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 ", "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 ", + "ex": "canPack on", + "desc": "Deprecated." + }, + { + "key": "configureByPopup", + "category": "Common Settings - less frequent", + "roles": [ + "super", + "composite", + "view", + "leaf" + ], + "types": "all", + "level": "full", + "fmt": "configureByPopup ", + "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 ", + "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 ", "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 ", "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 ", + "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 ", "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.. ", "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 ", "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 ", "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 ", "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 ", "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 ", "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. ", "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 \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.