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/trackDbLibrary.shtml src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml index 1a245417ff4..2d0614344d4 100644 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml @@ -1054,53 +1054,53 @@ <DIV class="sepFields"><span class="types bigBed bigPsl bigGenePred bigMethyl bigNarrowPeak bigMaf bigChain"></span> <div class="format"> <code>sepFields fieldName1,fieldName2 ...</code><BR> </div> <P>This setting changes the item details page and splits the table used for showing extra fields before any of the specified fields. It can be useful to visually separate extra fields into logical categories. </P> <P><B>Example:</B></P> <pre> sepFields pmid,spId </pre> </DIV> -<DIV class="mouseOverField"><span class="types bigBed bigPsl bigChain bigMaf bigMethyl bigNarrowPeak bigGenePred"></span> +<DIV class="mouseOverField"><span class="types bigBed bigPsl bigChain bigMaf bigMethyl bigNarrowPeak bigGenePred bigLolly"></span> <div class="format"> <code>mouseOverField <fieldName1></code><BR> </div> <P>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. </P> <P> 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 of the <a href="/goldenPath/help/bigBed.html">bigBed documentation</a>. The field name from your .as file is the field name for this statement. </P> <P><B>Example:</B></P> <pre> mouseOverField comment </pre> </DIV> -<DIV class="mouseOver"><span class="types bigBed bigPsl bigChain bigMaf bigMethyl bigNarrowPeak bigGenePred"></span> +<DIV class="mouseOver"><span class="types bigBed bigPsl bigChain bigMaf bigMethyl bigNarrowPeak bigGenePred bigLolly"></span> <div class="format"> <code>mouseOver <pattern></code><BR> </div> <P>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.</P> <P><B>Example:</B></P> <pre> mouseOver variant $name/$chrom:${chromStart} value $score </pre> @@ -3100,31 +3100,31 @@ <pre> transformFunc LOG</pre> </DIV> <DIV class="logo"><span class="types bigWig"></span> <div class="format"><code>logo on</code></div> <P>Enables <a target="_blank" href="https://kundajelab.github.io/dynseq-pages/"> dynseq display</a>, 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 <code>logo</code> dynseq display on the <a href="../bigWig.html#Ex4" target="_blank">bigWig</a> help page.</p> <P><B>Example:</B></P> <pre> logo on</pre> </DIV> -<DIV class="logoMaf"><span class="types bigWig bigMaf"></span> +<DIV class="logoMaf"><span class="types wig bigWig bigMaf"></span> <div class="format"><code>logoMaf <url/relativePath></code></div> <P>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.</p> <P><B>Example:</B></P> <pre> logoMaf https://hgdownload.gi.ucsc.edu/goldenPath/hg38/multiz470way/multiz470way.bigMaf</pre> </DIV> <DIV class="mouseOverFunction"><span class="types wig bigWig bedGraph"></span> <div class="format"><code>mouseOverFunction <noAverage></code></div> <P>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 @@ -3632,31 +3632,31 @@ bamColorMode off </pre> <P>No special coloring will be applied to items.</P> </DIV> <DIV class="bamSkipPrintQualScore"><span class="types bam"></span> <div class="format"><code>bamSkipPrintQualScore .</code></div> <P>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.</P> <P><B>Example:</B></P> <pre> bamSkipPrintQualScore .</pre> </DIV> -<DIV class="indelDoubleInsert"><span class="types bam"></span> +<DIV class="indelDoubleInsert"><span class="types bam psl bigPsl"></span> <div class="format"> <code>indelDoubleInsert <off/on></code><BR> <code>indelQueryInsert <off/on></code><BR> <code>indelPolyA <off/on></code></div> <P>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.</P> <UL> <LI> <code>indelDoubleInsert</code>: Use to highlight alignment gaps in both the target (reference) and query (tag) sequence with double (<B>=</B>) lines.</LI> <LI> <code>indelQueryInsert</code>: Use to highlight an insert in the query sequence only by drawing an orange (<B style="color:orange;">|</B>) or purple (<B style="color:purple;">|</B>) vertical line. Orange lines show unalignable regions in the middle of a sequence, @@ -5494,31 +5494,31 @@ <DIV class="motifTable"><span class="types factorSource"></span> <div class="format"><code>motifTable <table></code></div> <P> A <code>bed 6</code> table that holds motif regions to highlight within factorSource items.</P> </DIV> <DIV class="motifMapTable"><span class="types factorSource"></span> <div class="format"><code>motifMapTable <table></code></div> <P> If motif names differ from or are not unique for factorSource item names in the <code>motifTable</code>, this table can used to remap the names. This table has a simple 2 column format: char(255) factor, char(255) motif.</P> </DIV> -<DIV class="motifPwmTable"><span class="types factorSource bed6FloatScore"></span> +<DIV class="motifPwmTable"><span class="types factorSource bed6FloatScore bigBed"></span> <div class="format"><code>motifPwmTable <table></code></div> <P>When viewing the details of a factorSource track item containing a binding motif in the <code>motifTable</code>, the consensus motif sequence and sequence logo image can be displayed. This setting names the table holding the position weight matrices that provide this information.</P> </DIV> <DIV class="motifMaxWindow"><span class="types factorSource"></span> <div class="format"><code>motifMaxWindow <integer></code></div> <P>Display of highlighted motifs in a factorSource track can be limited using this setting. In large genomic regions motifs are not well distinguished in the display, and performance is improved by suppressing the feature.</P> </DIV> @@ -5832,44 +5832,44 @@ <!-- - - - - - - - bigBarChart settings - - - - - - - --> <DIV class="bigBarChart_intro"> <H3>bigBarChart: Bar charts of variables displayed on genomic regions</H3> <P> The bigBarChart format stores values of a set of variables for each genomic region in the file. BigBarChart files are created using the program bedToBigBed with a special AutoSQL file that defines the fields. The resulting files are in an indexed binary format that supports efficient remote access, so the file can be hosted on your web accessible server and displayed at UCSC. For the complete bigBarChart format definitions please see the <A HREF="../barChart.html">bigBarChart help page</A>.</P> </DIV> -<DIV class="barChartBars"><span class="types bigBarChart"></span> +<DIV class="barChartBars"><span class="types barChart bigBarChart"></span> <div class="format"><code>barChartBars <label1 label2...></code></div> <P>This setting is a list of labels for the categorical variables (bars). It is required for this track type. </P> </DIV> -<DIV class="barChartUnit"><span class="types bigBarChart"></span> +<DIV class="barChartUnit"><span class="types barChart bigBarChart"></span> <div class="format"><code>barChartUnit <unit></code></div> <P>The unit label is attached to values in the display, charts and plots of the track. </P> </DIV> -<DIV class="barChartLabel"><span class="types bigBarChart"></span> +<DIV class="barChartLabel"><span class="types barChart bigBarChart"></span> <div class="format"><code>barChartLabel <label></code></div> <P>This setting provides a label for the category selection list.</p> </P> </DIV> <DIV class="barChartMaxSize"><span class="types bigBarChart"></span> <div class="format"><code>barChartMaxSize <small/medium/large></code></div> <P>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. For dense data, it is helpful to reduce the barChart sizes, even when in relatively small genomic regions. This setting limits the size of the largest barChart to the selected value. When unset, the default value is "large". </P> </DIV> <DIV class="barChartSizeWindows"><span class="types bigBarChart"></span> @@ -5889,31 +5889,31 @@ <pre> barChartSizeWindows 500 8000</pre> <P>In this example, used when displaying barCharts on a 30,000 basepair viral genome, large charts appear in windows up to 499 bases, medium in windows from 500 to 7999 in size, and small when 8000 or more bases are shown in browser window. </P> </DIV> <DIV class="barChartStretchToItem"><span class="types bigBarChart"></span> <div class="format"><code>barChartStretchToItem on</code></div> <P>This setting extends the barCharts to cover the entire horizontal space available in the graph. This setting is typically used with bar charts with large number of bars so that it is possible to zoom in to see better the individual bars. </P> </DIV> -<DIV class="barChartMetric"><span class="types bigBarChart"></span> +<DIV class="barChartMetric"><span class="types barChart bigBarChart"></span> <div class="format"><code>barChartMetric <metric></code></div> <P>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).</p> </P> </DIV> <DIV class="barChartColors"><span class="types bigBarChart"></span> <div class="format"><code>barChartColors <color1 color2...></code></div> <P>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: <div class='dot' style='background: #000000'></div>black, <div class='dot' style='background: silver'></div>silver, <div class='dot' style='background: gray'></div>gray,