a470786ea3c54bfcfac6192a0aaacdb23c02a819 jcasper Thu Apr 23 08:20:45 2026 -0700 Fixing small typo in the trackDb changes doc, refs #36320 diff --git src/hg/htdocs/goldenPath/help/trackDb/changes.html src/hg/htdocs/goldenPath/help/trackDb/changes.html index a616d45e259..e128d99adc5 100755 --- src/hg/htdocs/goldenPath/help/trackDb/changes.html +++ src/hg/htdocs/goldenPath/help/trackDb/changes.html @@ -1,181 +1,181 @@ <!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>2026-04-22</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><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>2022-05-05</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>