0e4e0c0af65eea70f64edbc68348ce0972c4bbf4 braney Fri Aug 28 16:45:00 2026 -0700 Correct the track types listed for trackDb settings, and the hub settings list The "For Types" list in the trackDb docs was wrong for about sixty settings, so the docs named the wrong track types for settings that have always worked. Most named only the older type and left out its big* counterpart. The clearest case is the multiple-alignment family: a bigMaf track is drawn and configured by the same code as a wigMaf track, but only speciesOrder said so, while irows, itemFirstCharCase, speciesGroups, speciesCodonDefault, speciesDefaultOff, treeImage, pairwiseHeight and speciesUseFile all claimed wigMaf alone. The hapCluster settings said vcf and not vcfTabix. noScoreFilter said bed while its own example uses type bigBed 6 +. Six settings said "all" for something that only works on item tracks. Two documented settings do not exist. pslSequence describes a variable that was replaced by the baseColor family long before the setting was listed, and nothing has read either spelling since; it is removed. noStems is renamed to lollyNoStems, which is what the Browser actually reads. That one mattered: hubCheck builds its list of valid settings from trackDbHub.html, so it accepted the spelling that does nothing and rejected the one that works. Fourteen settings that work in hubs had no entry in the hub spec, so hubCheck reported them as unrecognized. They are listed now: chainColor, chainNormScoreAvailable, pairwiseHeight, barChartMatrixUrl, mouseOverFunction, intronGap, filterBy, baseColorTickColor, speciesGroups, speciesDefaultOff, speciesCodonDefault, itemFirstCharCase, irows, and canPack with configureByPopup and origAssembly. The last three, along with filterBy and baseColorTickColor, were marked "NOT FOR HUBS", which was wrong: the Browser reads them from a hub's trackDb the same way it reads them from ours. The type setting on the hub page listed every type the Browser knows, including ones that only work for tracks loaded into our own databases. It now shows only the types a hub can use. A hub-specific blurb for this already existed and had never been referenced. Three settings had no blurb at all, so the generated trackDbSettings.json never saw them: metadata, noInherit and useScore. Written, and the five hand-written copies in trackDbDoc.html that had drifted from the library are brought back into line. The library's header told the reader to always check their work in trackDbTestBlurbs.html, which was deleted in November 2025. It now points at "make settings" instead. That target regenerates trackDbSettings.yaml and .json, which are updated here, and its name map gains an entry so the hub-specific type blurb is still keyed as "type". refs #37908 diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml index a43af6f836c..a2c9f30b1d1 100644 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml @@ -10,55 +10,52 @@ - super - composite - view - leaf category: Common Settings context: trackDb level: required required: true summary: This is the name of the dataset and must be unique within the Genome Browser or dataHub. description: 'This is the name of the dataset and must be unique within the Genome Browser or dataHub. Typically this is the MariaDB table name or remote data file root name (without path or suffix). Must begin with a letter and contain only the following chars: [ a-zA-Z0-9_- ].' format: track examples: - track myFirstTrack -- name: type +- name: type_for_hubs types: - all roles: - super - composite - view - leaf category: Common Settings context: trackDb level: required required: true summary: Declares the format of the data and is used to determine display methods and options. description: 'Declares the format of the data and is used to determine display methods and options. - Valid settings: altGraphX , bam , bed , bed5FloatScore , bedGraph , bedRnaElements , bigBarChart , - bigBed , bigInteract , bigLolly , bigPsl , bigChain , bigMaf , bigWig , broadPeak , chain , clonePos - , coloredExon , ctgPos , downloadsOnly , encodeFiveC , expRatio , factorSource , genePred , gvf , - hic , ld2 , narrowPeak , netAlign , peptideMapping , psl , rmsk , snake , vcfTabix , wig , wigMaf - Not all track types are supported in hubs. The types specifically supported are called out at the - top of the Hub Track Database Definition page. In many cases the type setting includes additional + Valid settings for a hub: bam/cram , bigBarChart , bigBed , bigChain , bigGenePred , bigInteract , + bigLolly , bigMaf , bigNarrowPeak , bigPsl , bigWig , halSnake , hic , vcfTabix , vcfPhasedTrio . + Detailed descriptions of each type can be found below. In many cases the type setting includes additional parameters to further specify the data format. Some track types have additional setting requirements, to be discussed below.' format: type examples: - - type bed 6 + + - type bigBed 6 + - name: shortLabel types: - all roles: - super - composite - view - leaf category: Common Settings context: trackDb level: required required: true summary: Specifies the track's "short label", which is used in a number of places in the Browser to identify the track. description: Specifies the track's "short label", which is used in a number of places in the Browser @@ -249,30 +246,97 @@ context: trackDb level: base required: false summary: 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. description: '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. The order within the image can be dynamically changed by the user and will always depend upon which other tracks are currently visible. Typically the priority is set only for tracks that are on by default in order to move them ahead of other tracks. Prioritized tracks within a group or data hub are displayed in ascending priority order, followed by unprioritized tracks sorted alphabetically by short label. Tracks of the same priority within a group or hub are sorted by short label. Priority is a floating point number. Default: 0.' format: priority <float> examples: - priority 50 +- name: canPack + types: + - all + roles: + - super + - composite + - view + - leaf + category: Common Settings - less frequent + context: trackDb + level: deprecated + required: false + summary: Deprecated. + description: 'Deprecated. The track type usually implies whether pack and squish are offered, so this + setting is rarely needed. Most tracks can be displayed in all five visibilities modes. However on + some track types such as wiggles, the squish and pack modes offer no real advantage over the dense + and full modes. By default, these tracks will not offer the squish and pack vilibility settings. Nevertheless, + you can make your track offer these visibility choices by turning canPack on. Note: subtracks of composites + will always offer all five choices.' + format: canPack <off/on> + examples: + - canPack on +- name: configureByPopup + types: + - all + roles: + - super + - composite + - view + - leaf + category: Common Settings - less frequent + context: trackDb + level: full + required: false + summary: 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... + description: '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 a configuration dialog. While this + functionality works on the majority of track types, some configuration dialogs are too complex or + have too much embedded javascript control to be reliably configured through a pop-up. To turn off + the ability to configure the track via right-click, change this setting to "off". The user will still + be able to configure the track on the track''s configuration page. DEFAULT: on.' + format: configureByPopup <on/off> + examples: + - configureByPopup off +- name: origAssembly + types: + - all + roles: + - super + - composite + - view + - leaf + category: Common Settings - less frequent + context: trackDb + level: full + required: false + summary: The original assembly version for which the dataset was generated. + description: The original assembly version for which the dataset was generated. Datasets generated by + mapping to one genome assembly may prove useful enough to map to a more recent assembly. Ideally datasets + will be regenerated to map to the new assemblies coordinates, but sometimes this is not practical + or expedient. Therefore, the dataset may have its genome coordinates "lifted over" to the more recent + assembly. In some cases this results in an inferior but nevertheless useful representation. Such datasets + should have their original assembly defined with this setting. + format: origAssembly <db> + examples: + - origAssembly hg18 - name: altColor types: - all roles: - super - composite - view - leaf category: Common Settings - less frequent context: trackDb level: full required: false summary: Many track types allow setting a color range that varies from color to altColor . description: Many track types allow setting a color range that varies from color to altColor . For instance the CpG Island tracks use the altColor setting to display the weaker islands, while the stronger ones @@ -1125,30 +1189,44 @@ - bigBarChart roles: - leaf category: bigBarChart context: trackDb level: new required: false summary: 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. description: 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. It works with the barChartStatsUrl. The comma-separated list of columns refer to column names in the tab-separated-value file specified by barChartStatsUrl. See an example with images of barChartFacets on the barChart help page . format: barChartFacets <column1,column2,...columnN> examples: [] +- name: barChartMatrixUrl + types: + - bigBarChart + roles: + - leaf + category: bigBarChart + context: trackDb + level: full + required: false + summary: Specifies a data matrix file that provides data values for all samples. + description: Specifies a data matrix file that provides data values for all samples. Used together with + barChartSampleUrl to generate a box plot on the details page. + format: barChartMatrixUrl <url> + examples: [] - name: barChartStatsUrl types: - bigBarChart roles: - leaf category: bigBarChart context: trackDb level: new required: false summary: This setting associates a table in tab-separated-values with the barchart, with one line per bar. description: 'This setting associates a table in tab-separated-values with the barchart, with one line per bar. The first line of the file contains the table column names. The first column contains the name of the bar. The other columns can be in any order. If a color column is present it will be used for the colors of the bars using the hexadecimal #RRGGBB format. (Currently the same names and colors @@ -1570,55 +1648,64 @@ visualization is rendered by an ES6 module loaded on demand when the details page is viewed. The setting name has three dot-separated parts: The <jsonConfig> value is a JSON object with configuration for the visualization, such as titles and axis labels. Its keys are merged into the data object passed to the JavaScript function. Multiple fields can be visualized by using multiple detailsScript settings with different field names. Fields sharing the same <plotType> are grouped together and passed to a single JavaScript function call. The currently available plot type is histogram , which draws an SVG bar chart from data encoded as space-separated key=value pairs (logfmt format). The histogram plot type accepts the following JSON config keys: title (chart heading) and xLabel (x-axis label).' format: detailsScript.<plotType>.<fieldName> <jsonConfig> examples: - 'detailsScript.histogram.afrHist {"title":"AFR Allele Frequencies","xLabel":"Allele size (repeat copies)"} detailsScript.histogram.eurHist {"title":"EUR Allele Frequencies","xLabel":"Allele size (repeat copies)"}' - name: exonArrows types: - - genePred - bed + - bigBed + - genePred + - bigGenePred + - psl + - bigPsl + - chain + - bigChain + - narrowPeak + - bigNarrowPeak - broadPeak roles: - leaf category: bigBed - Item or Region Track Settings context: trackDb level: full required: false summary: 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. description: 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. Exon arrows are typically shown by default in these types of tracks, with the exception of tracks in the Regulation group. The arrows can be explicitly shown or hidden using this setting. format: exonArrows <on/off> examples: - exonArrows off - name: exonNumbers types: - genePred + - bigGenePred - bed - - psl - bigBed - - bigGenePred + - psl + - bigPsl roles: - leaf category: bigBed - Item or Region Track Settings context: trackDb level: full required: false summary: A mouseover that shows the exon and intron numbers can be explicitly shown or hidden using this setting. description: A mouseover that shows the exon and intron numbers can be explicitly shown or hidden using this setting. The default is "on" for the track types genePred and bigGenePred. format: exonNumbers <on/off> examples: - exonNumbers off - name: scoreFilter types: @@ -1659,127 +1746,135 @@ summary: Maximum number of items to display individually in full or pack or squish mode. description: 'Maximum number of items to display individually in full or pack or squish mode. When the maximum is exceeded, the track switches to coverage mode. Default: 1000. For type bigBed tracks, this setting can never be larger than the hg.conf setting bigBedMaxItems, which by default is 100,000 at UCSC. bigBedMaxItems is configured globally for a Genome Browser server and sets an upper limit on how many features can be loaded at most from a bigBed file, to avoid a single track making a Genome Browser view unusable at high zoom levels so it the upper limit for all maxItems settings of any tracks shown on a Genome Browser. If you have feedback on these values, please do not hesitate to contact us.' format: maxItems <integer> examples: - maxItems 25 - name: maxWindowCoverage types: - bed + - bigBed - genePred - - bam - - rmsk + - bigGenePred + - psl + - bigPsl + - chain + - bigChain - narrowPeak + - bigNarrowPeak - broadPeak - - bigWig + - bam + - rmsk - bedLogR + - vcf + - vcfTabix roles: - leaf category: bigBed - Item or Region Track Settings context: trackDb level: full required: false summary: 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... description: 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 will switch the track into density coverage plot when the window contains more than the specified number of bases. format: maxWindowCoverage <integer> examples: - maxWindowCoverage 10000000 - name: maxWindowToDraw types: - - bed - - genePred - - bam - - rmsk - - narrowPeak - - broadPeak - - bigWig - - bedLogR + - all roles: - leaf category: bigBed - Item or Region Track Settings context: trackDb level: full required: false summary: 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... description: 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 will trigger a choice to display a message asking users to zoom in to a smaller region. Depending on the current visibility of the bed track and which other tracks are being shown concurrently, the Browser may automatically reduce the display to pack or dense mode in some cases. The maxWindowToDraw setting allows you to force users to zoom in as an overriding message will block out the data display. Unlike the maxItems setting, which controls the display of vertical space and forces a display to dense when the maximum number of items is exceeded, the maxWindowToDraw setting dictates the number of bases to be displayed in a window before the track is obscured with a message explaining the requirement for zooming-in. Even without this setting, there are browser operations that will ultimately prevent too many items from being displayed by forcing a visualized summary in dense mode as noted. format: maxWindowToDraw <integer> examples: - maxWindowToDraw 10000000 - name: minGrayLevel types: - bed + - bigBed - broadPeak - narrowPeak + - bigNarrowPeak - bedLogR - - bigBed + - bigInteract roles: - leaf category: bigBed - Item or Region Track Settings context: trackDb level: full required: false summary: 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... description: 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 specifies the lightest shade to be used. This prevents the lowest scores from being displayed in too light of a color to easily view. Set the value in the range 1 - 9, lightest to darkest. format: minGrayLevel <1-9> examples: - minGrayLevel 4 - name: noScoreFilter types: - bed + - bigBed - bedGraph - bedLogR - gvf roles: - leaf category: bigBed - Item or Region Track Settings context: trackDb level: full required: false summary: By default, bed tracks with 5 or more standard bed fields that contain either a ' . description: By default, bed tracks with 5 or more standard bed fields that contain either a ' . ' or a ' + ' in the type setting will be filterable on score ; that is, they will have an assumed setting of " scoreFilter 0 ". To turn this old-style default off, include the " noScoreFilter " setting. format: noScoreFilter on examples: - "type bigBed 6 +\n noScoreFilter on" - name: spectrum types: - - all + - bed + - bigBed + - bigGenePred + - psl + - bigPsl roles: - leaf category: bigBed - Item or Region Track Settings context: trackDb level: base required: false summary: Replaces useScore . description: 'Replaces useScore . If your track is a bed 5 or greater, then the standard bed score field exists. This score, which is expected to vary from 0-1000, can be used to control the shading of bed items drawn in the Browser image. To activate this feature, set spectrum on . Lower scores will be shaded in light gray by default, while higher scores will trend towards black. This can be modified in a number of ways: Note: The file type must be type bigBed x where x is at least bigBed 5. If only type bigBed is used, the setting will not work as it is assumed to be a bigBed 3.' format: spectrum on examples: @@ -2089,30 +2184,65 @@ disable that default filter In order for filters to work, the track must be " type bigBed N + " or " type bigBed N . ". Including the "+" (for bigBed+ tracks) or a "." (for non-extended bigBed tracks) is required Filters are not supported in bed3 or bed4 files, even bed 3+x. The file must be at least a bed5 There should not be any white spaces between declared items after commas, e.x. "itemOne,itemTwo,itemThree" The default label can be customized with the filterLabel.<fieldName> parameter When using filter values in a field that incudes commas, an additional comma can be used to escape it. E.x. "fieldOne,fieldTwo,,fieldTwo,fieldThree"' format: filterValues.<fieldName> <value1,value2,value3...> examples: - filterValues.fieldName fieldValue1|alternativeName1,fieldValue2|alternativeName2... - filterValues.OddEven Odd,Even - "filterValues.OddEven Odd,Even\n filterType.OddEven singleList" - "filterValues.OddEven Odd,Even\n filterType.OddEven singleList\n filterValuesDefault.OddEven\ \ Odd" - filterValues.annotationType DNA-BR,AS,BS,BSi - filterValues.annotationType DNA-BR|DNA-binding region,AS|active site,BS|beta strand,BSi|binding site +- name: filterBy + types: + - bed + - bigBed + - genePred + - bigGenePred + - psl + - bigPsl + - bigLolly + - factorSource + roles: + - leaf + category: bigBed - Item or Region Track Settings + context: trackDb + level: full + required: false + summary: Another method of filtering items relies upon discrete values. + description: 'Another method of filtering items relies upon discrete values. One or more fields such + as name or score may contain a limited number of discrete values that can be filtered on. These discrete + values will be displayed in a dropdown list from which the user can choose one or more options. While + the maximum number of options in the list is not limited, displaying too many options can be confusing + for the user. Setting complexities: Because of this complexity, please remember to use the '' \ '' + continuation line to ensure the setting is readable: It is probable that this setting will be redefined + at some point, given that it is very complicated. However, this current format will be supported until + entirely replaced. The best way to understand this setting is with an example. This is an operational + example in the hg19 "Open Chrom Synth" track.' + format: "filterBy <field1:title=[+]opt1a...>\n [field2:title=[+]opt2a...]" + examples: + - "filterBy {field1}[:{Title1}]=[+]\\\n option1a[|label1a[{style1a}]],\\\n option1b[|label1b[{style1b}]],...\ + \ \\\n [{field2}[:{Title2}]=[+]\\\n option2a[|label2a[{style2a}]],,...]" + - "filterBy color:Validation_Level=\\\n 0|Validated_(OC_1){color:#000000},\\\n \ + \ 255|Open_Chromatin_(OC_2-3){color:#0000FF},\\\n 39168|DNase_low_(OC_2){color:#009900},\\\ + \n 10027008|FAIRE_low_(OC_3){color:#990000},\\\n 16711935|ChIP-seq_(OC_4){color:#FF00FF}\ + \ \\\n ocCode:OC_Code=+\\\n One:_Validated_(all),\\\n Two:_DNase_(all),\\\ + \n Three:_FAIRE_(all),\\\n Four:_ChIP_(all)" - name: filterLabel types: - bed - bigBed roles: - leaf category: bigBed - Item or Region Track Settings context: trackDb level: full required: false summary: When a user clicks on a track item in the Browser image, the item detail page is shown. description: 'When a user clicks on a track item in the Browser image, the item detail page is shown. This setting specifies an alternate label for the filter on that page. Without this setting, the label will be the description of the field as specified by the autoSql (.as) file. Some of the parameters modified by this are: filter.<fieldName> filterText.<fieldName> filterValues.<fieldName>' @@ -2275,46 +2405,58 @@ - leaf category: Item or Region Track Settings - less frequent context: trackDb level: full required: false summary: When a user clicks on a bed track item in the Browser image, the item detail page is shown. description: When a user clicks on a bed track item in the Browser image, the item detail page is shown. This setting specifies an alternate label for the item name on that page. Without this setting, the label will be "Item:". format: bedNameLabel <label> examples: - bedNameLabel Gene Id - name: exonArrowsDense types: - bed + - bigBed + - genePred + - bigGenePred + - psl + - bigPsl + - chain + - bigChain + - narrowPeak + - bigNarrowPeak + - broadPeak + - bam roles: - leaf category: Item or Region Track Settings - less frequent context: trackDb level: full required: false summary: On tracks that show exons or blocks within items, exon arrows allow the user to jump to the next exon/block outside the image. description: On tracks that show exons or blocks within items, exon arrows allow the user to jump to the next exon/block outside the image. Use this setting to display exon arrows even when the track is in dense mode. format: exonArrowsDense <off/on> examples: [] - name: itemImagePath types: - bed + - bigBed roles: - leaf category: Item or Region Track Settings - less frequent context: trackDb level: full required: false summary: Items can be associated with images and the images can be made visible with these two settings. description: Items can be associated with images and the images can be made visible with these two settings. The itemImagepath specifies a URL path to a directory with image files named in the format {name}.{suffix} . The name is retrieved from the table or remote data file. This image will be displayed on the item detaiIs page. If itemBigImagePath is also supplied, then a link to a larger image will be provided. If the path provided is local to the browser then the path should be relative. format: itemImagePath <path> <suffix> examples: - "itemImagePath images/myTrackImages png\n itemBigImagePath http://bigImages.com/myTrackImages jpg" @@ -2346,31 +2488,41 @@ - leaf category: Item or Region Track Settings - less frequent context: trackDb level: full required: false summary: This setting changes the meaning of the bed name field to "identifier description". description: This setting changes the meaning of the bed name field to "identifier description". If it is activated, the browser does not show the first word of the BED item name, but uses this first word for linking out to the item detail page. This allows putting both an identifier, like a gene ID, and its human-readable description into the BED item name field, separated by a space. format: linkIdInName on examples: - linkIdInName on - name: nextExonText types: - - all + - bed + - bigBed + - genePred + - bigGenePred + - psl + - bigPsl + - chain + - bigChain + - narrowPeak + - bigNarrowPeak + - broadPeak roles: - leaf category: Item or Region Track Settings - less frequent context: trackDb level: full required: false summary: For tracks that offer multiple block items such as gene models, the next/previous exon arrows are usually displayed by default in the Browser. description: For tracks that offer multiple block items such as gene models, the next/previous exon arrows are usually displayed by default in the Browser. The functionality of these tiny arrows is described by mouse-over "tool tips" that default to "Next Exon" and "Prev Exon". If the blocks do not represent exons, you can adjust the tool tip text to the appropriate information with these two settings. format: nextExonText <str> examples: @@ -2428,75 +2580,147 @@ format: type bigChain targetDb examples: [] - name: linkDataUrl types: - bigChain roles: - leaf category: bigChain - Pairwise Alignments context: trackDb level: full required: true summary: The location of a remote data file containing the chain link data. description: The location of a remote data file containing the chain link data. format: linkDataUrl <url/relativePath> examples: [] +- name: chainColor + types: + - chain + - bigChain + roles: + - leaf + category: bigChain - Pairwise Alignments + context: trackDb + level: full + required: false + summary: By default chains are colored by the alignment chromosome of the query species. + description: 'By default chains are colored by the alignment chromosome of the query species. This can + be overridden with this setting. The three options are: This setting affects chain but not netAlign + type tracks.' + format: chainColor <scheme> + examples: + - chainColor Black +- name: chainNormScoreAvailable + types: + - chain + - bigChain + - netAlign + - bed + roles: + - leaf + category: bigChain - Pairwise Alignments + context: trackDb + level: full + required: false + summary: A given chain or netAlign track may or may not have a populated normScore column. + description: A given chain or netAlign track may or may not have a populated normScore column. If the + column exists, then its value can be displayed in the item details page of the Browser by setting + chainNormScoreAvailable to yes . Item coloring based upon score as selected by the chainColor Normalized + Score setting also requires this setting to be yes . + format: chainNormScoreAvailable <yes/no> + examples: + - "chainNormScoreAvailable yes\n chainColor Normalized Score" - name: baseColorUseSequence types: - - all + - bed + - bigBed + - genePred + - psl + - bigPsl + - chain + - bigChain + - bam roles: - leaf category: bigChain - Pairwise Alignments context: trackDb level: full required: false summary: 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... description: 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 small region. format: "baseColorUseSequence <extFile {seqTable} /\n hgPcrResult / lfExtra / nameIsSequence\ \ / seq1Seq2 / ss / 2bit >" examples: [] - name: baseColorDefault types: - - all + - bed + - bigBed + - genePred + - bigGenePred + - psl + - bigPsl + - chain + - bigChain + - bam roles: - leaf category: bigChain - Pairwise Alignments context: trackDb level: full required: false summary: Specifies the default drawing mode. description: Specifies the default drawing mode. The itemBases , itemCodons , diffBases and diffCodons options are applicable only if the track has sequence, as specified by the baseColorUseSequence setting. The genomicCodons , itemCodons and diffCodons are applicable only if the track has CDS info, as specified by the baseColorUseCds setting. format: "baseColorDefault\n <diffBases/diffCodons/itemBases/itemCodons/genomicCodons>" examples: [] - name: bigGenePred types: - bigGenePred roles: - leaf category: bigGenePred - Gene Annotations context: trackDb level: null required: false summary: '' description: '' format: type bigGenePred examples: [] +- name: intronGap + types: + - genePred + - bigGenePred + - psl + - bigPsl + roles: + - leaf + category: bigGenePred - Gene Annotations + context: trackDb + level: full + required: false + summary: In drawing gene models, it can be useful to see "exon arrows" when the transcript extends beyond + the current window. + description: In drawing gene models, it can be useful to see "exon arrows" when the transcript extends + beyond the current window. This setting, which defaults to zero, ensures that these arrows will not + be drawn if the interceding intron gap is less than the stated number of bases. + format: intronGap <#bases> + examples: + - intronGap 12 - name: bigInteract types: - bigInteract roles: - leaf category: bigInteract context: trackDb level: null required: false summary: '' description: '' format: type bigInteract examples: [] - name: interactDirectional types: @@ -2585,57 +2809,171 @@ types: - bigMaf roles: - leaf category: bigMaf - Multiple Alignments context: trackDb level: null required: false summary: '' description: '' format: type bigMaf examples: [] - name: speciesOrder types: - wigMaf - - bed + - bigMaf roles: - leaf category: bigMaf - Multiple Alignments context: trackDb level: full required: false summary: Use speciesOrder to declare the order of the stacked alignments. description: Use speciesOrder to declare the order of the stacked alignments. If there are many species in your track, it may make sense to use the speciesGroups setting instead. format: speciesOrder <species1> [species2 ...] examples: [] - name: speciesLabels types: - wigMaf - - bed + - bigMaf roles: - leaf category: bigMaf - Multiple Alignments context: trackDb level: new required: false summary: Use speciesLabels to specify new labels that map to sequence names. description: Use speciesLabels to specify new labels that map to sequence names. format: speciesLabels <species1=newLabel1> [species2=newLabel2 ...] examples: - speciesLabels mm10=mouse_mm10 mm39=mouse_mm39 +- name: pairwiseHeight + types: + - wigMaf + - bigMaf + roles: + - leaf + category: bigMaf - Multiple Alignments + context: trackDb + level: full + required: false + summary: A wigMaf display in the Browser image is a stacked set of pairwise alignments to the target + genome. + description: A wigMaf display in the Browser image is a stacked set of pairwise alignments to the target + genome. Using this setting, you can change the height of each pairwise signal in the image. + format: pairwiseHeight <#> + examples: + - pairwiseHeight 10 +- name: speciesGroups + types: + - wigMaf + - bigMaf + roles: + - leaf + category: bigMaf - Multiple Alignments + context: trackDb + level: full + required: false + summary: You can include a list of "clades" to group the species into. + description: You can include a list of "clades" to group the species into. This option is an alternative + to speciesOrder , used when there are many species. Each speciesGroup in the list must have its own + setting (sGroup_<group>), followed by a list of species, specified as for speciesOrder. + format: speciesGroups <sgroup1> [sgroup2 ...] + examples: + - "speciesOrder panTro1 canFam1 mm5 rn3 \\\n galGal2 fr1 danRer1\n speciesGroups\ + \ Mammal Vertebrate\n sGroup_Mammal mm9 rn4\n sGroup_Vertebrate galGal2 fr1 danRer1" +- name: speciesDefaultOff + types: + - wigMaf + - bigMaf + roles: + - leaf + category: bigMaf - Multiple Alignments + context: trackDb + level: full + required: false + summary: 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... + description: 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 displayed. Each species is specified + as in the MAF file Organism names except embedded dots and/or spaces are replaced with underscores + (e.g. C. elegans -> c_elegans). + format: speciesDefaultOff <species1> [species2 ...] + examples: + - speciesDefaultOff galGal2 fr1 danRer1 +- name: speciesCodonDefault + types: + - wigMaf + - bigMaf + roles: + - leaf + category: bigMaf - Multiple Alignments + context: trackDb + level: full + required: false + summary: This setting, which is used with "frames", declares the default species for the codon reading + frame. + description: This setting, which is used with "frames", declares the default species for the codon reading + frame. + format: speciesCodonDefault <species> + examples: + - "speciesCodonDefault hg19\n frames myCodonFrames" +- name: itemFirstCharCase + types: + - wigMaf + - bigMaf + roles: + - leaf + category: bigMaf - Multiple Alignments + context: trackDb + level: full + required: false + summary: This controls if species names in the multiple alignment should be capitalized in the pairwise + display. + description: This controls if species names in the multiple alignment should be capitalized in the pairwise + display. Set " noChange " to avoid forcing the first letter to lower case. + format: itemFirstCharCase noChange + examples: + - itemFirstCharCase noChange +- name: irows + types: + - wigMaf + - bigMaf + roles: + - leaf + category: bigMaf - Multiple Alignments + context: trackDb + level: full + required: false + summary: 'By default, gaps in the non-reference species are filled with the placeholder character: Single + Line '' - '': No bases in the aligned species.' + description: 'By default, gaps in the non-reference species are filled with the placeholder character: + Single Line '' - '': No bases in the aligned species. Possibly due to a lineage-specific insertion + between the aligned blocks in the human genome or a lineage-specific deletion between the aligned + blocks in the aligning species. Double line '' = '': Aligning species has one or more unalignable + bases in the gap region. Possibly due to excessive evolutionary distance between species or independent + indels in the region between the aligned blocks in both species. Pale yellow coloring : Aligning species + has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, + due to lack of sequence in relevant portions of the aligning species. These display conventions make + it easier to visualize the columns in stacked alignments, but they also tend to clutter the display. + The user has the option to remove these placeholders by unchecking the "Display chains between alignments" + option. To set the default of this option to off, set irows to " off ".' + format: irows off + examples: + - irows off - name: frames types: - wigMaf - bigMaf roles: - leaf category: bigMaf - Multiple Alignments context: trackDb level: full required: false summary: A wigMaf or bigMaf track can display gene codon translation. description: A wigMaf or bigMaf track can display gene codon translation. The reading frame may differ between species. By providing the reading frames information in a separate table, the user can choose which frame to use when viewing the data. For bigMaf the value is expected to be a bigBed, for wigMaf it should be a table. Read about bigMaf supporting files on the help page. @@ -2667,31 +3005,33 @@ types: - bigNarrowPeak roles: - leaf category: bigNarrowPeak - Peaks context: trackDb level: null required: false summary: '' description: '' format: type bigNarrowPeak examples: [] - name: Filter types: - bed + - bigBed - narrowPeak + - bigNarrowPeak - broadPeak roles: - leaf category: bigNarrowPeak - Peaks context: trackDb level: full required: false summary: A number of numerical filters are available for bed tracks. description: 'A number of numerical filters are available for bed tracks. These are conveniently named by the field that is filtered on. The most common numerical filter is based on the standard bed field score , and is thus controlled by the scoreFilter setting. Other examples are pValueFilter, qValueFilter and signalFilter, which are filters on non-standard bed fields defined in the broadPeak and narrowPeak formats. These numerical filter settings should include the default value. If the numeric field is floating point, the default should contain at least one decimal place. By default the range of values for a numeric filter is 0 to 1000. However, you can explicitly set the upper and lower limits of the @@ -2708,112 +3048,136 @@ types: - bigPsl roles: - leaf category: bigPsl - Pairwise Alignments context: trackDb level: null required: false summary: '' description: '' format: type bigPsl examples: [] - name: baseColorUseCds types: - bed + - bigBed - genePred + - bigGenePred - psl - bigPsl roles: - leaf category: bigPsl - Pairwise Alignments context: trackDb level: full required: false summary: Specifies where coding sequence (CDS) coordinates can be found (if any) so that codons can be drawn when viewing a sufficiently small region. description: Specifies where coding sequence (CDS) coordinates can be found (if any) so that codons can be drawn when viewing a sufficiently small region. format: baseColorUseCds <given> examples: - baseColorUseCds given -- name: showDiffBasesAllScales +- name: baseColorTickColor types: - - all + - bed + - bigBed + - psl + - bigPsl roles: - leaf category: bigPsl - Pairwise Alignments context: trackDb level: full required: false - summary: Show base differences for all zoom levels. - description: Show base differences for all zoom levels. - format: showDiffBasesAllScales on - examples: [] -- name: pslSequence + summary: Sets the color of the tick marks that mark where item bases differ from the genome. + description: 'Sets the color of the tick marks that mark where item bases differ from the genome. Those + marks appear when the track draws with baseColorDefault diffBases and the view is zoomed out past + base level. Their default color is red. Both values are worked out from the item''s own color, so + this setting does nothing unless the track gives each item a color. In a hub the way to do that is + colorByStrand . Without it the setting is read and ignored, and the tick marks stay red. itemRgb does + not count here: it colors an item as it is drawn, but it does not give the track the per-item color + this setting reads.' + format: baseColorTickColor <lighterShade/contrastingColor> + examples: + - "colorByStrand 0,0,200 200,0,0\n baseColorDefault diffBases\n baseColorTickColor contrastingColor" +- name: showDiffBasesAllScales types: + - bed + - bigBed + - genePred - psl + - bigPsl + - chain + - bigChain + - bam roles: - leaf category: bigPsl - Pairwise Alignments context: trackDb - level: new + level: full required: false - summary: This setting specifies some display configuration options for psl tracks that also have sequence - loaded. - description: 'This setting specifies some display configuration options for psl tracks that also have - sequence loaded. all : Display nucleotide labels on all bases. different : Label only base differences. - no : Allow the user to select which of the other two options is preferred.' - format: pslSequence <no/all/different> - examples: - - pslSequence different + summary: Show base differences for all zoom levels. + description: Show base differences for all zoom levels. + format: showDiffBasesAllScales on + examples: [] - name: showCdsAllScales types: - psl + - bigPsl roles: - leaf category: bigPsl - Pairwise Alignments context: trackDb level: new required: false summary: Show CDS for PSL tracks at all zoom levels. description: Show CDS for PSL tracks at all zoom levels. format: showCdsAllScales on examples: [] - name: showCdsMaxZoom types: - psl + - bigPsl roles: - leaf category: bigPsl - Pairwise Alignments context: trackDb level: new required: false summary: Use this setting (a float) to specify the maximum zoom-out allowed for displaying the CDS for psl tracks. description: Use this setting (a float) to specify the maximum zoom-out allowed for displaying the CDS for psl tracks. In conjunction with this setting, showCdsAllScales must be set on and showDiffBasesMaxZoom should be set to a value not more than showCdsMaxZoom to make this display configuration useful. format: showCdsMaxZoom <basesPerPixel> examples: - "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 ." - name: showDiffBasesMaxZoom types: - - all + - bed + - bigBed + - genePred + - psl + - bigPsl + - chain + - bigChain + - bam roles: - leaf category: bigPsl - Pairwise Alignments context: trackDb level: new required: false summary: Show annotations highlighting base or codon differences only if current zoom level does not exceed basesPerPixel (a float). description: Show annotations highlighting base or codon differences only if current zoom level does not exceed basesPerPixel (a float). showDiffBasesAllScales should also be set to make this useful. format: showDiffBasesMaxZoom <basesPerPixel> examples: [] - name: bigWig types: - bigWig @@ -2853,30 +3217,49 @@ auto-scale . With this setting, tracks within the same group will share the same y-axis scaling. This means that the maximum and minimum values on the y-axis will be determined based on the data across all tracks within the same group. This can be useful when comparing multiple tracks and wanting to ensure consistency in scaling. The default is " off " which will set the track to use vertical viewing range setting . NOTE: These options can be misleading if a noisy, low signal erroneously appears as significant because there is no high signal in the view window. To use the group option declare the setting only in the parent bigWig composite, not in the individual children tracks. For Hi-C tracks, higher interaction scores are represented with more intense colors. When this setting is set to " off ", the score at which the color reaches maximum intensity is a fixed value that can be chosen with the saturationScore trackDb setting. When this setting is set to " on ", the maximum intensity score changes dynamically depending on the values in the current viewing window. The default value for this setting is " on ". The " group " option for autoScale is not available for Hi-C tracks.' format: autoScale <off/on/group> examples: - autoScale on +- name: mouseOverFunction + types: + - wig + - bigWig + - bedGraph + roles: + - leaf + category: bigWig - Signal Graphing Track Settings + context: trackDb + level: full + required: false + summary: Limit mouse over value display to only display the fundamental values without any averaging + of multiple data points. + description: Limit mouse over value display to only display the fundamental values without any averaging + of multiple data points. Display will show "zoom in to see values" when fundamental individual values + can not be shown. Useful for tracks where averaging values together is not a valid operation. + format: mouseOverFunction <noAverage> + examples: + - mouseOverFunction noAverage - name: maxHeightPixels types: - wig - bigWig - bedGraph - bigInteract roles: - leaf category: bigWig - Signal Graphing Track Settings context: trackDb level: base required: false summary: The amount of vertical viewing space for your signal track should be declared, though it is configurable by the user. description: The amount of vertical viewing space for your signal track should be declared, though it @@ -2928,33 +3311,31 @@ roles: - leaf category: bigWig - Signal Graphing Track Settings context: trackDb level: full required: false summary: The signal can be graphed as either " points " displayed at the signal value, or the default space-filling " bar ". description: The signal can be graphed as either " points " displayed at the signal value, or the default space-filling " bar ". format: graphTypeDefault points examples: - graphTypeDefault points - name: maxWindowToQuery types: - - bed - bigWig - - bedLogR roles: - leaf category: bigWig - Signal Graphing Track Settings context: trackDb level: full required: false summary: For bigWigs only When signal data is clicked in the Browser image, the details of the signal in the current viewing window are displayed. description: For bigWigs only When signal data is clicked in the Browser image, the details of the signal in the current viewing window are displayed. For bigWigs that reference remote data, the query can be a very expensive operation if the current window is large. To avoid overburdening the Browser, the size of the window to query should be limited. The value of this setting is the maximum window size in bases that should be queried to give the detailed signal numbers. format: maxWindowToQuery <integer> examples: [] @@ -3117,43 +3498,46 @@ examples: - "yLineOnOff on\n yLineMark 2.5\n gridDefault on" - name: bigLolly types: - bigLolly roles: - leaf category: bigLolly - Lollipop charts context: trackDb level: null required: false summary: '' description: '' format: type bigLolly examples: [] -- name: noStems +- name: lollyNoStems types: - bigLolly roles: - leaf category: bigLolly - Lollipop charts context: trackDb level: full required: false - summary: '' - description: '' - format: noStems <on/off> - examples: [] + summary: Draw the lollipop heads without the stems that normally connect them to the baseline. + description: Draw the lollipop heads without the stems that normally connect them to the baseline. This + setting was documented as noStems until August 2026. That spelling never worked, because the Browser + has always read lollyNoStems . A track using noStems draws its stems as usual. + format: lollyNoStems <on/off> + examples: + - lollyNoStems on - name: lollySizeField types: - bigLolly roles: - leaf category: bigLolly - Lollipop charts context: trackDb level: full required: false summary: '' description: '' format: lollySizeField <integer> examples: [] - name: lollyMaxSize types: @@ -3416,166 +3800,175 @@ category: vcfTabix - Variant Call Format Track Settings context: trackDb level: null required: false summary: If the bigDataUrl setting is included, the data at the location specified by that URL will be displayed. description: If the bigDataUrl setting is included, the data at the location specified by that URL will be displayed. Otherwise, a database table with a single column fileName can specify the location of a local file or a URL. If the database table includes a column seqName , a different VCF file or URL can be specified for each assembly sequence. format: type vcfTabix examples: [] - name: hapClusterEnabled types: - vcf + - vcfTabix roles: - leaf category: vcfTabix - Variant Call Format Track Settings context: trackDb level: full required: false summary: If the VCF file includes genotype columns for at least two individuals, then a haplotype sorting display is enabled by default. description: If the VCF file includes genotype columns for at least two individuals, then a haplotype sorting display is enabled by default. This option can be used to disable it if desired, for example if the genotypes have not been phased and a significant portion of the genotypes are heterozygous. More information about the haplotype sorting display can be found on our Configuring VCF tracks page. format: hapClusterEnabled <true|false> examples: [] - name: hapClusterMethod types: - vcf + - vcfTabix roles: - leaf category: vcfTabix - Variant Call Format Track Settings context: trackDb level: full required: false summary: 'Assuming hapClusterEnabled is true , this specifies how genotypes are ordered for display: centerWeighted : For diploid organisms, this separates the two hap...' description: 'Assuming hapClusterEnabled is true , this specifies how genotypes are ordered for display: centerWeighted : For diploid organisms, this separates the two haplotypes from each sample and dynamically clusters all haplotypes by similarity, weighted by proximity to a central variant. The clustering tree will be drawn in the left label area. This works best for phased genotypes. fileOrder : Genotypes are displayed in the order in which they appear in the VCF file. treeFile url : Genotypes are displayed in the order in which they appear in url , a Newick -formatted tree file whose leaf node IDs are the same as the genotype column IDs in the VCF file. The tree will be drawn in the left label area.' format: hapClusterMethod <centerWeighted|fileOrder|treeFile url > examples: [] - name: hapClusterColorBy types: - vcf + - vcfTabix roles: - leaf category: vcfTabix - Variant Call Format Track Settings context: trackDb level: full required: false summary: 'Assuming hapClusterEnabled is true , this specifies one of three ways that reference and alternate alleles are colored: altOnly : reference allele is white (...' description: 'Assuming hapClusterEnabled is true , this specifies one of three ways that reference and alternate alleles are colored: altOnly : reference allele is white (invisible), alternate allele is black. This emphasizes haplotypes with alternate alleles. (default) function : If the geneTrack setting is also provided, then reference allele is white (invisible) and alternate allele is red if the variant changes the protein sequence of a gene, green if the variant falls within a gene but does not change the protein sequence, blue if the variant falls within the UTR of a protein-coding gene or within a non-coding gene, and black if intronic or intergenic. refAlt : reference allele is blue, alternate allele is red. base : A is red, C is blue, G is green and T is magenta.' format: hapClusterColorBy <altOnly|function|refAlt|base> examples: [] - name: geneTrack types: - vcf + - vcfTabix - vcfPhasedTrio roles: - leaf category: vcfTabix - Variant Call Format Track Settings context: trackDb level: full required: false summary: This is for use with hapClusterColorBy function ; it specifies the gene track to use when determining the functional effect of each variant. description: This is for use with hapClusterColorBy function ; it specifies the gene track to use when determining the functional effect of each variant. format: geneTrack < track > examples: [] - name: hapClusterTreeAngle types: - vcf + - vcfTabix roles: - leaf category: vcfTabix - Variant Call Format Track Settings context: trackDb level: full required: false summary: Assuming hapClusterEnabled is true , this controls the shape of leaf clusters on the right of the tree (i.e. description: 'Assuming hapClusterEnabled is true , this controls the shape of leaf clusters on the right of the tree (i.e. the lines drawn to denote groups of identical local haplotypes): triangle for the < shape (default), rectangle for the [ shape.' format: hapClusterTreeAngle <triangle|rectangle> examples: [] - name: hapClusterHeight types: - vcf + - vcfTabix roles: - leaf category: vcfTabix - Variant Call Format Track Settings context: trackDb level: full required: false summary: Assuming hapClusterEnabled is true , this specifies the height in pixels of the haplotype sorting display. description: Assuming hapClusterEnabled is true , this specifies the height in pixels of the haplotype sorting display. format: hapClusterHeight < N > examples: [] - name: applyMinQual types: - vcf + - vcfTabix roles: - leaf category: vcfTabix - Variant Call Format Track Settings context: trackDb level: full required: false summary: If true , then variants whose QUAL column contains a value less than the minQual setting will not be displayed. description: If true , then variants whose QUAL column contains a value less than the minQual setting will not be displayed. format: applyMinQual <true|false> examples: [] - name: minQual types: - vcf + - vcfTabix roles: - leaf category: vcfTabix - Variant Call Format Track Settings context: trackDb level: full required: false summary: Assuming applyMinQual is true , this is the minimum QUAL value required for a variant to be displayed. description: Assuming applyMinQual is true , this is the minimum QUAL value required for a variant to be displayed. Assuming applyMinQual is true , this is the minimum QUAL value required for a variant to be displayed. format: minQual < Q > examples: [] - name: minFreq types: - vcf + - vcfTabix roles: - leaf category: vcfTabix - Variant Call Format Track Settings context: trackDb level: full required: false summary: The minimum minor allele frequency required for a variant to be displayed. description: The minimum minor allele frequency required for a variant to be displayed. By default this is 0.0 (i.e. display all variants). format: minFreq < F > examples: [] - name: vcfDoFilter types: - vcf - vcfTabix @@ -4706,15 +5099,81 @@ - name: isPcr types: - all roles: - genome category: genomes file settings context: genomes level: base required: false summary: Indicates the server and port to be used for the In-Silico PCR tool. description: Indicates the server and port to be used for the In-Silico PCR tool. See our documentation for more details about setting up In-Silico PCR for your hub. format: isPcr <url> <port> examples: - isPcr yourServer.yourInstitution.edu 17779 +- name: metadata + types: + - all + roles: + - super + - composite + - view + - leaf + category: Miscellaneous Deprecated Settings + context: trackDb + level: deprecated + required: false + summary: Deprecated. + description: 'Deprecated. Use meta instead. Attaches metadata to a track as a list of name=value pairs + on one line. Wrap a value that contains spaces in double quotes. A word starting with # ends the line, + so anything after it is a comment. The pairs are shown on the track description page and on the item + details page. The meta setting replaces this one. It keeps the metadata in a single file for the whole + hub, named by metaDb or metaTab in genomes.txt , instead of repeating it in every stanza. See the + metadata guide . The Browser still reads metadata , but meta wins when a stanza has both.' + format: metadata <name=value> [<name=value> ...] + examples: + - metadata cellType=K562 antibody=CTCF lab="Broad Institute" +- name: noInherit + types: + - all + roles: + - super + - composite + - view + - leaf + category: Miscellaneous Deprecated Settings + context: trackDb + level: deprecated + required: false + summary: Deprecated. + description: Deprecated. Placed on a subtrack, this stops the subtrack from taking settings from its + composite parent. Without it a subtrack inherits the parent's type and group , plus every parent setting + the subtrack does not define itself. The Browser only checks whether the setting is present, so any + value turns it on, including noInherit off . Defining a setting on the subtrack already overrides + the inherited value, so this setting is rarely needed. + format: noInherit on + examples: + - noInherit on +- name: useScore + types: + - bed + - bigBed + - bigGenePred + - psl + - bigPsl + roles: + - leaf + category: Miscellaneous Deprecated Settings + context: trackDb + level: deprecated + required: false + summary: Deprecated. + description: Deprecated. Use spectrum instead. Shades each item by its score field, so low scores draw + in light gray and high scores draw near black. spectrum on does the same thing and is the spelling + to use in a new track. The Browser treats the two names as one setting, and scoreMin , scoreMax and + minGrayLevel tune both the same way. In a trackDb file or a hub, any value turns the shading on, including + useScore 0 , because the Browser only checks whether the setting is present. In a custom track the + value is read, and 0 turns the shading off. + format: useScore 1 + examples: + - useScore 1