0e4e0c0af65eea70f64edbc68348ce0972c4bbf4 braney Fri Aug 28 16:45:00 2026 -0700 Correct the track types listed for trackDb settings, and the hub settings list The "For Types" list in the trackDb docs was wrong for about sixty settings, so the docs named the wrong track types for settings that have always worked. Most named only the older type and left out its big* counterpart. The clearest case is the multiple-alignment family: a bigMaf track is drawn and configured by the same code as a wigMaf track, but only speciesOrder said so, while irows, itemFirstCharCase, speciesGroups, speciesCodonDefault, speciesDefaultOff, treeImage, pairwiseHeight and speciesUseFile all claimed wigMaf alone. The hapCluster settings said vcf and not vcfTabix. noScoreFilter said bed while its own example uses type bigBed 6 +. Six settings said "all" for something that only works on item tracks. Two documented settings do not exist. pslSequence describes a variable that was replaced by the baseColor family long before the setting was listed, and nothing has read either spelling since; it is removed. noStems is renamed to lollyNoStems, which is what the Browser actually reads. That one mattered: hubCheck builds its list of valid settings from trackDbHub.html, so it accepted the spelling that does nothing and rejected the one that works. Fourteen settings that work in hubs had no entry in the hub spec, so hubCheck reported them as unrecognized. They are listed now: chainColor, chainNormScoreAvailable, pairwiseHeight, barChartMatrixUrl, mouseOverFunction, intronGap, filterBy, baseColorTickColor, speciesGroups, speciesDefaultOff, speciesCodonDefault, itemFirstCharCase, irows, and canPack with configureByPopup and origAssembly. The last three, along with filterBy and baseColorTickColor, were marked "NOT FOR HUBS", which was wrong: the Browser reads them from a hub's trackDb the same way it reads them from ours. The type setting on the hub page listed every type the Browser knows, including ones that only work for tracks loaded into our own databases. It now shows only the types a hub can use. A hub-specific blurb for this already existed and had never been referenced. Three settings had no blurb at all, so the generated trackDbSettings.json never saw them: metadata, noInherit and useScore. Written, and the five hand-written copies in trackDbDoc.html that had drifted from the library are brought back into line. The library's header told the reader to always check their work in trackDbTestBlurbs.html, which was deleted in November 2025. It now points at "make settings" instead. That target regenerates trackDbSettings.yaml and .json, which are updated here, and its name map gains an entry so the hub-specific type blurb is still keyed as "type". refs #37908 diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.json src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.json index dd8db21c28a..5fdf7dfaee7 100644 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.json +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.json @@ -14,61 +14,62 @@ "bigNarrowPeak - Peaks", "bigPsl - Pairwise Alignments", "bigWig - Signal Graphing Track Settings", "bigLolly - Lollipop charts", "hic - Hi-C contact matrices", "halSnake - Multiple Alignments", "vcfTabix - Variant Call Format Track Settings", "vcfPhasedTrio - Variant Call Format Track Settings", "superTrack - Folder Track Settings", "Composite Track Settings", "Composite - Subgroups Settings", "Composite - Views Settings", "Faceted Composite Settings", "Aggregate or Overlay Track Settings", "general hub file settings", - "genomes file settings" + "genomes file settings", + "Miscellaneous Deprecated Settings" ], "settings": [ { "key": "track", "category": "Common Settings", "roles": [ "super", "composite", "view", "leaf" ], "types": "all", "level": "required", "fmt": "track", "ex": "track myFirstTrack", "desc": "This is the name of the dataset and must be unique within the Genome Browser or dataHub." }, { "key": "type", "category": "Common Settings", "roles": [ "super", "composite", "view", "leaf" ], "types": "all", "level": "required", "fmt": "type", - "ex": "type bed 6 +", + "ex": "type bigBed 6 +", "desc": "Declares the format of the data and is used to determine display methods and options." }, { "key": "shortLabel", "category": "Common Settings", "roles": [ "super", "composite", "view", "leaf" ], "types": "all", "level": "required", "fmt": "shortLabel", "ex": "shortLabel Human mRNAs", @@ -180,30 +181,75 @@ { "key": "priority", "category": "Common Settings - less frequent", "roles": [ "super", "composite", "view", "leaf" ], "types": "all", "level": "base", "fmt": "priority <float>", "ex": "priority 50", "desc": "The priority is used to define the order of a track within its track group or data hub, as well as its default order within the Browser image." }, + { + "key": "canPack", + "category": "Common Settings - less frequent", + "roles": [ + "super", + "composite", + "view", + "leaf" + ], + "types": "all", + "level": "deprecated", + "fmt": "canPack <off/on>", + "ex": "canPack on", + "desc": "Deprecated." + }, + { + "key": "configureByPopup", + "category": "Common Settings - less frequent", + "roles": [ + "super", + "composite", + "view", + "leaf" + ], + "types": "all", + "level": "full", + "fmt": "configureByPopup <on/off>", + "ex": "configureByPopup off", + "desc": "Most track displays that can be configured by a user can also be configured from directly within the Browser image through a right-click option that pops up..." + }, + { + "key": "origAssembly", + "category": "Common Settings - less frequent", + "roles": [ + "super", + "composite", + "view", + "leaf" + ], + "types": "all", + "level": "full", + "fmt": "origAssembly <db>", + "ex": "origAssembly hg18", + "desc": "The original assembly version for which the dataset was generated." + }, { "key": "altColor", "category": "Common Settings - less frequent", "roles": [ "super", "composite", "view", "leaf" ], "types": "all", "level": "full", "fmt": "altColor <red,green,blue>", "ex": "altColor 0,0,255", "desc": "Many track types allow setting a color range that varies from color to altColor ." }, @@ -868,30 +914,44 @@ }, { "key": "barChartFacets", "category": "bigBarChart", "roles": [ "leaf" ], "types": [ "bigBarChart" ], "level": "new", "fmt": "barChartFacets <column1,column2,...columnN>", "ex": "", "desc": "This setting turns on the faceted selection on the track details and configure page which is useful for selecting which bars out of a large number to display." }, + { + "key": "barChartMatrixUrl", + "category": "bigBarChart", + "roles": [ + "leaf" + ], + "types": [ + "bigBarChart" + ], + "level": "full", + "fmt": "barChartMatrixUrl <url>", + "ex": "", + "desc": "Specifies a data matrix file that provides data values for all samples." + }, { "key": "barChartStatsUrl", "category": "bigBarChart", "roles": [ "leaf" ], "types": [ "bigBarChart" ], "level": "new", "fmt": "barChartStatsUrl <url>", "ex": "", "desc": "This setting associates a table in tab-separated-values with the barchart, with one line per bar." }, { @@ -1177,51 +1237,60 @@ "types": [ "bigBed" ], "level": "new", "fmt": "detailsScript.<plotType>.<fieldName> <jsonConfig>", "ex": "detailsScript.histogram.afrHist {\"title\":\"AFR Allele Frequencies\",\"xLabel\":\"Allele size (repeat copies)\"}\ndetailsScript.histogram.eurHist {\"title\":\"EUR Allele Frequencies\",\"xLabel\":\"Allele size (repeat copies)\"}", "desc": "Adds a custom JavaScript visualization to the item details page for a bigBed track." }, { "key": "exonArrows", "category": "bigBed - Item or Region Track Settings", "roles": [ "leaf" ], "types": [ - "genePred", "bed", + "bigBed", + "genePred", + "bigGenePred", + "psl", + "bigPsl", + "chain", + "bigChain", + "narrowPeak", + "bigNarrowPeak", "broadPeak" ], "level": "full", "fmt": "exonArrows <on/off>", "ex": "exonArrows off", "desc": "On tracks that show exons or blocks within features, exon arrows allow the user to jump to the next exon or block outside the image." }, { "key": "exonNumbers", "category": "bigBed - Item or Region Track Settings", "roles": [ "leaf" ], "types": [ "genePred", + "bigGenePred", "bed", - "psl", "bigBed", - "bigGenePred" + "psl", + "bigPsl" ], "level": "full", "fmt": "exonNumbers <on/off>", "ex": "exonNumbers off", "desc": "A mouseover that shows the exon and intron numbers can be explicitly shown or hidden using this setting." }, { "key": "scoreFilter", "category": "bigBed - Item or Region Track Settings", "roles": [ "leaf" ], "types": [ "bigBed" ], @@ -1243,106 +1312,114 @@ "psl" ], "level": "full", "fmt": "maxItems <integer>", "ex": "maxItems 25", "desc": "Maximum number of items to display individually in full or pack or squish mode." }, { "key": "maxWindowCoverage", "category": "bigBed - Item or Region Track Settings", "roles": [ "leaf" ], "types": [ "bed", + "bigBed", "genePred", - "bam", - "rmsk", + "bigGenePred", + "psl", + "bigPsl", + "chain", + "bigChain", "narrowPeak", + "bigNarrowPeak", "broadPeak", - "bigWig", - "bedLogR" + "bam", + "rmsk", + "bedLogR", + "vcf", + "vcfTabix" ], "level": "full", "fmt": "maxWindowCoverage <integer>", "ex": "maxWindowCoverage 10000000", "desc": "When too many individual bed items might be shown in the Browser image (such as might occur when a large region of a chromosome is viewed), maxWindowCoverage..." }, { "key": "maxWindowToDraw", "category": "bigBed - Item or Region Track Settings", "roles": [ "leaf" ], - "types": [ - "bed", - "genePred", - "bam", - "rmsk", - "narrowPeak", - "broadPeak", - "bigWig", - "bedLogR" - ], + "types": "all", "level": "full", "fmt": "maxWindowToDraw <integer>", "ex": "maxWindowToDraw 10000000", "desc": "When too many individual bed items might be shown in the Browser image (such as might occur when a large region of a chromosome is viewed), maxWindowToDraw w..." }, { "key": "minGrayLevel", "category": "bigBed - Item or Region Track Settings", "roles": [ "leaf" ], "types": [ "bed", + "bigBed", "broadPeak", "narrowPeak", + "bigNarrowPeak", "bedLogR", - "bigBed" + "bigInteract" ], "level": "full", "fmt": "minGrayLevel <1-9>", "ex": "minGrayLevel 4", "desc": "When a bed track contains the standard field score , and when that score is used to present items in gray or color scale (see spectrum ), this setting specif..." }, { "key": "noScoreFilter", "category": "bigBed - Item or Region Track Settings", "roles": [ "leaf" ], "types": [ "bed", + "bigBed", "bedGraph", "bedLogR", "gvf" ], "level": "full", "fmt": "noScoreFilter on", "ex": "type bigBed 6 +\n noScoreFilter on", "desc": "By default, bed tracks with 5 or more standard bed fields that contain either a ' ." }, { "key": "spectrum", "category": "bigBed - Item or Region Track Settings", "roles": [ "leaf" ], - "types": "all", + "types": [ + "bed", + "bigBed", + "bigGenePred", + "psl", + "bigPsl" + ], "level": "base", "fmt": "spectrum on", "ex": "spectrum on\n scoreMin 700\n scoreMax 900", "desc": "Replaces useScore ." }, { "key": "style", "category": "bigBed - Item or Region Track Settings", "roles": [ "leaf" ], "types": [ "bigBed" ], "level": "new", @@ -1498,30 +1575,51 @@ }, { "key": "filterValues", "category": "bigBed - Item or Region Track Settings", "roles": [ "leaf" ], "types": [ "bigBed" ], "level": "full", "fmt": "filterValues.<fieldName> <value1,value2,value3...>", "ex": "filterValues.fieldName fieldValue1|alternativeName1,fieldValue2|alternativeName2...", "desc": "There are a number of different filters available for bigBed data." }, + { + "key": "filterBy", + "category": "bigBed - Item or Region Track Settings", + "roles": [ + "leaf" + ], + "types": [ + "bed", + "bigBed", + "genePred", + "bigGenePred", + "psl", + "bigPsl", + "bigLolly", + "factorSource" + ], + "level": "full", + "fmt": "filterBy <field1:title=[+]opt1a...>\n [field2:title=[+]opt2a...]", + "ex": "filterBy {field1}[:{Title1}]=[+]\\\n option1a[|label1a[{style1a}]],\\\n option1b[|label1b[{style1b}]],... \\\n [{field2}[:{Title2}]=[+]\\\n option2a[|label2a[{style2a}]],,...]", + "desc": "Another method of filtering items relies upon discrete values." + }, { "key": "filterLabel", "category": "bigBed - Item or Region Track Settings", "roles": [ "leaf" ], "types": [ "bed", "bigBed" ], "level": "full", "fmt": "filterLabel.<fieldName> <label>", "ex": "filterValues.strand +,-\n filterLabel.strand Strand (Orientation)", "desc": "When a user clicks on a track item in the Browser image, the item detail page is shown." }, @@ -1622,45 +1720,57 @@ "bed", "bigBed" ], "level": "full", "fmt": "bedNameLabel <label>", "ex": "bedNameLabel Gene Id", "desc": "When a user clicks on a bed track item in the Browser image, the item detail page is shown." }, { "key": "exonArrowsDense", "category": "Item or Region Track Settings - less frequent", "roles": [ "leaf" ], "types": [ - "bed" + "bed", + "bigBed", + "genePred", + "bigGenePred", + "psl", + "bigPsl", + "chain", + "bigChain", + "narrowPeak", + "bigNarrowPeak", + "broadPeak", + "bam" ], "level": "full", "fmt": "exonArrowsDense <off/on>", "ex": "", "desc": "On tracks that show exons or blocks within items, exon arrows allow the user to jump to the next exon/block outside the image." }, { "key": "itemImagePath", "category": "Item or Region Track Settings - less frequent", "roles": [ "leaf" ], "types": [ - "bed" + "bed", + "bigBed" ], "level": "full", "fmt": "itemImagePath <path> <suffix>", "ex": "itemImagePath images/myTrackImages png\n itemBigImagePath http://bigImages.com/myTrackImages jpg", "desc": "Items can be associated with images and the images can be made visible with these two settings." }, { "key": "mergeSpannedItems", "category": "Item or Region Track Settings - less frequent", "roles": [ "leaf" ], "types": [ "bigBed" ], @@ -1678,31 +1788,43 @@ "types": [ "bed", "bigBed" ], "level": "full", "fmt": "linkIdInName on", "ex": "linkIdInName on", "desc": "This setting changes the meaning of the bed name field to \"identifier description\"." }, { "key": "nextExonText", "category": "Item or Region Track Settings - less frequent", "roles": [ "leaf" ], - "types": "all", + "types": [ + "bed", + "bigBed", + "genePred", + "bigGenePred", + "psl", + "bigPsl", + "chain", + "bigChain", + "narrowPeak", + "bigNarrowPeak", + "broadPeak" + ], "level": "full", "fmt": "nextExonText <str>", "ex": "nextExonText \"Next Match\"\n prevExonText \"Previous Match\"", "desc": "For tracks that offer multiple block items such as gene models, the next/previous exon arrows are usually displayed by default in the Browser." }, { "key": "scoreLabel", "category": "Item or Region Track Settings - less frequent", "roles": [ "leaf" ], "types": [ "bed", "bigBed", "bigPsl", @@ -1746,68 +1868,136 @@ }, { "key": "linkDataUrl", "category": "bigChain - Pairwise Alignments", "roles": [ "leaf" ], "types": [ "bigChain" ], "level": "full", "fmt": "linkDataUrl <url/relativePath>", "ex": "", "desc": "The location of a remote data file containing the chain link data." }, + { + "key": "chainColor", + "category": "bigChain - Pairwise Alignments", + "roles": [ + "leaf" + ], + "types": [ + "chain", + "bigChain" + ], + "level": "full", + "fmt": "chainColor <scheme>", + "ex": "chainColor Black", + "desc": "By default chains are colored by the alignment chromosome of the query species." + }, + { + "key": "chainNormScoreAvailable", + "category": "bigChain - Pairwise Alignments", + "roles": [ + "leaf" + ], + "types": [ + "chain", + "bigChain", + "netAlign", + "bed" + ], + "level": "full", + "fmt": "chainNormScoreAvailable <yes/no>", + "ex": "chainNormScoreAvailable yes\n chainColor Normalized Score", + "desc": "A given chain or netAlign track may or may not have a populated normScore column." + }, { "key": "baseColorUseSequence", "category": "bigChain - Pairwise Alignments", "roles": [ "leaf" ], - "types": "all", + "types": [ + "bed", + "bigBed", + "genePred", + "psl", + "bigPsl", + "chain", + "bigChain", + "bam" + ], "level": "full", "fmt": "baseColorUseSequence <extFile {seqTable} /\n hgPcrResult / lfExtra / nameIsSequence / seq1Seq2 / ss / 2bit >", "ex": "", "desc": "Specifies where item sequence can be found (if any) so that item sequence, or differences from genomic sequence, can be drawn when viewing a sufficiently sma..." }, { "key": "baseColorDefault", "category": "bigChain - Pairwise Alignments", "roles": [ "leaf" ], - "types": "all", + "types": [ + "bed", + "bigBed", + "genePred", + "bigGenePred", + "psl", + "bigPsl", + "chain", + "bigChain", + "bam" + ], "level": "full", "fmt": "baseColorDefault\n <diffBases/diffCodons/itemBases/itemCodons/genomicCodons>", "ex": "", "desc": "Specifies the default drawing mode." }, { "key": "bigGenePred", "category": "bigGenePred - Gene Annotations", "roles": [ "leaf" ], "types": [ "bigGenePred" ], "level": null, "fmt": "type bigGenePred", "ex": "", "desc": "" }, + { + "key": "intronGap", + "category": "bigGenePred - Gene Annotations", + "roles": [ + "leaf" + ], + "types": [ + "genePred", + "bigGenePred", + "psl", + "bigPsl" + ], + "level": "full", + "fmt": "intronGap <#bases>", + "ex": "intronGap 12", + "desc": "In drawing gene models, it can be useful to see \"exon arrows\" when the transcript extends beyond the current window." + }, { "key": "bigInteract", "category": "bigInteract", "roles": [ "leaf" ], "types": [ "bigInteract" ], "level": null, "fmt": "type bigInteract", "ex": "", "desc": "" }, { @@ -1890,52 +2080,142 @@ "bigMaf" ], "level": null, "fmt": "type bigMaf", "ex": "", "desc": "" }, { "key": "speciesOrder", "category": "bigMaf - Multiple Alignments", "roles": [ "leaf" ], "types": [ "wigMaf", - "bed" + "bigMaf" ], "level": "full", "fmt": "speciesOrder <species1> [species2 ...]", "ex": "", "desc": "Use speciesOrder to declare the order of the stacked alignments." }, { "key": "speciesLabels", "category": "bigMaf - Multiple Alignments", "roles": [ "leaf" ], "types": [ "wigMaf", - "bed" + "bigMaf" ], "level": "new", "fmt": "speciesLabels <species1=newLabel1> [species2=newLabel2 ...]", "ex": "speciesLabels mm10=mouse_mm10 mm39=mouse_mm39", "desc": "Use speciesLabels to specify new labels that map to sequence names." }, + { + "key": "pairwiseHeight", + "category": "bigMaf - Multiple Alignments", + "roles": [ + "leaf" + ], + "types": [ + "wigMaf", + "bigMaf" + ], + "level": "full", + "fmt": "pairwiseHeight <#>", + "ex": "pairwiseHeight 10", + "desc": "A wigMaf display in the Browser image is a stacked set of pairwise alignments to the target genome." + }, + { + "key": "speciesGroups", + "category": "bigMaf - Multiple Alignments", + "roles": [ + "leaf" + ], + "types": [ + "wigMaf", + "bigMaf" + ], + "level": "full", + "fmt": "speciesGroups <sgroup1> [sgroup2 ...]", + "ex": "speciesOrder panTro1 canFam1 mm5 rn3 \\\n galGal2 fr1 danRer1\n speciesGroups Mammal Vertebrate\n sGroup_Mammal mm9 rn4\n sGroup_Vertebrate galGal2 fr1 danRer1", + "desc": "You can include a list of \"clades\" to group the species into." + }, + { + "key": "speciesDefaultOff", + "category": "bigMaf - Multiple Alignments", + "roles": [ + "leaf" + ], + "types": [ + "wigMaf", + "bigMaf" + ], + "level": "full", + "fmt": "speciesDefaultOff <species1> [species2 ...]", + "ex": "speciesDefaultOff galGal2 fr1 danRer1", + "desc": "To control which of the stacked pairwise alignments are displayed or hidden by default, use speciesDefaultOff to list the species alignments that will not be..." + }, + { + "key": "speciesCodonDefault", + "category": "bigMaf - Multiple Alignments", + "roles": [ + "leaf" + ], + "types": [ + "wigMaf", + "bigMaf" + ], + "level": "full", + "fmt": "speciesCodonDefault <species>", + "ex": "speciesCodonDefault hg19\n frames myCodonFrames", + "desc": "This setting, which is used with \"frames\", declares the default species for the codon reading frame." + }, + { + "key": "itemFirstCharCase", + "category": "bigMaf - Multiple Alignments", + "roles": [ + "leaf" + ], + "types": [ + "wigMaf", + "bigMaf" + ], + "level": "full", + "fmt": "itemFirstCharCase noChange", + "ex": "itemFirstCharCase noChange", + "desc": "This controls if species names in the multiple alignment should be capitalized in the pairwise display." + }, + { + "key": "irows", + "category": "bigMaf - Multiple Alignments", + "roles": [ + "leaf" + ], + "types": [ + "wigMaf", + "bigMaf" + ], + "level": "full", + "fmt": "irows off", + "ex": "irows off", + "desc": "By default, gaps in the non-reference species are filled with the placeholder character: Single Line ' - ': No bases in the aligned species." + }, { "key": "frames", "category": "bigMaf - Multiple Alignments", "roles": [ "leaf" ], "types": [ "wigMaf", "bigMaf" ], "level": "full", "fmt": "frames <table/url>", "ex": "frames myCodonFrames", "desc": "A wigMaf or bigMaf track can display gene codon translation." }, @@ -1964,130 +2244,157 @@ "bigNarrowPeak" ], "level": null, "fmt": "type bigNarrowPeak", "ex": "", "desc": "" }, { "key": "Filter", "category": "bigNarrowPeak - Peaks", "roles": [ "leaf" ], "types": [ "bed", + "bigBed", "narrowPeak", + "bigNarrowPeak", "broadPeak" ], "level": "full", "fmt": "<column>Filter <low>[:<high>]", "ex": "scoreFilter 100", "desc": "A number of numerical filters are available for bed tracks." }, { "key": "bigPsl", "category": "bigPsl - Pairwise Alignments", "roles": [ "leaf" ], "types": [ "bigPsl" ], "level": null, "fmt": "type bigPsl", "ex": "", "desc": "" }, { "key": "baseColorUseCds", "category": "bigPsl - Pairwise Alignments", "roles": [ "leaf" ], "types": [ "bed", + "bigBed", "genePred", + "bigGenePred", "psl", "bigPsl" ], "level": "full", "fmt": "baseColorUseCds <given>", "ex": "baseColorUseCds given", "desc": "Specifies where coding sequence (CDS) coordinates can be found (if any) so that codons can be drawn when viewing a sufficiently small region." }, { - "key": "showDiffBasesAllScales", + "key": "baseColorTickColor", "category": "bigPsl - Pairwise Alignments", "roles": [ "leaf" ], - "types": "all", + "types": [ + "bed", + "bigBed", + "psl", + "bigPsl" + ], "level": "full", - "fmt": "showDiffBasesAllScales on", - "ex": "", - "desc": "Show base differences for all zoom levels." + "fmt": "baseColorTickColor <lighterShade/contrastingColor>", + "ex": "colorByStrand 0,0,200 200,0,0\n baseColorDefault diffBases\n baseColorTickColor contrastingColor", + "desc": "Sets the color of the tick marks that mark where item bases differ from the genome." }, { - "key": "pslSequence", + "key": "showDiffBasesAllScales", "category": "bigPsl - Pairwise Alignments", "roles": [ "leaf" ], "types": [ - "psl" + "bed", + "bigBed", + "genePred", + "psl", + "bigPsl", + "chain", + "bigChain", + "bam" ], - "level": "new", - "fmt": "pslSequence <no/all/different>", - "ex": "pslSequence different", - "desc": "This setting specifies some display configuration options for psl tracks that also have sequence loaded." + "level": "full", + "fmt": "showDiffBasesAllScales on", + "ex": "", + "desc": "Show base differences for all zoom levels." }, { "key": "showCdsAllScales", "category": "bigPsl - Pairwise Alignments", "roles": [ "leaf" ], "types": [ - "psl" + "psl", + "bigPsl" ], "level": "new", "fmt": "showCdsAllScales on", "ex": "", "desc": "Show CDS for PSL tracks at all zoom levels." }, { "key": "showCdsMaxZoom", "category": "bigPsl - Pairwise Alignments", "roles": [ "leaf" ], "types": [ - "psl" + "psl", + "bigPsl" ], "level": "new", "fmt": "showCdsMaxZoom <basesPerPixel>", "ex": "baseColorDefault genomicCodons\n baseColorUseCds given\n showDiffBasesMaxZoom 10000.0\n showCdsMaxZoom 10000.0\n baseColorUseCds table hgFixed.transMapGeneUcscGenes\n baseColorUseSequence lfExtra\n baseColorDefault diffCodons\n baseColorTickColor lighterShade\n showDiffBasesAllScales .\n showCdsAllScales .", "desc": "Use this setting (a float) to specify the maximum zoom-out allowed for displaying the CDS for psl tracks." }, { "key": "showDiffBasesMaxZoom", "category": "bigPsl - Pairwise Alignments", "roles": [ "leaf" ], - "types": "all", + "types": [ + "bed", + "bigBed", + "genePred", + "psl", + "bigPsl", + "chain", + "bigChain", + "bam" + ], "level": "new", "fmt": "showDiffBasesMaxZoom <basesPerPixel>", "ex": "", "desc": "Show annotations highlighting base or codon differences only if current zoom level does not exceed basesPerPixel (a float)." }, { "key": "bigWig", "category": "bigWig - Signal Graphing Track Settings", "roles": [ "leaf" ], "types": [ "bigWig" ], "level": null, @@ -2100,30 +2407,46 @@ "category": "bigWig - Signal Graphing Track Settings", "roles": [ "leaf" ], "types": [ "wig", "bigWig", "bedGraph", "hic" ], "level": "base", "fmt": "autoScale <off/on/group>", "ex": "autoScale on", "desc": "This setting is available for both the graph types of tracks (wig, bigWig, bedGraph) and the Hi-C heatmap tracks (hic)." }, + { + "key": "mouseOverFunction", + "category": "bigWig - Signal Graphing Track Settings", + "roles": [ + "leaf" + ], + "types": [ + "wig", + "bigWig", + "bedGraph" + ], + "level": "full", + "fmt": "mouseOverFunction <noAverage>", + "ex": "mouseOverFunction noAverage", + "desc": "Limit mouse over value display to only display the fundamental values without any averaging of multiple data points." + }, { "key": "maxHeightPixels", "category": "bigWig - Signal Graphing Track Settings", "roles": [ "leaf" ], "types": [ "wig", "bigWig", "bedGraph", "bigInteract" ], "level": "base", "fmt": "maxHeightPixels <max:default:min>", "ex": "maxHeightPixels 100:16:8", @@ -2172,33 +2495,31 @@ "bigWig", "bedGraph" ], "level": "full", "fmt": "graphTypeDefault points", "ex": "graphTypeDefault points", "desc": "The signal can be graphed as either \" points \" displayed at the signal value, or the default space-filling \" bar \"." }, { "key": "maxWindowToQuery", "category": "bigWig - Signal Graphing Track Settings", "roles": [ "leaf" ], "types": [ - "bed", - "bigWig", - "bedLogR" + "bigWig" ], "level": "full", "fmt": "maxWindowToQuery <integer>", "ex": "", "desc": "For bigWigs only When signal data is clicked in the Browser image, the details of the signal in the current viewing window are displayed." }, { "key": "negateValues", "category": "bigWig - Signal Graphing Track Settings", "roles": [ "leaf" ], "types": [ "wig", "bigWig", @@ -2320,42 +2641,42 @@ { "key": "bigLolly", "category": "bigLolly - Lollipop charts", "roles": [ "leaf" ], "types": [ "bigLolly" ], "level": null, "fmt": "type bigLolly", "ex": "", "desc": "" }, { - "key": "noStems", + "key": "lollyNoStems", "category": "bigLolly - Lollipop charts", "roles": [ "leaf" ], "types": [ "bigLolly" ], "level": "full", - "fmt": "noStems <on/off>", - "ex": "", - "desc": "" + "fmt": "lollyNoStems <on/off>", + "ex": "lollyNoStems on", + "desc": "Draw the lollipop heads without the stems that normally connect them to the baseline." }, { "key": "lollySizeField", "category": "bigLolly - Lollipop charts", "roles": [ "leaf" ], "types": [ "bigLolly" ], "level": "full", "fmt": "lollySizeField <integer>", "ex": "", "desc": "" }, @@ -2592,144 +2913,153 @@ "types": [ "vcfTabix" ], "level": null, "fmt": "type vcfTabix", "ex": "", "desc": "If the bigDataUrl setting is included, the data at the location specified by that URL will be displayed." }, { "key": "hapClusterEnabled", "category": "vcfTabix - Variant Call Format Track Settings", "roles": [ "leaf" ], "types": [ - "vcf" + "vcf", + "vcfTabix" ], "level": "full", "fmt": "hapClusterEnabled <true|false>", "ex": "", "desc": "If the VCF file includes genotype columns for at least two individuals, then a haplotype sorting display is enabled by default." }, { "key": "hapClusterMethod", "category": "vcfTabix - Variant Call Format Track Settings", "roles": [ "leaf" ], "types": [ - "vcf" + "vcf", + "vcfTabix" ], "level": "full", "fmt": "hapClusterMethod <centerWeighted|fileOrder|treeFile url >", "ex": "", "desc": "Assuming hapClusterEnabled is true , this specifies how genotypes are ordered for display: centerWeighted : For diploid organisms, this separates the two hap..." }, { "key": "hapClusterColorBy", "category": "vcfTabix - Variant Call Format Track Settings", "roles": [ "leaf" ], "types": [ - "vcf" + "vcf", + "vcfTabix" ], "level": "full", "fmt": "hapClusterColorBy <altOnly|function|refAlt|base>", "ex": "", "desc": "Assuming hapClusterEnabled is true , this specifies one of three ways that reference and alternate alleles are colored: altOnly : reference allele is white (..." }, { "key": "geneTrack", "category": "vcfTabix - Variant Call Format Track Settings", "roles": [ "leaf" ], "types": [ "vcf", + "vcfTabix", "vcfPhasedTrio" ], "level": "full", "fmt": "geneTrack < track >", "ex": "", "desc": "This is for use with hapClusterColorBy function ; it specifies the gene track to use when determining the functional effect of each variant." }, { "key": "hapClusterTreeAngle", "category": "vcfTabix - Variant Call Format Track Settings", "roles": [ "leaf" ], "types": [ - "vcf" + "vcf", + "vcfTabix" ], "level": "full", "fmt": "hapClusterTreeAngle <triangle|rectangle>", "ex": "", "desc": "Assuming hapClusterEnabled is true , this controls the shape of leaf clusters on the right of the tree (i.e." }, { "key": "hapClusterHeight", "category": "vcfTabix - Variant Call Format Track Settings", "roles": [ "leaf" ], "types": [ - "vcf" + "vcf", + "vcfTabix" ], "level": "full", "fmt": "hapClusterHeight < N >", "ex": "", "desc": "Assuming hapClusterEnabled is true , this specifies the height in pixels of the haplotype sorting display." }, { "key": "applyMinQual", "category": "vcfTabix - Variant Call Format Track Settings", "roles": [ "leaf" ], "types": [ - "vcf" + "vcf", + "vcfTabix" ], "level": "full", "fmt": "applyMinQual <true|false>", "ex": "", "desc": "If true , then variants whose QUAL column contains a value less than the minQual setting will not be displayed." }, { "key": "minQual", "category": "vcfTabix - Variant Call Format Track Settings", "roles": [ "leaf" ], "types": [ - "vcf" + "vcf", + "vcfTabix" ], "level": "full", "fmt": "minQual < Q >", "ex": "", "desc": "Assuming applyMinQual is true , this is the minimum QUAL value required for a variant to be displayed." }, { "key": "minFreq", "category": "vcfTabix - Variant Call Format Track Settings", "roles": [ "leaf" ], "types": [ - "vcf" + "vcf", + "vcfTabix" ], "level": "full", "fmt": "minFreq < F >", "ex": "", "desc": "The minimum minor allele frequency required for a variant to be displayed." }, { "key": "vcfDoFilter", "category": "vcfTabix - Variant Call Format Track Settings", "roles": [ "leaf" ], "types": [ "vcf", "vcfTabix", @@ -3599,18 +3929,66 @@ "fmt": "blat <url> <port>", "ex": "blat yourServer.yourInstitution.edu 17777", "desc": "Indicates the server and port to be used for the BLAT tool." }, { "key": "isPcr", "category": "genomes file settings", "roles": [ "genome" ], "types": "all", "level": "base", "fmt": "isPcr <url> <port>", "ex": "isPcr yourServer.yourInstitution.edu 17779", "desc": "Indicates the server and port to be used for the In-Silico PCR tool." + }, + { + "key": "metadata", + "category": "Miscellaneous Deprecated Settings", + "roles": [ + "super", + "composite", + "view", + "leaf" + ], + "types": "all", + "level": "deprecated", + "fmt": "metadata <name=value> [<name=value> ...]", + "ex": "metadata cellType=K562 antibody=CTCF lab=\"Broad Institute\"", + "desc": "Deprecated." + }, + { + "key": "noInherit", + "category": "Miscellaneous Deprecated Settings", + "roles": [ + "super", + "composite", + "view", + "leaf" + ], + "types": "all", + "level": "deprecated", + "fmt": "noInherit on", + "ex": "noInherit on", + "desc": "Deprecated." + }, + { + "key": "useScore", + "category": "Miscellaneous Deprecated Settings", + "roles": [ + "leaf" + ], + "types": [ + "bed", + "bigBed", + "bigGenePred", + "psl", + "bigPsl" + ], + "level": "deprecated", + "fmt": "useScore 1", + "ex": "useScore 1", + "desc": "Deprecated." } ] }