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 It is obsolete, but deleting the row was the wrong way to say so. 118 psl and 6 bigPsl native tracks set it, and so do three public-hub bigPsl tracks.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 The library blurb is restored too, rewritten to say the setting is obsolete and to map its three values onto baseColorDefault, which replaced it in 8d32ba75938 in 2006.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/changes.html src/hg/htdocs/goldenPath/help/trackDb/changes.html index a91db488194..6bd0d98f46e 100755 --- src/hg/htdocs/goldenPath/help/trackDb/changes.html +++ src/hg/htdocs/goldenPath/help/trackDb/changes.html @@ -1,332 +1,361 @@ <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd"> <HTML> <HEAD> <META HTTP-EQUIV="Content-Type" CONTENT="text/html;CHARSET=iso-8859-1"> <META name="description" content="UCSC Track Database Definition Changes"> <META name="keywords" content="tracDb, tracks, UCSC, bioinformatics"> <TITLE>UCSC Track Database Definition History</TITLE> <LINK REL="STYLESHEET" HREF="/style/HGStyle.css"> <LINK REL="STYLESHEET" HREF="trackDbDoc.css"> <script type="text/javascript" src="/js/jquery.js"></script> <script type="text/javascript" src="/js/staticDoc.js"></script> <script type="text/javascript" src="/js/utils.js"></script> <script type="text/javascript" src="trackDbDoc.js"></script> </HEAD> <BODY> <A NAME="TOP"></A> <!-- Format everthing inside this narrower "pageWidth" window --> <div class="pageWidth"> <!--#include virtual="../../../cgi-bin/hgMenubar"--> <!--Content Tables--> <!--outer table is for border purposes--> <div class="contentBorder"> <div class="lightBlueBar"> <div class="lightBlueBarTitle"> Track Database Definition Change History</div> </div> <!-- Finally to the content --> <div class="borderGuard"> <DIV class="trackDbDoc_intro"> <H1>Track Database Definition</H1> <p>This document summarizes the changes to the <a href="trackDbHub.html">UCSC Genome Browser Hub TrackDb specification</a>.<p> <TABLE class="settingsTable" id="Common_Settings"> <tbody> <tr valign="TOP"> <th width="100">Date</th> <th width="15%">Track Types</th> <th width="15%">Link to Doc</th> <th>Change</th> </tr> +<tr> + <td>2026-08-31</td> + <td>bigPsl, bigGenePred, bigBarChart, bigLolly</td> + <td><a href="trackDbHub.html#searchIndex">searchIndex</a>, + <a href="trackDbHub.html#searchTrix">searchTrix</a>, + <a href="trackDbHub.html#mouseOver">mouseOver</a>, + <a href="trackDbHub.html#mouseOverField">mouseOverField</a>, + <a href="trackDbHub.html#indelDoubleInsert">indelDoubleInsert</a>, + <a href="trackDbHub.html#indelQueryInsert">indelQueryInsert</a>, + <a href="trackDbHub.html#indelPolyA">indelPolyA</a></td> + <td>Documentation fix, continuing the "For Types" corrections below. Each of these + settings works on types its entry did not name. <code>searchIndex</code> gains + <code>bigPsl</code>, <code>bigGenePred</code> and <code>bigBarChart</code>, and + <code>searchTrix</code> gains <code>bigGenePred</code>; both are read on the + bigBed-backed search path, whatever the flavor. <code>mouseOver</code> and + <code>mouseOverField</code> gain <code>bigLolly</code>. The three + <code>indel*</code> settings named only <code>bam</code> in the library, though this + page has listed them under <code>bigPsl</code> for years; they are read for every + track that draws linked features, so <code>psl</code> and <code>bigPsl</code> are + named now. <code>searchIndex</code> and <code>searchTrix</code> also drop + <code>bed</code>, which never worked: a track in one of our own database tables + configures search through the <code>hgFindSpec</code> table instead. No browser + behavior changed.</td> +</tr> <tr> <td>2026-08-28</td> <td>bigLolly</td> <td><a href="trackDbHub.html#lollyNoStems">lollyNoStems</a></td> <td>Renamed in the documentation, from <code>noStems</code>. The Browser has always read <code>lollyNoStems</code>, so a track that set <code>noStems</code> drew its stems as usual. <code>hubCheck</code> takes its list of valid settings from this page, so it accepted the spelling that did nothing and rejected the one that works. If your hub sets <code>noStems</code>, change it to <code>lollyNoStems</code>.</td> </tr> <tr> <td>2026-08-28</td> <td>all</td> <td><a href="trackDbHub.html#type">type</a></td> <td>The list of valid types on this page now shows only the types a hub can use. It had been showing the full list, which includes types that only work for tracks loaded into our own databases. The three hub types missing from the shorter list, <code>bigGenePred</code>, <code>bigNarrowPeak</code> and <code>vcfPhasedTrio</code>, have been added.</td> </tr> <tr> <td>2026-08-28</td> <td>all</td> <td><a href="trackDbHub.html#canPack">canPack</a>, <a href="trackDbHub.html#configureByPopup">configureByPopup</a>, <a href="trackDbHub.html#origAssembly">origAssembly</a></td> <td>Now listed on this page, and no longer marked as unavailable to hubs. The Browser reads all three from a hub's trackDb the same way it reads them from ours, so the old note was wrong. <code>canPack</code> is still marked deprecated: the track type usually decides whether pack and squish are offered, so you rarely need to set it.</td> </tr> <tr> <td>2026-08-28</td> <td>bigMaf, bigGenePred</td> <td><a href="trackDbHub.html#speciesGroups">speciesGroups</a>, <a href="trackDbHub.html#speciesDefaultOff">speciesDefaultOff</a>, <a href="trackDbHub.html#speciesCodonDefault">speciesCodonDefault</a>, <a href="trackDbHub.html#itemFirstCharCase">itemFirstCharCase</a>, <a href="trackDbHub.html#irows">irows</a>, <a href="trackDbHub.html#intronGap">intronGap</a></td> <td>Now listed on this page. A bigMaf track is drawn and configured by the same code as a wigMaf track, so the five multiple-alignment settings have always worked on it, but only <code>speciesOrder</code> was documented that way. <code>intronGap</code> is read for every track type that draws linked features, bigGenePred included. Nothing about their behavior changed.</td> </tr> <tr> <td>2026-08-28</td> <td>bigBed, bigGenePred, bigPsl, bigLolly</td> <td><a href="trackDbHub.html#filterBy">filterBy</a></td> <td>Now listed on this page, and no longer marked as unavailable to hubs. The Browser applies <code>filterBy</code> to bigBed-backed tracks when it loads them, so it has worked in hubs for some time. If you avoided it because of the old note, you can use it now.</td> </tr> <tr> <td>2026-08-28</td> <td>bigBed, bigPsl</td> <td><a href="trackDbHub.html#baseColorTickColor">baseColorTickColor</a></td> <td>Now listed on this page, and no longer marked as unavailable to hubs. It has always worked in hubs. The entry now also states the requirement that was missing: the tick color is worked out from each item's own color, so the setting does nothing unless the track sets <code>colorByStrand</code>. <code>itemRgb</code> does not satisfy it.</td> </tr> <tr> <td>2026-08-28</td> <td>bigChain, bigMaf, bigBarChart, bigWig</td> <td><a href="trackDbHub.html#chainColor">chainColor</a>, <a href="trackDbHub.html#chainNormScoreAvailable">chainNormScoreAvailable</a>, <a href="trackDbHub.html#pairwiseHeight">pairwiseHeight</a>, <a href="trackDbHub.html#barChartMatrixUrl">barChartMatrixUrl</a>, <a href="trackDbHub.html#mouseOverFunction">mouseOverFunction</a></td> <td>Now listed on this page. All five have worked in hubs for years, but none had an entry here, so <code>hubCheck</code> reported them as unrecognized settings. Nothing about their behavior changed.</td> </tr> <tr> <td>2026-08-28</td> <td>bigBed, bigGenePred, bigPsl, bigChain, bigNarrowPeak, bigMaf, vcfTabix</td> <td><a href="trackDbHub.html#spectrum">spectrum</a> and 25 others</td> <td>Documentation fix: the "For Types" list was wrong for 26 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 <code>big*</code> counterpart, for example <code>noScoreFilter</code> said <code>bed</code> while its own example uses <code>type bigBed 6 +</code>, and the <code>hapCluster*</code> settings said <code>vcf</code> and not <code>vcfTabix</code>. Six others said "all" for a setting that only works on item tracks. No browser behavior changed.</td> </tr> <tr> <td>2026-08-28</td> <td>bigPsl</td> - <td>pslSequence</td> - <td>Removed. This setting has never done anything. The variable it described was - replaced by the <a href="trackDbHub.html#baseColorUseSequence">baseColorUseSequence</a> - family long before the setting was listed here. Use - <code>baseColorUseSequence</code> and - <a href="trackDbHub.html#baseColorDefault">baseColorDefault</a> instead.</td> + <td><a href="trackDbHub.html#pslSequence">pslSequence</a></td> + <td>Marked deprecated. This setting has never done anything. The variable it + described was replaced by the + <a href="trackDbHub.html#baseColorUseSequence">baseColorUseSequence</a> family long + before the setting was listed here. Use <code>baseColorUseSequence</code> and + <a href="trackDbHub.html#baseColorDefault">baseColorDefault</a> instead: + <code>pslSequence all</code> is now <code>baseColorDefault itemBases</code>, and + <code>pslSequence different</code> is now <code>baseColorDefault diffBases</code>. + The entry is kept rather than deleted so that <code>hubCheck</code> tells you the + setting is deprecated, instead of reporting it as an unrecognized setting and + guessing at a typo.</td> </tr> <tr> <td>2026-07-31</td> <td>faceted composite</td> <td><a href="trackDbHub.html#maxCheckboxes">maxCheckboxes</a></td> <td>Documentation fix: this setting was previously listed here as <code>maxCheckBoxes</code>, with a capital B. Setting names are case sensitive and the browser has always read it as <code>maxCheckboxes</code>, so hubs that used the capitalized spelling fell back to the default of 20 facet values. If your hub sets <code>maxCheckBoxes</code>, change it to <code>maxCheckboxes</code>.</td> </tr> <tr> <td>2026-07-08</td> <td><b>genomes.txt setting</b></td> <td><a href="trackDbHub.html#codonTable">codonTable</a></td> <td>New <code>codonTable</code> genome-stanza setting (an assembly hub <code>genomes.txt</code> setting, not a track setting) assigns NCBI genetic codes to individual sequences for amino acid display, e.g. <code>codonTable default=1 NC_017929.1=13</code>. Affects the base position track three-frame translation, codon-colored tracks such as gene predictions, and details pages. Sequences named chrM/chrMT still default to the vertebrate mitochondrial code.</td> </tr> <tr> <td>2026-06-02</td> <td>bigBed, bigGenePred</td> <td><a href="trackDbHub.html#colorFields">colorFields</a></td> <td>New <code>colorFields</code> setting adds a <b>Color by:</b> dropdown to the track controls page, letting users switch among multiple pre-computed color schemes stored as extra bigBed fields containing <code>R,G,B</code> strings. The special name <code>default="label"</code> renames the standard itemRgb option. When a non-default scheme is selected, a <em>(Coloring by: label)</em> suffix appears in the track long label.</td> </tr> <tr> <td>2026-05-08</td> <td>bed, bigBed</td> <td><a href="trackDbHub.html#filterPriority">filterPriority</a> / <a href="trackDbHub.html#highlightPriority">highlightPriority</a></td> <td>New <code>filterPriority.<fieldName></code> setting controls the display order of filter controls on the track configuration page. A companion <code>highlightPriority.<fieldName></code> setting orders highlight controls.</td> </tr> <tr> <td>2026-04-22</td> <td>faceted composite tracks</td> <td><a href="trackDbHub.html#subtrackUrls">subtrackUrls</a></td> <td>An update for the subtrackUrls option for faceted composites, which enables links out to other resources in the faceted table.</td> </tr> <tr> <td>2026-04-10</td> <td>vcf, vcfTabix, vcfPhasedTrio</td> <td><a href="trackDbHub.html#sampleMetadataFile">sampleMetadataFile</a></td> <td>Add per-sample metadata columns to the VCF genotype details table. Points to a tab-separated file with a <code>#sample</code> header line; columns are appended to the genotype table on the item details page.</td> </tr> <tr> <td>2026-04-08</td> <td>bigBed</td> <td><a href="trackDbHub.html#detailsScript">detailsScript</a></td> <td>Add custom JavaScript visualizations (e.g. histograms) to the item details page. An ES6 module is loaded on demand and renders into the extra fields table. First plot type: histogram, for logfmt-encoded allele frequency data.</td> </tr> <tr> <td>2026-03-09</td> <td>bigBed</td> <td><a href="trackDbHub.html#faceted_composite">faceted composite</a></td> <td>An alternate UI for composite tracks with a very large number of subtracks.</td> </tr> <tr> <td>2026-01-12</td> <td>bigBed</td> <td><a href="trackDbHub.html#style">style</a></td> <td>Activates the positional heatmap display mode for a track that meets the schema.</td> </tr> <tr> <td>2026-01-11</td> <td>hic</td> <td><a href="trackDbHub.html#hicArcLimit">hicArcLimit</a></td> <td>Limit the number of arcs displayed in a Hi-C plot, favoring those with the highest scores</td> </tr> <tr> <td>2025-03-31</td> <td>interact, bigInteract</td> <td><a href="trackDbHub.html#detailBoxesEnabled">detailBoxesEnabled</a></td> <td>Used to suppress the link/boxes in interact tracks that would go to a details page.</td> </tr> <tr> <td>2025-03-06</td> <td>hic</td> <td><a href="trackDbHub.html#bigDataUrl">bigDataUrl</a></td> <td>Added hic to the list of supported file types for bigDataUrl.</td> </tr> <tr> <td>2024-06-11</td> <td>bigBed, bigGenePred, bigChain, bigPsl</td> <td><a href="trackDbHub.html#highlight">highlightValues.*</a></td> <td>Allow user to highlight certain features in yellow, if they contain certain values in an extraField</td> </tr> <tr> <td>2024-01-22</td> <td>bigWig</td> <td><a href="trackDbHub.html#setColorWith">setColorWith</a></td> <td>Color a signal plot from a bigWig file by the ranges in a bigBed file</td> </tr> <tr> <td>2023-11-08</td> <td>bigBed, bigGenePred, bigChain, bigPsl</td> <td><a href="../decorator.html">decorator.*</a></td> <td>Semi-transparently overlay annotations, e.g. protein domains on transcripts, mutations on exons, or summits on chip-seq peaks</td> </tr> <tr> <td>2023-10-16</td> <td>bigGenePred, bigChain, bigPsl</td> <td><a href="../decorator.html">mouseOver, mouseOverField</a></td> <td>mouseOver works for all bigBed-based file formats</td> </tr> <tr> <td>2023-06-27</td> <td>all</td> <td><a href="trackDbHub.html#maxItems">maxItems</a></td> <td>Change: <tt>maxItems</tt>, increased default to 10,000, 10x more items can be shown.</td> </tr> <tr> <td>2023-04-04</td> <td>all</td> <td><a href="trackDbHub.html#downloadUrl">downloadUrl</a></td> <td>New: <tt>downloadUrl <fileType> <URL></tt><br>Shows a link where user can download a file. On the UCSC browser, the link is shown above the description page. Right now this is used for GFF files on gene tracks.</td> </tr> <tr> <td>2022-09-30</td> <td>bigBed, BAM</td> <td><a href="trackDbHub.html#doWiggle">doWiggle</a></td> <td>New: <tt>doWiggle on</tt><br>Instead of showing the features, show coverage of features, as a 'wiggle' (signal) style track. Can be switched off by the user on the track config page.</td> </tr> <tr> <td>2022-09-22</td> <td>bigGenePred</td> <td><a href="trackDbHub.html#colorByStrand">colorByStrand</a></td> <td>Change: <tt>colorByStrand</tt> can now be used by bigGenePred-type tracks.</td> </tr> <tr> <td>2022-06-30</td> <td>bigPsl, bigChain</td> <td><a href="trackDbHub.html#otherTwoBitUrl">otherTwoBitUrl</a></td> <td>New: <tt>otherTwoBitUrl <URL></tt><br>This statement allows one to store query sequences in a separate twoBit file rather than in the annotation file itself, which can reduce the size of the annotation file.</td> </tr> <tr> <td>2022-05-14</td> <td>bigWig</td> <td><a href="trackDbHub.html#logo">logo</a></td> <td>New: <tt>logo on</tt><br>Motif logo of the genome sequence, as a "dynseq" display, see <a href='../bigWig.html#Ex4'>the example</a>.</td> </tr> <tr> <td>2022-05-11</td> <td><b>genomes.txt setting</b></td> <td><a href="../assemblyHubHelp.html#chromAuthority">chromAuthority</a></td> <td>New <code>chromAuthority</code> genome-stanza setting (an assembly hub <code>genomes.txt</code> setting, not a track setting) chooses which <code>chromAlias</code> name column is displayed by default for the assembly's sequences, e.g. <code>chromAuthority ucsc</code>.</td> </tr> <tr> <td>2022-05-05</td> <td>bigMaf, maf</td> <td><a href="trackDbHub.html#logoMaf">logoMaf</a></td> <td>New: <tt>logoMaf on</tt><br>Motif logo on MAF/bigMaf alignment tracks. Zooming in on alignment shows nucleotides scaled by phyloP conservation.</td> </tr> <tr> <td>2019-05</td> <td>all</td> <td><a href="../hgTracksHelp.html#UseOneFile">useOneFile</a></td> <td><tt>useOneFile on</tt><br>Adding the 'useOneFile on' line to the hub.txt section of a hub allows the contents of all three files to be referenced inside of one file.</td> </tr> </tbody> </table> </div> </div> </BODY></HTML>