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/trackDbHub.v3.html src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html index 1fc0748b9bd..fc59ea703fb 100755 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html @@ -257,31 +257,31 @@
  Common trackDb settings
-
 Common Settings
track
+
type
shortLabel
longLabel
bigDataUrl <url/relativePath>
html
@@ -293,30 +293,39 @@

+ + + + + + +
 Common Optional Settings
color <red,green,blue>
priority <float>
+
canPack <off/on>
+
+
configureByPopup <on/off>
+
+
origAssembly <db>
+
altColor <red,green,blue>
boxedCfg <on/off>
chromosomes <chr1,chr2,...>
darkerLabels on
@@ -535,30 +544,35 @@
barChartSizeWindows <largeMax> <smallMin>
barChartStretchToItem on
barChartFacets on
+ +
barChartMatrixUrl <url> +
+
barChartStatsUrl on
singleCellColumnNames off
@@ -739,30 +753,34 @@ filterLimits.<fieldName> <low>[:<high>]
filterText.<fieldName> <default search string>
filterType.<fieldName> <wildcard/regexp>
filterValues.<fieldName> <value1,value2,value3...>
filterValuesDefault.<fieldName> <value1,value2,value3...>
filterType.<fieldName> <single/singleList/multiple/multipleListOr/multipleListAnd/multipleListOnlyOr/multipleListOnlyAnd>
+
+ filterBy <field1:title=[+]opt1a...> [field2:title=[+]opt2a...]
+
filterLabel.<fieldName> <label>
filterPriority.<fieldName> <number>
@@ -847,30 +865,36 @@  bigChain - Genome-wide Pairwise Alignments
type bigChain targetDb
bigDataUrl <url/relativePath>
linkDataUrl <url/relativePath>
otherTwoBitUrl <url/relativePath>
+
chainColor <scheme>
+
+
chainNormScoreAvailable <yes/no>
+
baseColorUseSequence < <extFile {seqTable} <extFile> / hgPcrResult / lfExtra / nameIsSequence / seq1Seq2 / ss / 2bit >
baseColorDefault <diffBases/diffCodons/itemBases/itemCodons/genomicCodons>
indelDoubleInsert <off/on>
indelQueryInsert <off/on>
indelPolyA <off/on>
@@ -881,30 +905,33 @@ + + + + + + +
 bigGenePred - Gene Annotations
type bigGenePred
bigDataUrl <url/relativePath>
+
intronGap <#bases>
+
baseColorDefault <diffBases/diffCodons/itemBases/itemCodons/genomicCodons>
labelFields <fieldName[,fieldName]>
defaultLabelFields <fieldName[,fieldName]>
labelSeparator <text>

Additional settings defined in other sections are also @@ -967,30 +994,48 @@  bigMaf - Multiple alignments

type bigMaf
bigDataUrl <url/relativePath>
speciesOrder <species1> [species2 …]
speciesLabels <species1=newLabel1> [species2=newLabel2 …]
+
pairwiseHeight <#>
+
+
speciesGroups <sgroup1> [sgroup2 …]
+
+
speciesDefaultOff <species1> [species2 ...]
+
+
speciesCodonDefault <species>
+
+
itemFirstCharCase noChange
+
+
irows off
+
frames <url/relativePath>
summary <tableName/url>


@@ -1026,45 +1071,45 @@ type bigPsl + - @@ -1082,30 +1127,33 @@

 bigNarrowPeak - Peaks
bigDataUrl <url/relativePath>
baseColorUseCds <given>
baseColorUseSequence < <extFile {seqTable} <extFile> / hgPcrResult / lfExtra / nameIsSequence / seq1Seq2 / ss >
baseColorDefault <diffBases/diffCodons/itemBases/itemCodons/genomicCodons>
+
baseColorTickColor <lighterShade/contrastingColor>
+
showDiffBasesAllScales on
indelDoubleInsert <off/on>
indelQueryInsert <off/on>
indelPolyA <off/on>
-
pslSequence <no/all/different>
-
showCdsAllScales on
showCdsMaxZoom <basesPerPixel>
showDiffBasesMaxZoom <basesPerPixel>
labelFields <fieldName[,fieldName]>
defaultLabelFields <fieldName[,fieldName]>
+
 bigWig - Signal graphing track settings
type bigWig <#> <#>
autoScale <off/on/group>
+
mouseOverFunction <noAverage>
+
maxHeightPixels <max:default:min>
viewLimits <lower:upper>
viewLimitsMax <lower:upper>
alwaysZero <off/on>
@@ -1164,32 +1212,32 @@

-
 bigLolly - lollipop graphs
type bigLolly
bigDataUrl <url/relativePath>
-
noStems <on/off> +
+
lollyNoStems <on/off>
lollySizeField <integer>
lollyMaxSize <integer>
lollyField <integer>
@@ -1780,32 +1828,33 @@

Miscellaneous Deprecated Settings

- - + +
SettingFor TypesNotes
metadata all
noInheritall
useScorebed, factorSource, bed5FloatScore, broadPeakReplaced with spectrum.bed, bigBed, bigGenePred, psl, bigPslReplaced with spectrum, which + sets the same flag and takes the same type list.