92af4b0363b70062f69a5730648b20bd8e52a317
braney
  Mon Aug 31 13:34:03 2026 -0700
Drop bed from searchIndex and searchTrix, and deprecate pslSequence instead of deleting it

This is the reverse of the earlier passes. Instead of asking what a type list
is missing, it asks which declared type nothing supports.

searchIndex and searchTrix both declared bed. Neither works on a SQL bed table.
The trackDb read for searchIndex is at bigBedFind.c:270 and it then needs a bbi
file, from bigDataUrl or from the table's fileName, which a plain bed table does
not have. searchTrix has two readers: bigBedFind.c:312 reads it from trackDb on
the bigBed path, while hgFind.c:2393 reads it from hgFindSpec, which is how a
SQL track gets trix search. Native usage agrees, with zero bed tracks for
either setting. searchIndex also gains bigPsl, bigGenePred and bigBarChart, and
searchTrix gains bigGenePred, all of which have real usage.

pslSequence was deleted outright in 0e4e0c0af65. It is obsolete, but deleting
the row was the wrong way to say so. 118 psl and 6 bigPsl native tracks set it,
and so do three public-hub bigPsl tracks. hubCheck takes its vocabulary from
this page, so with no row those hub authors would be told the setting "is not
recognized. Check for typos", with a spelling suggestion, which is the wrong
advice for a setting they took from our own documentation. The row is back at
level-deprecated, which makes hubCheck say "is deprecated" instead, the way it
already does for canPack, useScore, metadata and noInherit. Verified by running
hubCheck against both spellings of the page. The library blurb is restored too,
rewritten to say the setting is obsolete and to map its three values onto
baseColorDefault, which replaced it in 8d32ba75938 in 2006.

chainMinScore is deliberately left alone. It was proposed for deletion on the
grounds that nothing reads it. Nothing does, but our own automation writes it:
asmHubChainNetTrackDb.pl:101 and chainNetCompositeTrackDb.pl:186 emit
"chainMinScore 5000" into the chainNet composite stanza, and findScores.pl
converts -minScore into it. 40,920 native bed stanzas and 16 chain tracks carry
it today. It records the minScore the chains were built with. Removing its
documentation would leave those stanzas with an undocumented setting.

changes.html gains a row for the type lists corrected across all three of these
commits, and its existing pslSequence row is rewritten: it said the setting was
removed, which is no longer what happened. Since the earlier commit has not
shipped to the RR, no reader ever saw the "Removed" wording.

trackDbSettings.yaml and .json are regenerated, and now hold 263 settings.

refs #37908

diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.json src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.json
index cc5c25ea2c7..4cd7823d864 100644
--- src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.json
+++ src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.json
@@ -1,4003 +1,4020 @@
 {
  "version": "v3",
  "categories": [
   "Common Settings",
   "Common Settings - less frequent",
   "bam - Compressed Alignment Track Settings",
   "bigBarChart",
   "bigBed - Item or Region Track Settings",
   "Item or Region Track Settings - less frequent",
   "bigChain - Pairwise Alignments",
   "bigGenePred - Gene Annotations",
   "bigInteract",
   "bigMaf - Multiple Alignments",
   "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",
   "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 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",
    "desc": "Specifies the track's \"short label\", which is used in a number of places in the Browser to identify the track."
   },
   {
    "key": "longLabel",
    "category": "Common Settings",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": "required",
    "fmt": "longLabel",
    "ex": "longLabel Human mRNAs from GenBank",
    "desc": "Specifies the track's \"long label\", which is also used in numerous places in the Browser to identify a track."
   },
   {
    "key": "bigDataUrl",
    "category": "Common Settings",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": [
     "bigBarChart",
     "bigBed",
     "bigChain",
     "bigInteract",
     "bigLolly",
     "bigMaf",
     "bigPsl",
     "bigWig",
     "bam",
     "hic",
     "vcfTabix",
     "vcfPhasedTrio"
    ],
    "level": "required",
    "fmt": "bigDataUrl <url/relativePath>",
    "ex": "bigDataUrl http://vizhub.wustl.edu/VizHub/hg19/biBrainH3K4me1.bb",
    "desc": "The location of a remote data file containing the bulk of the data for the track."
   },
   {
    "key": "html",
    "category": "Common Settings",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": "base",
    "fmt": "html",
    "ex": "html docs/myFirstTrack.html",
    "desc": "Use the html path/to/explain.html to specify the file that contains the complete description of a track in HTML format."
   },
   {
    "key": "visibility",
    "category": "Common Settings",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": "required",
    "fmt": "visibility",
    "ex": "visibility dense",
    "desc": "Visibility (i.e."
   },
   {
    "key": "meta",
    "category": "Common Settings",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": "full",
    "fmt": "meta",
    "ex": "",
    "desc": "Meta specifies the metadata tag for this track."
   },
   {
    "key": "color",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": "base",
    "fmt": "color <red,green,blue>",
    "ex": "color 255,0,0",
    "desc": "Many track types allow the color of the data displayed in the image to be specified with this setting."
   },
   {
    "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 ."
   },
   {
    "key": "boxedCfg",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": "full",
    "fmt": "boxedCfg <on/off>",
    "ex": "boxedCfg on",
    "desc": "Configuration controls can be placed inside a box on the configuration page."
   },
   {
    "key": "chromosomes",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": "full",
    "fmt": "chromosomes <chr1,chr2,...>",
    "ex": "chromosomes chr1,chr7,chr18,chr19,chr22,chrX,chrM",
    "desc": "Some datasets do not contain data for all chromosomes of a genome."
   },
   {
    "key": "darkerLabels",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": "full",
    "fmt": "darkerLabels on",
    "ex": "",
    "desc": "If this setting is \"on\", the color of the left labels on the track display will have a somewhat darker color than the track display itself."
   },
   {
    "key": "dataVersion",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": "full",
    "fmt": "dataVersion <str>",
    "ex": "dataVersion May 2011 <em>beta</em>",
    "desc": "Many tracks undergo multiple revisions over time."
   },
   {
    "key": "directUrl_for_hubs",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": "full",
    "fmt": "directUrl <url>",
    "ex": "directUrl http://mygenes.org/cgi-bin/geneView/%s",
    "desc": "By default, items shown in the Browser image can be linked to a details page giving information about that item."
   },
   {
    "key": "downloadUrl",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": "full",
    "fmt": "downloadUrl <label> <URL>",
    "ex": "downloadUrl GFF https://mywebsite.com/ucscTrack.gff.gz",
    "desc": "While description HTML pages can contain download instructions, having external file download links directly specified in trackDb makes it possible show thes..."
   },
   {
    "key": "iframeUrl",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": "full",
    "fmt": "iframeUrl <url>",
    "ex": "iframeUrl https://www.ncbi.nlm.nih.gov/nuccore/$$\n    iframeOptions height='600' width='1024'",
    "desc": "This setting allows integrating an external html page into the default details page, as an iframe."
   },
   {
    "key": "iframeOptions",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": "full",
    "fmt": "iframeOptions <string>",
    "ex": "iframeOptions width='800' height='800' scrolling='yes'",
    "desc": "When iframeUrl is used, this statement specifies a string that is inserted literally into the HTML <iframe> tag."
   },
   {
    "key": "mouseOver",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": [
     "bigBed",
     "bigPsl",
     "bigChain",
     "bigMaf",
     "bigMethyl",
     "bigNarrowPeak",
     "bigGenePred",
     "bigLolly"
    ],
    "level": "full",
    "fmt": "mouseOver <pattern>",
    "ex": "mouseOver variant $name/$chrom:${chromStart} value $score",
    "desc": "For bigBed files with more than 8 fields (not counting any extra bigBed fields), this adds mouse over text from a pattern based on the values of fields in th..."
   },
   {
    "key": "mouseOverField",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": [
     "bigBed",
     "bigPsl",
     "bigChain",
     "bigMaf",
     "bigMethyl",
     "bigNarrowPeak",
     "bigGenePred",
     "bigLolly"
    ],
    "level": "full",
    "fmt": "mouseOverField <fieldName1>",
    "ex": "mouseOverField comment",
    "desc": "For bigBed files with more than 8 fields (not counting any extra bigBed fields), this adds mouse over text that are different from the \"name\" field of a bigB..."
   },
   {
    "key": "multiRegionsBedUrl",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": null,
    "fmt": "multiRegionsBedUrl <url/relativePath>",
    "ex": "multiRegionsBedUrl covidMuts.regions.bed",
    "desc": "This setting causes a link to appear on the track configuration and items details pages to launch a multi-region custom regions view , where the regions are..."
   },
   {
    "key": "onlyVisibility",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": "new",
    "fmt": "onlyVisibility <dense|squish|pack|full>",
    "ex": "track coverage\n   onlyVisibility dense",
    "desc": "Restricts a track to a single display mode."
   },
   {
    "key": "otherDb",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": "full",
    "fmt": "otherDb <otherDb>",
    "ex": "otherDb mm10",
    "desc": "Track types that show pairwise alignments often need to declare the other species/assembly included in the alignment."
   },
   {
    "key": "otherTwoBitUrl",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": [
     "chain",
     "bigChain",
     "psl",
     "bigPsl"
    ],
    "level": "new",
    "fmt": "otherTwoBitUrl <url/relativePath>",
    "ex": "otherTwoBitUrl https://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit",
    "desc": "For pairwise alignment tracks this can specify where to find the query sequence This setting can be used in psl, bigPsl, chain, and bigChain tracks."
   },
   {
    "key": "pennantIcon",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": "full",
    "fmt": "pennantIcon <iconFile>/<text color> [html [tip]] \n[; <iconFile>/<text color> [html [tip]]]",
    "ex": "pennantIcon 18.jpg ../goldenPath/help/liftOver.html \"lifted from hg18\"",
    "desc": "Certain tracks can be visually flagged in the Browser menu by use of an icon or text label and a link to a description of the flags meaning."
   },
   {
    "key": "tableBrowser",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": null,
    "fmt": "tableBrowser <off/on/noGenome/tbNoGenome> [table1 ...]",
    "ex": "tableBrowser off decipherRaw knownToDecipher",
    "desc": "The Table Browser (and REST API ) typically allow querying and downloading of some or all of the raw data for a track."
   },
   {
    "key": "url_for_hubs",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": "all",
    "level": "full",
    "fmt": "url <url>",
    "ex": "url https://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&db=$n&term=$$&extra=$<field2>\n    urlLabel NCBI Details:",
    "desc": "Many tracks allow an external link when an individual track data item is examined."
   },
   {
    "key": "urls",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": [
     "bigBed",
     "bigBarChart"
    ],
    "level": "full",
    "fmt": "urls <fieldName1>=\"<url1>\" <fieldName2>=\"<url2>\" ...",
    "ex": "urls pmid=\"https://www.ncbi.nlm.nih.gov/pubmed/$$\" spId=\"http://www.uniprot.org/uniprot/$$\"",
    "desc": "This is similar to the url tag, but allows urls on fields that are not the \"name\" field."
   },
   {
    "key": "skipEmptyFields",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": [
     "bigBed",
     "bigPsl",
     "bigGenePred",
     "bigMethyl",
     "bigNarrowPeak",
     "bigMaf",
     "bigChain"
    ],
    "level": "full",
    "fmt": "skipEmptyFields on",
    "ex": "",
    "desc": "If this setting is \"on\", the item details page will not show fields that have empty values."
   },
   {
    "key": "skipFields",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": [
     "bigBed",
     "bigPsl",
     "bigGenePred",
     "bigMethyl",
     "bigNarrowPeak",
     "bigMaf",
     "bigChain"
    ],
    "level": "full",
    "fmt": "skipFields <fieldName1>,<fieldName2> ...",
    "ex": "skipFields mouseOver,labelField,hiddenField",
    "desc": "This setting can be used to suppress extra fields on the item details page."
   },
   {
    "key": "sepFields",
    "category": "Common Settings - less frequent",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": [
     "bigBed",
     "bigPsl",
     "bigGenePred",
     "bigMethyl",
     "bigNarrowPeak",
     "bigMaf",
     "bigChain"
    ],
    "level": "full",
    "fmt": "sepFields fieldName1,fieldName2 ...",
    "ex": "sepFields pmid,spId",
    "desc": "This setting changes the item details page and splits the table used for showing extra fields before any of the specified fields."
   },
   {
    "key": "bam",
    "category": "bam - Compressed Alignment Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bam"
    ],
    "level": null,
    "fmt": "type bam",
    "ex": "",
    "desc": "Declares configuration settings for a track of type bam."
   },
   {
    "key": "refUrl",
    "category": "bam - Compressed Alignment Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bam"
    ],
    "level": "full",
    "fmt": "refUrl <url>/%s",
    "ex": "",
    "desc": ""
   },
   {
    "key": "bigDataIndex",
    "category": "bam - Compressed Alignment Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bam",
     "vcfTabix",
     "vcfPhasedTrio"
    ],
    "level": "full",
    "fmt": "bigDataIndex <url/relativePath>",
    "ex": "bigDataIndex http://vizhub.wustl.edu/VizHub/hg19/biBrainH3K4me1.bam.bai",
    "desc": "The location of a remote data file containing the index."
   },
   {
    "key": "bamColorMode",
    "category": "bam - Compressed Alignment Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bam"
    ],
    "level": "full",
    "fmt": "bamColorMode <strand/gray/tag/off>",
    "ex": "",
    "desc": "There are numerous ways to color bam tracks to highlight certain aspects of the data."
   },
   {
    "key": "bamGrayMode",
    "category": "bam - Compressed Alignment Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bam"
    ],
    "level": "full",
    "fmt": "bamGrayMode <aliQual/baseQual/unpaired>",
    "ex": "",
    "desc": "When bamColorMode is set to \"gray\", you can highlight one of the following: Refer to the SAM format details for a discussion of these values."
   },
   {
    "key": "bamColorTag",
    "category": "bam - Compressed Alignment Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bam"
    ],
    "level": "full",
    "fmt": "bamColorTag <XX>",
    "ex": "",
    "desc": "You can also use RGB data associated with individual tags within the bam file itself."
   },
   {
    "key": "noColorTag",
    "category": "bam - Compressed Alignment Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bam"
    ],
    "level": "full",
    "fmt": "noColorTag .",
    "ex": "bamColorMode strand\n    noColorTag",
    "desc": "The bam coloring options are all user-configurable within the browser."
   },
   {
    "key": "bamSkipPrintQualScore",
    "category": "bam - Compressed Alignment Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bam"
    ],
    "level": "full",
    "fmt": "bamSkipPrintQualScore .",
    "ex": "bamSkipPrintQualScore .",
    "desc": "Any bam tag can be displayed on the details page by clicking on it in the Browser image."
   },
   {
    "key": "indelDoubleInsert",
    "category": "bam - Compressed Alignment Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bam",
     "psl",
     "bigPsl"
    ],
    "level": "full",
    "fmt": "indelDoubleInsert <off/on>",
    "ex": "baseColorUseSequence genbank\n    indelDoubleInsert on\n    indelQueryInsert on\n    indelPolyA on",
    "desc": "Insertion and deletion differences between tag sequences and the reference genome can be highlighted with the use of these settings."
   },
   {
    "key": "minAliQual",
    "category": "bam - Compressed Alignment Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bam"
    ],
    "level": "full",
    "fmt": "minAliQual <#>",
    "ex": "minAliQual 20",
    "desc": "When the Browser image is zoomed in to the level where individual tags are visible, the tags in a bam file can be filtered to show only those with a minimum..."
   },
   {
    "key": "pairEndsByName",
    "category": "bam - Compressed Alignment Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bam"
    ],
    "level": "full",
    "fmt": "pairEndsByName .",
    "ex": "",
    "desc": "Some high-throughput sequencing technologies result in \"paired end\" tags, which are two individual bam records joined by their name."
   },
   {
    "key": "pairSearchRange",
    "category": "bam - Compressed Alignment Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bam"
    ],
    "level": "full",
    "fmt": "pairSearchRange <#>",
    "ex": "pairedEndsByName .\n    pairSearchRange 5000",
    "desc": "Searching to join pairs of tags by name will be limited to a maximum distance (default: 20,000 bases)."
   },
   {
    "key": "showNames",
    "category": "bam - Compressed Alignment Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bam"
    ],
    "level": "full",
    "fmt": "showNames <on/off>",
    "ex": "showNames off",
    "desc": "When the Browser image is zoomed in to the level where individual tags are viewable, the query name for each tag is shown by default."
   },
   {
    "key": "doWiggle",
    "category": "bam - Compressed Alignment Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bam"
    ],
    "level": "full",
    "fmt": "doWiggle on",
    "ex": "doWiggle on",
    "desc": "The doWiggle setting enables the BAM data to be displayed as a bar graph where the height is proportional to the number of reads mapped to each genomic posit..."
   },
   {
    "key": "bigBarChart",
    "category": "bigBarChart",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBarChart"
    ],
    "level": null,
    "fmt": "type bigBarChart",
    "ex": "",
    "desc": ""
   },
   {
    "key": "barChartBars",
    "category": "bigBarChart",
    "roles": [
     "leaf"
    ],
    "types": [
     "barChart",
     "bigBarChart"
    ],
    "level": "full",
    "fmt": "barChartBars <label1 label2...>",
    "ex": "",
    "desc": "This setting is a list of labels for the categorical variables (bars)."
   },
   {
    "key": "barChartColors",
    "category": "bigBarChart",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBarChart"
    ],
    "level": "full",
    "fmt": "barChartColors <color1 color2...>",
    "ex": "",
    "desc": "This setting is a list of colors, one for each category (bar)."
   },
   {
    "key": "barChartLabel",
    "category": "bigBarChart",
    "roles": [
     "leaf"
    ],
    "types": [
     "barChart",
     "bigBarChart"
    ],
    "level": "full",
    "fmt": "barChartLabel <label>",
    "ex": "",
    "desc": "This setting provides a label for the category selection list."
   },
   {
    "key": "barChartMaxSize",
    "category": "bigBarChart",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBarChart"
    ],
    "level": "full",
    "fmt": "barChartMaxSize <small/medium/large>",
    "ex": "",
    "desc": "BarChart track display selects one of three sizes (small, medium, or large) to display barCharts, based on size of the genomic region in the current window."
   },
   {
    "key": "barChartSizeWindows",
    "category": "bigBarChart",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBarChart"
    ],
    "level": "full",
    "fmt": "barChartSizeWindows <largeMax> <smallMin>",
    "ex": "barChartSizeWindows 500 8000",
    "desc": "This setting provides a way to choose the basepair thresholds which determine the barChart sizes (small, medium, or large charts)."
   },
   {
    "key": "barChartStretchToItem",
    "category": "bigBarChart",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBarChart"
    ],
    "level": "new",
    "fmt": "barChartStretchToItem on",
    "ex": "",
    "desc": "This setting extends the barCharts to cover the entire horizontal space available in the graph."
   },
   {
    "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."
   },
   {
    "key": "singleCellColumnNames",
    "category": "bigBarChart",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBarChart"
    ],
    "level": "new",
    "fmt": "singleCellColumnNames off",
    "ex": "",
    "desc": "This setting changes cell count to count in the track details page for the column named count in the facets file specified by barChartStatsUrl ."
   },
   {
    "key": "barChartMerge",
    "category": "bigBarChart",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBarChart"
    ],
    "level": "new",
    "fmt": "barChartMerge on",
    "ex": "",
    "desc": "This setting enables the merge button inside of the faceted selections."
   },
   {
    "key": "barChartMetric",
    "category": "bigBarChart",
    "roles": [
     "leaf"
    ],
    "types": [
     "barChart",
     "bigBarChart"
    ],
    "level": "full",
    "fmt": "barChartMetric <metric>",
    "ex": "",
    "desc": "This setting provides a label for details page information about the barChart values presented."
   },
   {
    "key": "barChartUnit",
    "category": "bigBarChart",
    "roles": [
     "leaf"
    ],
    "types": [
     "barChart",
     "bigBarChart"
    ],
    "level": "full",
    "fmt": "barChartUnit <unit>",
    "ex": "",
    "desc": "The unit label is attached to values in the display, charts and plots of the track."
   },
   {
    "key": "barChartCategoryUrl",
    "category": "bigBarChart",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBarChart"
    ],
    "level": "full",
    "fmt": "barChartCategoryUrl <url>",
    "ex": "",
    "desc": "Specifies a tab-separated file that provides labels and optionally colors for the categories (bars)."
   },
   {
    "key": "barChartSampleUrl",
    "category": "bigBarChart",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBarChart"
    ],
    "level": "full",
    "fmt": "barChartSampleUrl <url>",
    "ex": "",
    "desc": "Specifies a tab-separated file that provides categories for samples in the barChartMatrixUrl file."
   },
   {
    "key": "barChartBarMinPadding",
    "category": "bigBarChart",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBarChart"
    ],
    "level": "new",
    "fmt": "barChartBarMinPadding <num>",
    "ex": "",
    "desc": "Sets the minimum pixel width between bars to <num> pixels."
   },
   {
    "key": "barChartBarMinWidth",
    "category": "bigBarChart",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBarChart"
    ],
    "level": "new",
    "fmt": "barChartBarMinWidth <num>",
    "ex": "",
    "desc": "Sets the minimum pixel width of the bars in the chart to <num> pixels."
   },
   {
    "key": "maxLimit",
    "category": "bigBarChart",
    "roles": [
     "leaf"
    ],
    "types": [
     "bedGraph",
     "bigBarChart"
    ],
    "level": "full",
    "fmt": "maxLimit <#>",
    "ex": "maxLimit 5000",
    "desc": "The upper limit of the data range in a track is specified with this setting."
   },
   {
    "key": "bigBed",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBed"
    ],
    "level": null,
    "fmt": "type bigBed <3-12> [+/.]",
    "ex": "type bigBed 9 +",
    "desc": "Type bigBed declares the number of standard \"bed\" fields in the data."
   },
   {
    "key": "itemRgb",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bed",
     "bigBed",
     "bedDetail",
     "bedGraph",
     "bedLogR"
    ],
    "level": "base",
    "fmt": "itemRgb on",
    "ex": "itemRgb on",
    "desc": "In bed formats supporting at least 9 standard bed fields, this setting can be used to activate item coloring using the value in the ninth field, itemRgb ."
   },
   {
    "key": "colorFields",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBed",
     "bigGenePred"
    ],
    "level": "new",
    "fmt": "colorFields default=\"<label>\" <fieldName1>=\"<label1>\" <fieldName2>=\"<label2>\" ...",
    "ex": "colorFields default=\"Kozak strength\" colorByEvidence=\"Evidence type\" colorByHlaClass=\"HLA class\"",
    "desc": "Enables a Color by: dropdown in the track controls that lets the user switch among multiple pre-computed color schemes without leaving the track display."
   },
   {
    "key": "colorByStrand",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bed",
     "bigBed"
    ],
    "level": "base",
    "fmt": "colorByStrand <red,green,blue> <red,green,blue>",
    "ex": "colorByStrand 255,0,0 0,0,255",
    "desc": "To color items differently by the strand they align to, use the colorByStrand setting."
   },
   {
    "key": "denseCoverage",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBed"
    ],
    "level": "full",
    "fmt": "denseCoverage <maxVal>",
    "ex": "denseCoverage 100",
    "desc": "bigBed specific Type bigBed tracks in dense mode do a density plot based on maximum coverage seen at each pixel."
   },
   {
    "key": "labelOnFeature",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bed",
     "bigBed"
    ],
    "level": "full",
    "fmt": "labelOnFeature <on/off>",
    "ex": "labelOnFeature on",
    "desc": "Usually, labels (the BED name field) are drawn next to the features."
   },
   {
    "key": "extraDetailsTable",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBed"
    ],
    "level": "deprecated",
    "fmt": "extraDetailsTable <url/relativePath>",
    "ex": "",
    "desc": "This setting was renamed June 2022."
   },
   {
    "key": "extraTableFields",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBed"
    ],
    "level": "deprecated",
    "fmt": "extraTableFields <fieldName1|table title,fieldName2|table title,...>",
    "ex": "extraTableFields _jsonField1|JSON Title Example,tableField2|NON-JSON Title Example",
    "desc": "This setting was renamed June 2022."
   },
   {
    "key": "detailsStaticTable",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBed"
    ],
    "level": "new",
    "fmt": "detailsStaticTable <url/relativePath>",
    "ex": "",
    "desc": "Provides a template to a tab separated text file where $<fieldName> strings will be substituted for data in the bigBed and displayed as an HTML table."
   },
   {
    "key": "detailsDynamicTable",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBed"
    ],
    "level": "new",
    "fmt": "detailsDynamicTable <fieldName1|table title,fieldName2|table title,...>",
    "ex": "detailsDynamicTable _jsonField1|JSON Title Example,tableField2|NON-JSON Title Example",
    "desc": "Tells the system that the data in <fieldName1,...> contains an encoded table that should be turned into a standard HTML table on the details page for that item."
   },
   {
    "key": "detailsScript",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "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": [
     "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",
     "bigBed",
     "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"
    ],
    "level": "full",
    "fmt": "scoreFilter <low>[:<high>]",
    "ex": "scoreFilter 300\n    scoreFilterLimits 200:1000",
    "desc": "Type bigBed tracks can be filtered on the standard bed field score ."
   },
   {
    "key": "maxItems",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bed",
     "bigBed",
     "broadPeak",
     "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",
     "bigGenePred",
     "psl",
     "bigPsl",
     "chain",
     "bigChain",
     "narrowPeak",
     "bigNarrowPeak",
     "broadPeak",
     "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": "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",
     "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": [
     "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",
    "fmt": "style <heatmap>",
    "ex": "style heatmap",
    "desc": "BigBed tracks can be created with a variety of extra fields."
   },
   {
    "key": "thickDrawItem",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bed",
     "bigBed"
    ],
    "level": "full",
    "fmt": "thickDrawItem <off/on>",
    "ex": "thickDrawItem on",
    "desc": "In bed tracks that have 8 or more standard bed fields, portions of items in tracks such as gene models can be drawn thicker to differentiate exon regions fro..."
   },
   {
    "key": "decorator",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bed",
     "bigBed",
     "genePred",
     "bigGenePred",
     "psl",
     "bigPsl"
    ],
    "level": "new",
    "fmt": "decorator.default.*",
    "ex": "",
    "desc": "Decorators allow annotation to be placed on top of BED 12+, bigBed, PSL, and bigGenePred tracks by highlighting regions and adding glyphs on top of them."
   },
   {
    "key": "searchIndex",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
-    "bed",
-    "bigBed"
+    "bigBed",
+    "bigPsl",
+    "bigGenePred",
+    "bigBarChart"
    ],
    "level": "full",
    "fmt": "searchIndex <str>",
    "ex": "searchIndex name",
    "desc": "Specifies the list of field names on which a index has been made."
   },
   {
    "key": "searchTrix",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
-    "bed",
-    "bigBed"
+    "bigBed",
+    "bigGenePred"
    ],
    "level": "full",
    "fmt": "searchTrix <url/relativePath>",
    "ex": "searchTrix url or relative path",
    "desc": "Specifies the URL to a TRIX file that maps free text to a set of indices that are assumed to have indicies in the associated bigBed file."
   },
   {
    "key": "labelFields",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBarChart",
     "bigBed",
     "bigGenePred",
     "bigNarrowPeak",
     "bigPsl"
    ],
    "level": "full",
    "fmt": "labelFields < fieldName[,fieldName] >",
    "ex": "",
    "desc": "A list of fields from the bigBed based file that can be used as a label."
   },
   {
    "key": "defaultLabelFields",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBarChart",
     "bigBed",
     "bigGenePred",
     "bigNarrowPeak",
     "bigPsl"
    ],
    "level": "full",
    "fmt": "defaultLabelFields < fieldName[,fieldName] >",
    "ex": "",
    "desc": "A list of fields from the bigBed based file that should be used as a label by default."
   },
   {
    "key": "labelSeparator",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBed",
     "bigGenePred",
     "bigNarrowPeak",
     "bigPsl"
    ],
    "level": "full",
    "fmt": "labelSeparator < text >",
    "ex": "",
    "desc": "One or more characters to use as the field separator between multiple labels."
   },
   {
    "key": "filter",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bed",
     "bigBed"
    ],
    "level": "full",
    "fmt": "filter.<fieldName> <default integer>",
    "ex": "filter.score 0",
    "desc": "There are a number of different filters available for bigBed data."
   },
   {
    "key": "filterText",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBed"
    ],
    "level": "full",
    "fmt": "filterText.<fieldName> <default search string>",
    "ex": "filterText.geneName *BRCA*",
    "desc": "There are a number of different filters available for bigBed data."
   },
   {
    "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."
   },
   {
    "key": "filterPriority",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bed",
     "bigBed"
    ],
    "level": "new",
    "fmt": "filterPriority.<fieldName> <number>",
    "ex": "filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,...\n    filterValues.annot pLoF,missense,synonymous,other\n    filterValues.FILTER PASS,InbreedingCoeff,RF,AC0\n    filterPriority.variation_type 1\n    filterPriority.annot 2\n    filterPriority.FILTER 3",
    "desc": "Sets the display order of filters on the track configuration page."
   },
   {
    "key": "highlight",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bed",
     "bigBed"
    ],
    "level": "new",
    "fmt": "highlight.<fieldName> <default integer>",
    "ex": "highlight.blockCount 4",
    "desc": "Similar to filters, There are a number of different highlights available for bigBed data."
   },
   {
    "key": "highlightText",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBed"
    ],
    "level": "new",
    "fmt": "highlightText.<fieldName> <default search string>",
    "ex": "highlightText.name NM*",
    "desc": "Similar to filters, There are a number of different highlights available for bigBed data."
   },
   {
    "key": "highlightValues",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBed"
    ],
    "level": "new",
    "fmt": "highlightValues.<fieldName> <value1,value2,value3...>",
    "ex": "highlightValues.OddEven Odd",
    "desc": "Similar to filters, There are a number of different highlights available for bigBed data."
   },
   {
    "key": "highlightColor",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBed"
    ],
    "level": "new",
    "fmt": "highlightColor <hexcolor>",
    "ex": "highlightColor #ff0000",
    "desc": "Sets the default color for all of the various highlights defined in this stanza"
   },
   {
    "key": "highlightPriority",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bed",
     "bigBed"
    ],
    "level": "new",
    "fmt": "highlightPriority.<fieldName> <number>",
    "ex": "highlightValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,...\n    highlightValues.annot pLoF,missense,synonymous,other\n    highlightValues.FILTER PASS,InbreedingCoeff,RF,AC0\n    highlightPriority.variation_type 1\n    highlightPriority.annot 2\n    highlightPriority.FILTER 3",
    "desc": "Sets the display order of highlights on the track configuration page."
   },
   {
    "key": "bedNameLabel",
    "category": "Item or Region Track Settings - less frequent",
    "roles": [
     "leaf"
    ],
    "types": [
     "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",
     "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",
     "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"
    ],
    "level": "full",
    "fmt": "mergeSpannedItems <on/off>",
    "ex": "mergeSpannedItems on",
    "desc": "Allows merging all track items that extend beyond both sides of the current viewing window into one bed item in the display."
   },
   {
    "key": "linkIdInName",
    "category": "Item or Region Track Settings - less frequent",
    "roles": [
     "leaf"
    ],
    "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": [
     "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",
     "bigGenePred",
     "bigNarrowPeak"
    ],
    "level": "full",
    "fmt": "scoreLabel <label>",
    "ex": "scoreLabel Log of binding Score * 1000",
    "desc": "When a user clicks on a track item in the Browser image, the item detail page is shown."
   },
   {
    "key": "showTopScorers",
    "category": "Item or Region Track Settings - less frequent",
    "roles": [
     "leaf"
    ],
    "types": [
     "bed",
     "bed5FloatScoreWithFdr",
     "bed5FloatScore"
    ],
    "level": "full",
    "fmt": "showTopScorers #",
    "ex": "showTopScorers 20",
    "desc": "Use this setting to show a list of some number of top-scoring items in a region of the genome, when looking at an individual item in the item details page."
   },
   {
    "key": "bigChain",
    "category": "bigChain - Pairwise Alignments",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigChain"
    ],
    "level": null,
    "fmt": "type bigChain targetDb",
    "ex": "",
    "desc": ""
   },
   {
    "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": [
     "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": [
     "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": ""
   },
   {
    "key": "interactDirectional",
    "category": "bigInteract",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigInteract"
    ],
    "level": "full",
    "fmt": "interactDirectional <true|offsetSource|offsetTarget|clusterSource|clusterTarget>",
    "ex": "",
    "desc": "This setting is used when the interaction has an orientation (direction of effect)."
   },
   {
    "key": "interactUp",
    "category": "bigInteract",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigInteract"
    ],
    "level": "full",
    "fmt": "interactUp <true|false>",
    "ex": "",
    "desc": "This setting flips the curved full visibility display so that the peak of the curves is 'up' (hills instead of valleys)."
   },
   {
    "key": "detailsBoxesEnabled",
    "category": "bigInteract",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigInteract"
    ],
    "level": "new",
    "fmt": "detailsBoxesEnabled <true|false>",
    "ex": "",
    "desc": "This setting controls the default behavior for suppressing the \"box\" links to hgc details pages that appear on the lines connecting interacting regions."
   },
   {
    "key": "interactMultiRegion",
    "category": "bigInteract",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigInteract"
    ],
    "level": "full",
    "fmt": "interactMultiRegion <true|padding>",
    "ex": "",
    "desc": "This setting causes a link to appear on the details page that appears when an interaction is clicked on."
   },
   {
    "key": "endsVisible",
    "category": "bigInteract",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigInteract"
    ],
    "level": "full",
    "fmt": "endsVisible two",
    "ex": "",
    "desc": "This setting makes the default behavior for the track show only interactions with both ends in the window."
   },
   {
    "key": "bigMaf",
    "category": "bigMaf - Multiple Alignments",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigMaf"
    ],
    "level": null,
    "fmt": "type bigMaf",
    "ex": "",
    "desc": ""
   },
   {
    "key": "speciesOrder",
    "category": "bigMaf - Multiple Alignments",
    "roles": [
     "leaf"
    ],
    "types": [
     "wigMaf",
     "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",
     "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."
   },
   {
    "key": "summary",
    "category": "bigMaf - Multiple Alignments",
    "roles": [
     "leaf"
    ],
    "types": [
     "wigMaf",
     "bigMaf"
    ],
    "level": "full",
    "fmt": "summary <tableName/url>",
    "ex": "summary hg17Maf8waySummary",
    "desc": "This setting contains a table name containing a MAF summary table, or a url that points to a bigBed containing that information."
   },
   {
    "key": "bigNarrowPeak",
    "category": "bigNarrowPeak - Peaks",
    "roles": [
     "leaf"
    ],
    "types": [
     "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": "baseColorTickColor",
    "category": "bigPsl - Pairwise Alignments",
    "roles": [
     "leaf"
    ],
    "types": [
     "bed",
     "bigBed",
     "psl",
     "bigPsl"
    ],
    "level": "full",
    "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": "showDiffBasesAllScales",
    "category": "bigPsl - Pairwise Alignments",
    "roles": [
     "leaf"
    ],
    "types": [
     "bed",
     "bigBed",
     "genePred",
     "psl",
     "bigPsl",
     "chain",
     "bigChain",
     "bam"
    ],
    "level": "full",
    "fmt": "showDiffBasesAllScales on",
    "ex": "",
    "desc": "Show base differences for all zoom levels."
   },
+  {
+   "key": "pslSequence",
+   "category": "bigPsl - Pairwise Alignments",
+   "roles": [
+    "leaf"
+   ],
+   "types": [
+    "psl",
+    "bigPsl"
+   ],
+   "level": "deprecated",
+   "fmt": "pslSequence <no/all/different>",
+   "ex": "",
+   "desc": "Obsolete."
+  },
   {
    "key": "showCdsAllScales",
    "category": "bigPsl - Pairwise Alignments",
    "roles": [
     "leaf"
    ],
    "types": [
     "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",
     "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": [
     "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,
    "fmt": "type bigWig <#> <#>",
    "ex": "",
    "desc": "The remote data files of type bigWig must declare the expected signal range for the data."
   },
   {
    "key": "autoScale",
    "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",
    "desc": "The amount of vertical viewing space for your signal track should be declared, though it is configurable by the user."
   },
   {
    "key": "viewLimits",
    "category": "bigWig - Signal Graphing Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "wig",
     "bigWig",
     "bedGraph"
    ],
    "level": "base",
    "fmt": "viewLimits <lower:upper>",
    "ex": "viewLimits 5:20\n    viewLimitsMax0:100",
    "desc": "The data of most interest in a graph track may be contained within a narrow range."
   },
   {
    "key": "alwaysZero",
    "category": "bigWig - Signal Graphing Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "wig",
     "bedGraph",
     "bigWig"
    ],
    "level": "full",
    "fmt": "alwaysZero  <off/on>",
    "ex": "",
    "desc": "When autoScale is set to \"on\" or \"group\" in the signal track, additionally setting alwaysZero to \"on\" will ensure that the y=0 value will be in view at all t..."
   },
   {
    "key": "graphTypeDefault",
    "category": "bigWig - Signal Graphing Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "wig",
     "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": [
     "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",
     "bedGraph"
    ],
    "level": "full",
    "fmt": "negateValues <on>",
    "ex": "",
    "desc": "Negate the values in the wiggle, meaning that positive values become negative and vice-versa."
   },
   {
    "key": "setColorWith",
    "category": "bigWig - Signal Graphing Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigWig"
    ],
    "level": "full",
    "fmt": "setColorWith <url/relativePath>",
    "ex": "setColorWith url or relative path",
    "desc": "Specifies the URL to a bed 9 bigBed file."
   },
   {
    "key": "smoothingWindow",
    "category": "bigWig - Signal Graphing Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "wig",
     "bigWig",
     "bedGraph"
    ],
    "level": "full",
    "fmt": "smoothingWindow <off/1-16>",
    "ex": "smoothingWindow 4",
    "desc": "Often signal information is chunky, because a single value is given for a number of bases."
   },
   {
    "key": "transformFunc",
    "category": "bigWig - Signal Graphing Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "wig",
     "bigWig",
     "bedGraph",
     "bed"
    ],
    "level": "full",
    "fmt": "transformFunc <NONE/LOG>",
    "ex": "transformFunc LOG",
    "desc": "The track's signal can be presented in log scale with this user-configurable setting."
   },
   {
    "key": "logo",
    "category": "bigWig - Signal Graphing Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigWig"
    ],
    "level": "new",
    "fmt": "logo on",
    "ex": "logo on",
    "desc": "Enables dynseq display , which graphs the signal as reference base nucleotide letters with their heights equal to the signal value within the bigWig track."
   },
   {
    "key": "logoMaf",
    "category": "bigWig - Signal Graphing Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "wig",
     "bigWig",
     "bigMaf"
    ],
    "level": "new",
    "fmt": "logoMaf <url/relativePath>",
    "ex": "logoMaf https://hgdownload.gi.ucsc.edu/goldenPath/hg38/multiz470way/multiz470way.bigMaf",
    "desc": "The argument to logoMaf is the path to a MAF alignment (either a table or bigMaf)."
   },
   {
    "key": "windowingFunction",
    "category": "bigWig - Signal Graphing Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "wig",
     "bigWig",
     "bedGraph"
    ],
    "level": "full",
    "fmt": "windowingFunction  <mean/mean+whiskers/maximum/minimum>",
    "ex": "windowingFunction mean",
    "desc": "Depending upon how large of a genomic region is displayed in the Browser image, it may be necessary to summarize the actual signal."
   },
   {
    "key": "yLineMark",
    "category": "bigWig - Signal Graphing Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "wig",
     "bigWig",
     "bedGraph"
    ],
    "level": "full",
    "fmt": "yLineMark <#>",
    "ex": "yLineOnOff on\n    yLineMark 2.5\n    gridDefault on",
    "desc": "It can be useful to draw a line across the track's signal graph at some fixed y coordinate."
   },
   {
    "key": "bigLolly",
    "category": "bigLolly - Lollipop charts",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigLolly"
    ],
    "level": null,
    "fmt": "type bigLolly",
    "ex": "",
    "desc": ""
   },
   {
    "key": "lollyNoStems",
    "category": "bigLolly - Lollipop charts",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigLolly"
    ],
    "level": "full",
    "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": ""
   },
   {
    "key": "lollyMaxSize",
    "category": "bigLolly - Lollipop charts",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigLolly"
    ],
    "level": "full",
    "fmt": "lollyMaxSize <integer>",
    "ex": "",
    "desc": ""
   },
   {
    "key": "lollyField",
    "category": "bigLolly - Lollipop charts",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigLolly"
    ],
    "level": "full",
    "fmt": "lollyField <integer>",
    "ex": "",
    "desc": ""
   },
   {
    "key": "yAxisLabel",
    "category": "bigLolly - Lollipop charts",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigLolly"
    ],
    "level": "full",
    "fmt": "yAxisLabel.<integer> <integer> <on/off> <R,G,B> <string>",
    "ex": "",
    "desc": ""
   },
   {
    "key": "yAxisNumLabels",
    "category": "bigLolly - Lollipop charts",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigLolly"
    ],
    "level": "full",
    "fmt": "yAxisNumLabels.<on/off> <integer>",
    "ex": "",
    "desc": ""
   },
   {
    "key": "hic",
    "category": "hic - Hi-C contact matrices",
    "roles": [
     "leaf"
    ],
    "types": [
     "hic"
    ],
    "level": null,
    "fmt": "type hic",
    "ex": "",
    "desc": ""
   },
   {
    "key": "drawMode",
    "category": "hic - Hi-C contact matrices",
    "roles": [
     "leaf"
    ],
    "types": [
     "hic"
    ],
    "level": "full",
    "fmt": "drawMode <triangle|square|arc>",
    "ex": "",
    "desc": "This setting controls the default display mode for the hic track."
   },
   {
    "key": "normalization",
    "category": "hic - Hi-C contact matrices",
    "roles": [
     "leaf"
    ],
    "types": [
     "hic"
    ],
    "level": "full",
    "fmt": "normalization <NONE|VC|VC_SQRT|KR>",
    "ex": "",
    "desc": "This setting controls which method is the default for normalizing the raw scores from the .hic file."
   },
   {
    "key": "resolution",
    "category": "hic - Hi-C contact matrices",
    "roles": [
     "leaf"
    ],
    "types": [
     "hic"
    ],
    "level": "full",
    "fmt": "resolution <Auto|integer>",
    "ex": "",
    "desc": "This setting controls the default size of the bins that the Hi-C contact results are grouped into."
   },
   {
    "key": "saturationScore",
    "category": "hic - Hi-C contact matrices",
    "roles": [
     "leaf"
    ],
    "types": [
     "hic"
    ],
    "level": "full",
    "fmt": "saturationScore <float>",
    "ex": "",
    "desc": "The saturationScore setting is part of how the color shades of the heatmap are displayed."
   },
   {
    "key": "hicDistanceMin",
    "category": "hic - Hi-C contact matrices",
    "roles": [
     "leaf"
    ],
    "types": [
     "hic"
    ],
    "level": "new",
    "fmt": "hicDistanceMin <integer>",
    "ex": "",
    "desc": "Hi-C tracks have a setting that controls the minimum interaction distance in nucleotides for the heatmap."
   },
   {
    "key": "hicDistanceMax",
    "category": "hic - Hi-C contact matrices",
    "roles": [
     "leaf"
    ],
    "types": [
     "hic"
    ],
    "level": "new",
    "fmt": "hicDistanceMax <integer>",
    "ex": "",
    "desc": "Hi-C tracks have a setting that controls the maximum interaction distance in nucleotides for the heatmap."
   },
   {
    "key": "hicArcLimit",
    "category": "hic - Hi-C contact matrices",
    "roles": [
     "leaf"
    ],
    "types": [
     "hic"
    ],
    "level": "new",
    "fmt": "hicArcLimit <integer>",
    "ex": "",
    "desc": "The \"arc\" display mode for Hi-C tracks can become difficult to read if too many arcs are being drawn, particularly if many of them have scores close to the s..."
   },
   {
    "key": "hicArcLimitEnabled",
    "category": "hic - Hi-C contact matrices",
    "roles": [
     "leaf"
    ],
    "types": [
     "hic"
    ],
    "level": "new",
    "fmt": "hicArcLimitEnabled <true|false>",
    "ex": "",
    "desc": "The \"arc\" display mode for Hi-C tracks can become difficult to read if too many arcs are being drawn, so there is an option to limit the display to the N hig..."
   },
   {
    "key": "halSnake",
    "category": "halSnake - Multiple Alignments",
    "roles": [
     "leaf"
    ],
    "types": [
     "halSnake"
    ],
    "level": null,
    "fmt": "type halSnake",
    "ex": "",
    "desc": "If the bigDataUrl setting is included, the data at the location specified by that URL will be displayed."
   },
   {
    "key": "showSnpWidth",
    "category": "halSnake - Multiple Alignments",
    "roles": [
     "leaf"
    ],
    "types": [
     "halSnake"
    ],
    "level": "full",
    "fmt": "showSnpWidth < integer >",
    "ex": "",
    "desc": "The maximum width (in bases) of a window where the halSnake will show SNPs between the reference and the other species."
   },
   {
    "key": "otherSpecies",
    "category": "halSnake - Multiple Alignments",
    "roles": [
     "leaf"
    ],
    "types": [
     "halSnake"
    ],
    "level": "full",
    "fmt": "otherSpecies <otherSpecies>",
    "ex": "otherSpecies tweeter",
    "desc": "The name of the other assembly in the pairwise alignment for this track."
   },
   {
    "key": "vcfTabix",
    "category": "vcfTabix - Variant Call Format Track Settings",
    "roles": [
     "leaf"
    ],
    "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",
     "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",
     "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",
     "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",
     "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",
     "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",
     "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",
     "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",
     "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",
     "vcfPhasedTrio"
    ],
    "level": "full",
    "fmt": "vcfDoFilter <on/off>",
    "ex": "",
    "desc": "Turn on/off the FILTER options available by default for VCF tracks"
   },
   {
    "key": "vcfDoQual",
    "category": "vcfTabix - Variant Call Format Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "vcf",
     "vcfTabix",
     "vcfPhasedTrio"
    ],
    "level": "full",
    "fmt": "vcfDoQual <on/off>",
    "ex": "",
    "desc": "Turns on/off the QUAL filter options available by default for VCF tracks"
   },
   {
    "key": "vcfDoMaf",
    "category": "vcfTabix - Variant Call Format Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "vcf",
     "vcfTabix",
     "vcfPhasedTrio"
    ],
    "level": "full",
    "fmt": "vcfDoMaf <on/off>",
    "ex": "",
    "desc": "Turns on/off the Minor Allele Frequency filter options available by default for VCF tracks"
   },
   {
    "key": "sampleMetadataFile",
    "category": "vcfTabix - Variant Call Format Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "vcf",
     "vcfTabix",
     "vcfPhasedTrio"
    ],
    "level": "new",
    "fmt": "sampleMetadataFile <url>",
    "ex": "#sample\tPopulation\tSuperpopulation\tRegion\nHG00096\tGBR\tEUR\tEurope\nHG00099\tGBR\tEUR\tEurope\nNA18939\tJPT\tEAS\tEast Asia",
    "desc": "Specifies a tab-separated file that provides metadata columns for VCF samples."
   },
   {
    "key": "vcfPhasedTrio",
    "category": "vcfPhasedTrio - Variant Call Format Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "vcfPhasedTrio"
    ],
    "level": null,
    "fmt": "type vcfPhasedTrio",
    "ex": "",
    "desc": "There are no extra options that can appear on the type vcfPhasedTrio line."
   },
   {
    "key": "vcfChildSample",
    "category": "vcfPhasedTrio - Variant Call Format Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "vcfPhasedTrio"
    ],
    "level": "full",
    "fmt": "vcfChildSample <sampleName|altName>",
    "ex": "",
    "desc": "The VCF Genotype column ID of the \"child\" sample, followed optionally by a \"|\" character and an alias for the display."
   },
   {
    "key": "vcfParentSamples",
    "category": "vcfPhasedTrio - Variant Call Format Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "vcfPhasedTrio"
    ],
    "level": "full",
    "fmt": "vcfParentSamples <sampleName|altName,sampleName|altName>",
    "ex": "",
    "desc": "A comma separated (no spaces) list of the VCF Genotype column IDs of the \"parents\", followed optionally by a \"|\" character and an alias for the display."
   },
   {
    "key": "vcfUseAltSampleNames",
    "category": "vcfPhasedTrio - Variant Call Format Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "vcfPhasedTrio"
    ],
    "level": "full",
    "fmt": "vcfUseAltSampleNames <on/off>",
    "ex": "",
    "desc": "Make the display use the aliases as the default labels for each haplotype lane instead of the ID from the VCF."
   },
   {
    "key": "superTrack",
    "category": "superTrack - Folder Track Settings",
    "roles": [
     "super"
    ],
    "types": [
     "superTrack"
    ],
    "level": "base",
    "fmt": "superTrack on show",
    "ex": "",
    "desc": "To declare a supertrack, simply add this setting to a track definition that will hold a few standard settings."
   },
   {
    "key": "parent_supertrack",
    "category": "superTrack - Folder Track Settings",
    "roles": [
     "super"
    ],
    "types": [
     "superTrack"
    ],
    "level": "base",
    "fmt": "parent <superTrack>",
    "ex": "",
    "desc": "Membership in a supertrack, composite, or aggregate track is declared by the child, not the supertrack itself with a line such as parent superTrack1 ."
   },
   {
    "key": "parent",
    "category": "Composite Track Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "compositeTrack"
    ],
    "level": "base",
    "fmt": "parent <composite> [off/on]",
    "ex": "",
    "desc": "Membership in a composite is declared by the subtrack child, not the composite itself, through this setting."
   },
   {
    "key": "compositeTrack",
    "category": "Composite Track Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "compositeTrack"
    ],
    "level": "base",
    "fmt": "compositeTrack on",
    "ex": "",
    "desc": "To declare a composite, simply add this setting to a track definition, along with a few standard settings."
   },
   {
    "key": "allButtonPair",
    "category": "Composite Track Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "compositeTrack"
    ],
    "level": "full",
    "fmt": "allButtonPair on",
    "ex": "",
    "desc": "When a simple composite track presents a short list of subtracks, it can be convenient for the user to have an easy way to select or deselect all of them."
   },
   {
    "key": "centerLabelsDense",
    "category": "Composite Track Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "compositeTrack"
    ],
    "level": "full",
    "fmt": "centerLabelsDense <off/on>",
    "ex": "",
    "desc": "By default, only the composite track's single center label is shown when the subtracks are displayed together in the Browser dense mode."
   },
   {
    "key": "dragAndDrop",
    "category": "Composite Track Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "compositeTrack"
    ],
    "level": "full",
    "fmt": "dragAndDrop subTracks",
    "ex": "",
    "desc": "When you have many subtracks in a composite track, it may be useful on the Track Setting page, also known as the hgTrackUi configuration page, to rearrange t..."
   },
   {
    "key": "hideEmptySubtracks",
    "category": "Composite Track Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "compositeTrack"
    ],
    "level": "full",
    "fmt": "hideEmptySubtracks <on/off>",
    "ex": "",
    "desc": "When you have many subtracks in a composite track, it may be useful to limit the display to only those with data in the current viewing window."
   },
   {
    "key": "hideEmptySubtracksMultiBedUrl",
    "category": "Composite Track Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "compositeTrack"
    ],
    "level": "full",
    "fmt": "hideEmptySubtracksMultiBedUrl file.bb",
    "ex": "",
    "desc": "For large composites, especially those where each subtrack may be sparse, substantial performance improvements can be gained by creating an index file of the..."
   },
   {
    "key": "hideEmptySubtracksSourcesUrl",
    "category": "Composite Track Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "compositeTrack"
    ],
    "level": "full",
    "fmt": "hideEmptySubtracksSourcesUrl file.tab",
    "ex": "",
    "desc": "This setting is used in conjunction with the hideEmptySubtracksMultiBedUrl setting, described above."
   },
   {
    "key": "hideEmptySubtracksLabel",
    "category": "Composite Track Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "compositeTrack"
    ],
    "level": "full",
    "fmt": "hideEmptySubtracksLabel <label>",
    "ex": "",
    "desc": "This setting is used in conjunction with the hideEmptySubtracks setting to customize the label preceding the selection checkbox on the track configuration page."
   },
   {
    "key": "subGroupN",
    "category": "Composite - Subgroups Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "subGroups"
    ],
    "level": "base",
    "fmt": "subGroup1 <gTag1> <gTitle1> <mTag1a=mTitle1a>\n                        [mTag1b=mTitle1b...]",
    "ex": "",
    "desc": "Up to 9 subgroups may be declared, one per line."
   },
   {
    "key": "subGroups",
    "category": "Composite - Subgroups Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "subGroups"
    ],
    "level": "base",
    "fmt": "subGroups <gTag1=mTag1?> [gTag2= mTag2?]",
    "ex": "",
    "desc": "The subtracks themselves declare their membership in a group with the subGroups setting."
   },
   {
    "key": "dimensions",
    "category": "Composite - Subgroups Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "subGroups"
    ],
    "level": "base",
    "fmt": "dimensions <dimX=gTag#> [dimY=gTag#] [dimA=gTag# ...]",
    "ex": "",
    "desc": "In order to define the type of UI desired for selecting subtracks based upon groups, additional settings are needed at the composite level."
   },
   {
    "key": "filterComposite",
    "category": "Composite - Subgroups Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "subGroups"
    ],
    "level": "full",
    "fmt": "filterComposite <dim[A/B/C][=one]> [dimB dimC ...]",
    "ex": "",
    "desc": "For the \"abc\" dimensions, rows of checkboxes will be shown by default."
   },
   {
    "key": "dimensionAchecked",
    "category": "Composite - Subgroups Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "subGroups"
    ],
    "level": "full",
    "fmt": "dimension<?>checked <mTag1a>\n                                [mTag1b ...]",
    "ex": "",
    "desc": "One more complication in the selection process is determining which subgroup options are selected by default."
   },
   {
    "key": "sortOrder",
    "category": "Composite - Subgroups Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "subGroups"
    ],
    "level": "full",
    "fmt": "sortOrder <gTag#=+/-> [gTag#=- ...]",
    "ex": "",
    "desc": "When declaring subgroups, it is often useful to sort the subtrack list by those subgroups."
   },
   {
    "key": "view",
    "category": "Composite - Views Settings",
    "roles": [
     "view"
    ],
    "types": [
     "view"
    ],
    "level": "base",
    "fmt": "subGroup1 view <Views> <vTag1a=vTitle1a> [vTag1b=vTitle1b...]",
    "ex": "",
    "desc": "A view is always declared both as a subgroup and in a track stanza itself."
   },
   {
    "key": "parent_view",
    "category": "Composite - Views Settings",
    "roles": [
     "view"
    ],
    "types": [
     "view"
    ],
    "level": "base",
    "fmt": "subGroups view=<vTag1>...",
    "ex": "",
    "desc": "A subtrack declares its membership in a view both as subgroup membership and with a parent setting that refers to the view track name."
   },
   {
    "key": "viewUi",
    "category": "Composite - Views Settings",
    "roles": [
     "view"
    ],
    "types": [
     "view"
    ],
    "level": "full",
    "fmt": "viewUi on",
    "ex": "",
    "desc": "If subtracks within a view are configurable, then the view will have the configuration controls for it in a box beneath the view's visibility drop down."
   },
   {
    "key": "configurable",
    "category": "Composite - Views Settings",
    "roles": [
     "view"
    ],
    "types": [
     "view",
     "composite"
    ],
    "level": "full",
    "fmt": "configurable <off/on>",
    "ex": "",
    "desc": "Tracks are configurable by default if their track type supports this, and views and composites are configurable if their children's track type supports this."
   },
   {
    "key": "faceted",
    "category": "Faceted Composite Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "faceted",
     "composite"
    ],
    "level": null,
    "fmt": "compositeTrack faceted",
    "ex": "",
    "desc": "This version of the compositeTrack setting indicates that the UI for this composite track should be handled with facets."
   },
   {
    "key": "metaDataUrl",
    "category": "Faceted Composite Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "faceted",
     "composite"
    ],
    "level": "new",
    "fmt": "metaDataUrl <url>",
    "ex": "accession       group        cell_type\nDRX118406       CellLine     iPSC\nDRX118407       CellLine     iPSC\nDRX118408       CellLine     iMeLC",
    "desc": "The URL here points to the tsv file that provides facet information."
   },
   {
    "key": "primaryKey",
    "category": "Faceted Composite Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "faceted",
     "composite"
    ],
    "level": "new",
    "fmt": "primaryKey <field>",
    "ex": "",
    "desc": "This setting is required and works in tandem with the file specified in the metaDataUrl setting."
   },
   {
    "key": "maxCheckboxes",
    "category": "Faceted Composite Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "faceted",
     "composite"
    ],
    "level": "new",
    "fmt": "maxCheckboxes <integer>",
    "ex": "",
    "desc": "Frequently a facet may have a long list of possible values - too many to display at once in the track selection interface."
   },
   {
    "key": "dataTypes",
    "category": "Faceted Composite Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "faceted",
     "composite"
    ],
    "level": "new",
    "fmt": "dataTypes <name1(|\"table title\") name2(|\"table title\") ...>",
    "ex": "dataTypes sig|\"Raw signal\" peak|Peaks",
    "desc": "This optional setting identifies a list of datatypes available for each sample in the metadata file (one sample per row)."
   },
   {
    "key": "defaultSortField",
    "category": "Faceted Composite Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "faceted",
     "composite"
    ],
    "level": "new",
    "fmt": "defaultSortField <name>",
    "ex": "defaultSortField tissue",
    "desc": "This optional setting chooses which field in the metadata table will be used to sort the table of subtracks when the page is first loaded."
   },
   {
    "key": "subtrackUrls",
    "category": "Faceted Composite Settings",
    "roles": [
     "composite"
    ],
    "types": [
     "faceted",
     "composite"
    ],
    "level": "new",
    "fmt": "subtrackUrls <field1>=<url1> <field2>=<url2> ...",
    "ex": "subtrackUrls accession=https://www.ncbi.nlm.nih.gov/sra/$$ project=https://www.ncbi.nlm.nih.gov/bioproject/$$",
    "desc": "For some faceted composites, each subtrack is associated with a particular cell line or other accession that is described in more detail at another resource..."
   },
   {
    "key": "container",
    "category": "Aggregate or Overlay Track Settings",
    "roles": [
     "composite",
     "view",
     "leaf"
    ],
    "types": [
     "container",
     "multiWig"
    ],
    "level": "full",
    "fmt": "container multiWig",
    "ex": "",
    "desc": "Signal overlay tracks are declared much like simple composites."
   },
   {
    "key": "parent_container",
    "category": "Aggregate or Overlay Track Settings",
    "roles": [
     "composite",
     "view",
     "leaf"
    ],
    "types": [
     "container",
     "multiWig"
    ],
    "level": "base",
    "fmt": "parent <containerTrack>",
    "ex": "",
    "desc": "Membership in a container track is declared at the subtrack level."
   },
   {
    "key": "aggregate",
    "category": "Aggregate or Overlay Track Settings",
    "roles": [
     "composite",
     "view",
     "leaf"
    ],
    "types": [
     "container",
     "multiWig"
    ],
    "level": "full",
    "fmt": "aggregate <transparentOverlay/stacked/solidOverlay/none>",
    "ex": "",
    "desc": "It is important to declare an aggregation method; otherwise, this set of tracks displays as a composite would, with additional restrictions."
   },
   {
    "key": "showSubtrackColorOnUi",
    "category": "Aggregate or Overlay Track Settings",
    "roles": [
     "composite",
     "view",
     "leaf"
    ],
    "types": [
     "container",
     "multiWig"
    ],
    "level": "full",
    "fmt": "showSubtrackColorOnUi on",
    "ex": "",
    "desc": "Subtracks in an overlay have individual colors."
   },
   {
    "key": "hub",
    "category": "general hub file settings",
    "roles": [
     "hub"
    ],
    "types": "all",
    "level": "base",
    "fmt": "hub <str>",
    "ex": "hub myRnaSeqData",
    "desc": "A short, unique identifier for the hub used internally by the Genome Browser software to identify your hub."
   },
   {
    "key": "shortLabel",
    "category": "general hub file settings",
    "roles": [
     "hub"
    ],
    "types": "all",
    "level": "base",
    "fmt": "shortLabel <str>",
    "ex": "shortLabel ENCODE3 RNA-seq Data",
    "desc": "A short description of the hub."
   },
   {
    "key": "longLabel",
    "category": "general hub file settings",
    "roles": [
     "hub"
    ],
    "types": "all",
    "level": "base",
    "fmt": "longLabel <str>",
    "ex": "longLabel Comment describing this hub contents",
    "desc": "A longer, more descriptive label for the hub."
   },
   {
    "key": "genomesFile",
    "category": "general hub file settings",
    "roles": [
     "hub"
    ],
    "types": "all",
    "level": "base",
    "fmt": "genomesFile <url/relativePath>",
    "ex": "genomesFile genomes.txt",
    "desc": "References the next definition file in this hub that will describe the assemblies and tracks available at this hub."
   },
   {
    "key": "email",
    "category": "general hub file settings",
    "roles": [
     "hub"
    ],
    "types": "all",
    "level": "base",
    "fmt": "email <email address>",
    "ex": "email contactEmail@institution.edu",
    "desc": "Provides users with a contact point for questions related to the hub."
   },
   {
    "key": "descriptionUrl",
    "category": "general hub file settings",
    "roles": [
     "hub"
    ],
    "types": "all",
    "level": "base",
    "fmt": "descriptionUrl <url/relativePath>",
    "ex": "descriptionUrl castorBeanHubDescription.html",
    "desc": "Specify a relative path or URL link to a webpage (e.g."
   },
   {
    "key": "useOneFile",
    "category": "general hub file settings",
    "roles": [
     "hub"
    ],
    "types": "all",
    "level": "base",
    "fmt": "useOneFile <on>",
    "ex": "useOneFile on",
    "desc": "If the hub only has tracks on a single genome, useOneFile allows all hub and track configuration settings to be in a single file."
   },
   {
    "key": "genome",
    "category": "genomes file settings",
    "roles": [
     "genome"
    ],
    "types": "all",
    "level": "base",
    "fmt": "genome <str>",
    "ex": "genome ricCom1",
    "desc": "For hubs on native assemblies, use the UCSC database name (e.g."
   },
   {
    "key": "trackDb",
    "category": "genomes file settings",
    "roles": [
     "genome"
    ],
    "types": "all",
    "level": "base",
    "fmt": "trackDb <url/relativePath>",
    "ex": "trackDb ricCom1/trackDb.txt",
    "desc": "Relative path or URL to the file that defines the tracks for the assembly specified by the genome setting."
   },
   {
    "key": "groups",
    "category": "genomes file settings",
    "roles": [
     "genome"
    ],
    "types": "all",
    "level": "base",
    "fmt": "groups <url/relativePath>",
    "ex": "groups ricCom1/groups.txt",
    "desc": "Relative path or URL that points to a file defining track groups, which are collections of related tracks displayed together under the main Genome Browser im..."
   },
   {
    "key": "description",
    "category": "genomes file settings",
    "roles": [
     "genome"
    ],
    "types": "all",
    "level": "base",
    "fmt": "description <str>",
    "ex": "description July 2011 Castor bean",
    "desc": "Description of the assembly version that is displayed on the Gateway page and title pages for this assembly."
   },
   {
    "key": "twoBitPath",
    "category": "genomes file settings",
    "roles": [
     "genome"
    ],
    "types": "all",
    "level": "base",
    "fmt": "twoBitPath <url/relativePath>",
    "ex": "twoBitPath ricCom1/ricCom1.2bit",
    "desc": "Relative path or URL to the .2bit sequence file for the assembly."
   },
   {
    "key": "chromAlias",
    "category": "genomes file settings",
    "roles": [
     "genome"
    ],
    "types": "all",
    "level": "base",
    "fmt": "chromAlias <url/relativePath>",
    "ex": "chromAlias thisGenome.chromAlias.txt",
    "desc": "Enables the Genome Browser to automatically convert chromosome names in submitted custom track data from alternate naming schemes to the names used in the as..."
   },
   {
    "key": "chromAliasBb",
    "category": "genomes file settings",
    "roles": [
     "genome"
    ],
    "types": "all",
    "level": "base",
    "fmt": "chromAliasBb <url/relativePath>",
    "ex": "chromAliasBb thisGenome.chromAlias.bb",
    "desc": "Like chromAlias , except the file is in the compressed, binary bigBed format."
   },
   {
    "key": "chromSizes",
    "category": "genomes file settings",
    "roles": [
     "genome"
    ],
    "types": "all",
    "level": "base",
    "fmt": "chromSizes <url/relativePath>",
    "ex": "chromSizes thisGenome.chromSizes.txt",
    "desc": "Defines a file to be used when displaying the sequences contained in an assembly."
   },
   {
    "key": "chromAuthority",
    "category": "genomes file settings",
    "roles": [
     "genome"
    ],
    "types": "all",
    "level": "base",
    "fmt": "chromAuthority <str>",
    "ex": "chromAuthority ucsc",
    "desc": "Indicates which chromosome naming scheme from the chromAlias file to be used as the default in the Genome Browser display."
   },
   {
    "key": "codonTable",
    "category": "genomes file settings",
    "roles": [
     "genome"
    ],
    "types": "all",
    "level": "new",
    "fmt": "codonTable default=<id> <sequenceName>=<id> ...",
    "ex": "codonTable default=1 NC_017929.1=13",
    "desc": "By default the Genome Browser translates codons to amino acids with the standard genetic code, except for sequences named chrM or chrMT , which use the verte..."
   },
   {
    "key": "organism",
    "category": "genomes file settings",
    "roles": [
     "genome"
    ],
    "types": "all",
    "level": "base",
    "fmt": "organism <str>",
    "ex": "organism Orangutan",
    "desc": "Common name of the organism, displayed alongside the description on title pages."
   },
   {
    "key": "defaultPos",
    "category": "genomes file settings",
    "roles": [
     "genome"
    ],
    "types": "all",
    "level": "base",
    "fmt": "defaultPos <chr:start-end>",
    "ex": "defaultPos chr7:155799529-155812871",
    "desc": "Defines the initial view in the Genome Browser, usually highlighting a popular gene or region of interest."
   },
   {
    "key": "orderKey",
    "category": "genomes file settings",
    "roles": [
     "genome"
    ],
    "types": "all",
    "level": "base",
    "fmt": "orderKey <int>",
    "ex": "orderKey 4800",
    "desc": "Controls the ordering of assemblies in the pull-down menu."
   },
   {
    "key": "scientificName",
    "category": "genomes file settings",
    "roles": [
     "genome"
    ],
    "types": "all",
    "level": "base",
    "fmt": "scientificName <str>",
    "ex": "scientificName Ricinus communis",
    "desc": "Scientific name of organism, displayed alongside the description on title pages."
   },
   {
    "key": "htmlPath",
    "category": "genomes file settings",
    "roles": [
     "genome"
    ],
    "types": "all",
    "level": "base",
    "fmt": "htmlPath <url/relativePath>",
    "ex": "htmlPath ricCom1/description.html",
    "desc": "Points to an HTML file with assembly information."
   },
   {
    "key": "transBlat",
    "category": "genomes file settings",
    "roles": [
     "genome"
    ],
    "types": "all",
    "level": "base",
    "fmt": "transBlat <url> <port>",
    "ex": "transBlat yourServer.yourInstitution.edu 17778",
    "desc": "Indicates the server and port to be used for the \"translated DNA/RNA\" options in the BLAT interface."
   },
   {
    "key": "blat",
    "category": "genomes file settings",
    "roles": [
     "genome"
    ],
    "types": "all",
    "level": "base",
    "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."
   }
  ]
 }