Sarcopterygii wigMaf sGroup_Spirurina wigMaf sGroup_Strongylida wigMaf sGroup_Sudan_1976-9 wigMaf sGroup_Tylenchina wigMaf sGroup_vertebrate wigMaf sGroup_Vertebrate wigMaf sGroup_Vertebrates wigMaf sGroup_Virus wigMaf sGroup_worm wigMaf sGroup_Xenarthra bigMaf sGroup_Zaire wigMaf sGroup_Zaire(DRC)_1976-7 wigMaf *Filter bed narrowPeak broadPeak *FilterLimits bed narrowPeak broadPeak *FilterByRange bed narrowPeak broadPeak *FilterLabel bed narrowPeak broadPeak big* sampleColorFile vcf vcfTabix scoreFilter broadPeak narrowPeak bed interaction bedlogR peptideMapping bigBed bigPsl scoreFilterByRange bed peptideMapping bigBed bigPsl scoreFilterLimits broadPeak narrowPeak bed interaction bedlogR peptideMapping bigBed bigPsl scoreFilterMax bed bedlogR peptideMapping bigBed bigPsl scoreMax bed bedlogR interaction peptideMapping narrowPeak bigBed bigPsl scoreMin broadPeak narrowPeak bed bedlogR interaction peptideMapping bigBed bigPsl scoreLabel bed bigBed bigPsl bigGenePred bigLolly searchIndex bigBed bigPsl bigGenePred bigBarChart searchTrix bigBed bigPsl bigGenePred searchTrixContext bigBed bigPsl bigGenePred selectSubject psl bigPsl seqTable bed settingsByView * sepFields bigBed bigPsl bigGenePred shortLabel * showCdsAllScales psl bigPsl chain bigChain showCdsMaxZoom psl bigPsl chain bigChain showCfg * showDiffBasesAllScales * showDiffBasesMaxZoom * showHardyWeinberg vcf vcfTabix showNames bam showSubtrackColorOnUi * showTopScorers bed5FloatScoreWithFdr bed5FloatScore bed signalFilter bed narrowPeak broadPeak signalFilterLimits bed narrowPeak broadPeak skipFields bigBed bigPsl bigGenePred bigLolly skipEmptyFields bigBed bigPsl smoothingWindow wig bed5FloatScore bedGraph bigWig snpExceptions bed snpExceptionDesc bed snpMode wigMaf maf snpSeq bed snpSeqFile bed snpTable bed wigMaf snpVersion bed sortOrder * sourceTable factorSource bed spanList * speciesCodonDefault wigMafProt wigMaf bigMaf speciesDefaultOff wigMaf bigMaf speciesDefaultOn wigMaf bigMaf speciesGroups wigMafProt wigMaf bigMaf speciesLabels wigMafProt wigMaf bigMaf speciesOrder bed maf wigMaf bigMaf speciesTarget wigMaf speciesTree wigMaf speciesUseFile wigMafProt wigMaf spectrum * squishyPackField bigBed bigGenePred squishyPackPoint bigBed bigGenePred stripPrefix bam subGroup1 * subGroup2 * subGroup3 * subGroup4 * subGroup5 * subGroup6 * subGroup7 * subGroup8 * subGroup9 * subGroups * subGroupMetaTables * subTrack * subgroups bed summary wigMaf bigMaf superTrack * symbolTable bed genePred pubsArticleTable bed psl bigPsl pubsSequenceTable bed psl bigPsl pubsMarkerTable bed psl bigPsl pubsPslTrack bed psl bigPsl thickDrawItem bed table * tableBrowser * tdbType customTracks track * trackHandler * transMapGene psl bigPsl transMapInfo psl bigPsl transMapSrc psl bigPsl transMapTypeDesc psl bigPsl transMapSrcSet psl bigPsl transformFunc bed bigBed bedGraph wig bigWig barChart bigBarChart treeImage wigMaf bigMaf twoBit snake txInfo genePred type * url * url2 bed genePred bigBarChart url2Label bed genePred bigBarChart urlLabel * urlName genePred psl bigPsl urls bigBed bed bigPsl genePred psl bigBarChart bigGenePred bigLolly useScore * vcfDoFilter vcf vcfTabix vcfPhasedTrio vcfDoQual vcf vcfTabix vcfPhasedTrio vcfDoMaf vcf vcfTabix vcfPhasedTrio view * viewLimits * viewLimitsMax bed bedGraph wig bigWig viewUi * visibility * visibilityViewDefaults * wgEncode * wgEncodeGencodeVersion genePred wgEncodeGencodeAttrs genePred wgEncodeGencodeExonSupport genePred wgEncodeGencodeGeneSource genePred wgEncodeGencodeTranscriptSource genePred wgEncodeGencodeHgnc genePred wgEncodeGencodePdb genePred wgEncodeGencodePubMed genePred wgEncodeGencodeRefSeq genePred wgEncodeGencodeTag genePred wgEncodeGencodeTranscriptSupport genePred wgEncodeGencodeUniProt genePred wgEncodeGencodePolyAFeature genePred wgEncodeGencodeAnnotationRemark genePred wgEncodeGencodeTranscriptionSupportLevel genePred wgEncodeGencodeEntrezGene genePred maxTransEnabled * wibFile customTracks wigColorBy wig wigFile customTracks wiggle wigMaf windowingFunction * xrefDataUrl * yalePseudoAssoc * yaleUrl * yalePseudoUrl * yLinOnOff wigMaf yLineMark * yLineOnOff * yAxisNumLabels bigBed bigLolly