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 It is obsolete, but deleting the row was the wrong way to say so. 118 psl and 6 bigPsl native tracks set it, and so do three public-hub bigPsl tracks.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 The library blurb is restored too, rewritten to say the setting is obsolete and to map its three values onto baseColorDefault, which replaced it in 8d32ba75938 in 2006.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 @@ -33,30 +33,54 @@ <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. @@ -125,36 +149,41 @@ <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>