2c66cf38bdd66fd2c5cb9a5a23de69ca2c24bec5 braney Mon Aug 31 13:14:15 2026 -0700 Add the track types that a code read confirms for nine trackDb settings This is the first part of the Tier B pass on the "For Types" lists. Tier B holds the settings that real tracks use on a type the docs never mention. Usage alone is not proof, because a setting can be set on a track and do nothing there, so each row here was confirmed by finding the code that reads the setting and showing that it serves the added type. The barChart family, barChartBars, barChartLabel, barChartMetric and barChartUnit, listed bigBarChart alone. cfgTypeFromTdb sends both barChart and bigBarChart to cfgBarChart, and barChartUi.c serves the pair, so barChart is added to all four. indelDoubleInsert listed bam. One blurb covers it and indelQueryInsert and indelPolyA. indelEnabled (hui.c:1586) takes a trackDb and never looks at the type, and linkedFeaturesDrawAt calls it at simpleTracks.c:4391, so the whole linked-features family reaches it and not only bamTrack.c. psl and bigPsl are added: they are the two types with real usage, 3494 and 2338 tracks, and the hub spec has listed all three settings under bigPsl for years, so the hub page and the library have disagreed about this. mouseOver and mouseOverField gain bigLolly, which lollyTrack.c reads at lines 384 and 377. motifPwmTable gains bigBed, read on the bigBed details path at hgc/bigBedClick.c:584. logoMaf gains wig, read off tg->tdb with no type gate at wigTrack.c:2029, in a file that serves plain wig as well as bigWig. trackDbSettings.yaml and .json are regenerated. refs #37908 diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml index a2c9f30b1d1..28ce9e1236d 100644 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml @@ -513,59 +513,61 @@ resizing of iframes is not trivial, as they have to be resized with javascript, across domains. We recommend keeping the size static and to use scrollbars. Example: iframeOptions width=''800'' height=''800'' scrolling=''yes'' This example fixes the size to 800x800 pixels and activates scrollbars.' format: iframeOptions <string> examples: - iframeOptions width='800' height='800' scrolling='yes' - name: mouseOver types: - bigBed - bigPsl - bigChain - bigMaf - bigMethyl - bigNarrowPeak - bigGenePred + - bigLolly roles: - super - composite - view - leaf category: Common Settings - less frequent context: trackDb level: full required: false summary: 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... description: 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 the file. The pattern is constructed with fieldnames from the .as file, preceded by the dollar sign ($) and optional curly braces ({}), and can include arbitrary text between the field names. When field names may be prefixes or overlap with one another, as in the below example, curly braces can be used to more clearly define the field name to be used. format: mouseOver <pattern> examples: - mouseOver variant $name/$chrom:${chromStart} value $score - name: mouseOverField types: - bigBed - bigPsl - bigChain - bigMaf - bigMethyl - bigNarrowPeak - bigGenePred + - bigLolly roles: - super - composite - view - leaf category: Common Settings - less frequent context: trackDb level: full required: false summary: 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... description: 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 bigBed file. If the field is empty then the mouse over will fallback to the name field. To make this work, create a bigBed file with at least 8 columns and put the text for the mouse over into an extra bigBed field as explained in example 3 @@ -966,30 +968,32 @@ - leaf category: bam - Compressed Alignment Track Settings context: trackDb level: full required: false summary: Any bam tag can be displayed on the details page by clicking on it in the Browser image. description: Any bam tag can be displayed on the details page by clicking on it in the Browser image. The details include quality scores by default. If these scores are not relevant for this particular bam, they may be excluded from the details page with this setting. format: bamSkipPrintQualScore . examples: - bamSkipPrintQualScore . - name: indelDoubleInsert types: - bam + - psl + - bigPsl roles: - leaf category: bam - Compressed Alignment Track Settings context: trackDb level: full required: false summary: Insertion and deletion differences between tag sequences and the reference genome can be highlighted with the use of these settings. description: Insertion and deletion differences between tag sequences and the reference genome can be highlighted with the use of these settings. These options may be set by the user. format: indelDoubleInsert <off/on> examples: - "baseColorUseSequence genbank\n indelDoubleInsert on\n indelQueryInsert on\n indelPolyA on" - name: minAliQual types: @@ -1080,60 +1084,62 @@ - name: bigBarChart types: - bigBarChart roles: - leaf category: bigBarChart context: trackDb level: null required: false summary: '' description: '' format: type bigBarChart examples: [] - name: barChartBars types: + - barChart - bigBarChart roles: - leaf category: bigBarChart context: trackDb level: full required: false summary: This setting is a list of labels for the categorical variables (bars). description: This setting is a list of labels for the categorical variables (bars). It is required for this track type. format: barChartBars <label1 label2...> examples: [] - name: barChartColors types: - bigBarChart roles: - leaf category: bigBarChart context: trackDb level: full required: false summary: This setting is a list of colors, one for each category (bar). description: 'This setting is a list of colors, one for each category (bar). Colors are specified as RGB values (255,255,255 or #FFFFFF) or by name (the 16 HTML color names defined in HTML 4.01). The named HTML colors are: black, silver, gray, white, maroon, red, purple, fuchsia, green, lime, olive, yellow, navy, blue, teal, aqua.' format: barChartColors <color1 color2...> examples: [] - name: barChartLabel types: + - barChart - bigBarChart roles: - leaf category: bigBarChart context: trackDb level: full required: false summary: This setting provides a label for the category selection list. description: This setting provides a label for the category selection list. format: barChartLabel <label> examples: [] - name: barChartMaxSize types: - bigBarChart roles: @@ -1259,44 +1265,46 @@ - bigBarChart roles: - leaf category: bigBarChart context: trackDb level: new required: false summary: This setting enables the merge button inside of the faceted selections. description: This setting enables the merge button inside of the faceted selections. It is particularly useful when there are many bars and many facets. It allows bars that differ only in that one facet to be merged together. See an example with images of barChartMerge on the barChart help page . format: barChartMerge on examples: [] - name: barChartMetric types: + - barChart - bigBarChart roles: - leaf category: bigBarChart context: trackDb level: full required: false summary: This setting provides a label for details page information about the barChart values presented. description: This setting provides a label for details page information about the barChart values presented. These are typically summary values, derived from many samples (often the median value). format: barChartMetric <metric> examples: [] - name: barChartUnit types: + - barChart - bigBarChart roles: - leaf category: bigBarChart context: trackDb level: full required: false summary: The unit label is attached to values in the display, charts and plots of the track. description: The unit label is attached to values in the display, charts and plots of the track. format: barChartUnit <unit> examples: [] - name: barChartCategoryUrl types: - bigBarChart roles: @@ -3425,30 +3433,31 @@ category: bigWig - Signal Graphing Track Settings context: trackDb level: new required: false summary: Enables dynseq display , which graphs the signal as reference base nucleotide letters with their heights equal to the signal value within the bigWig track. description: Enables dynseq display , which graphs the signal as reference base nucleotide letters with their heights equal to the signal value within the bigWig track. If not sufficiently zoomed in, the bigWig will revert to bars instead of letters by default. See a working example of the logo dynseq display on the bigWig help page. format: logo on examples: - logo on - name: logoMaf types: + - wig - bigWig - bigMaf roles: - leaf category: bigWig - Signal Graphing Track Settings context: trackDb level: new required: false summary: The argument to logoMaf is the path to a MAF alignment (either a table or bigMaf). description: The argument to logoMaf is the path to a MAF alignment (either a table or bigMaf). If set and zoomed into base level, the wiggle will be drawn as a sequence logo calculated by counting the number of each nucleotide aligned to that base, which will be scaled by the value in the wiggle. format: logoMaf <url/relativePath> examples: - logoMaf https://hgdownload.gi.ucsc.edu/goldenPath/hg38/multiz470way/multiz470way.bigMaf