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 It is obsolete, but deleting the row was the wrong way to say so. 118 psl and 6 bigPsl native tracks set it, and so do three public-hub bigPsl tracks.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 The library blurb is restored too, rewritten to say the setting is obsolete and to map its three values onto baseColorDefault, which replaced it in 8d32ba75938 in 2006.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/trackDbLibrary.shtml src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml index ad1f694d7e6..6e5550b8eaf 100644 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml @@ -2395,49 +2395,49 @@ bigBed 5. If only <b>type bigBed</b> is used, the setting will not work as it is assumed to be a bigBed 3.</p> <P><B>Example:</B></P> <pre> spectrum on scoreMin 700 scoreMax 900</pre> <P>In this example, the track description will be displayed in blue, but the track will remain a gray scale. Items with scores less than or equal to 700 will be shown in very light gray, those with scores between 700 and 900 will display in increasingly darker shades of gray, and items with scores greater than or equal to 900 above will display in black.</P> </DIV> -<DIV class="searchIndex"><span class="types bed bigBed"></span> +<DIV class="searchIndex"><span class="types bigBed bigPsl bigGenePred bigBarChart"></span> <div class="format"><code>searchIndex <str></code></div> <P> Specifies the list of field names on which a index has been made. When a user enters a string in the position search box of the browser, this index will be searched to find that name, and if the string is in the index, the user will either be navigated to that position in the browser, or if there are more than one matches of that string, will be give a list of the positions to choose from. See <A HREF="../bigBed.html#Ex3">HERE</A> for instructions on how to build an index for a bigBed file. The searchIndex setting requires the input BED data to be case-senstive sorted (<code>sort -k1,1 -k2,2n</code>), where newer versions of the tool bedToBigBed (available <a href="http://hgdownload.gi.ucsc.edu/admin/exe/">here</a>) are enhanced to catch improper input. <P><B>Example:</B></P> <pre> searchIndex name</pre> </DIV> -<DIV class="searchTrix"><span class="types bed bigBed"></span> +<DIV class="searchTrix"><span class="types bigBed bigGenePred"></span> <div class="format"><code>searchTrix <url/relativePath></code></div> <P> Specifies the URL to a TRIX file that maps free text to a set of indices that are assumed to have indicies in the associated bigBed file. See <a href="../trix.html">here</a> for instructions on how to build a TRIX file and a <a href="../hubQuickStartSearch.html">Searchable Track Hub Quick Start Guide</a> here.</li> <P><B>Example:</B></P> <pre> searchTrix url or relative path </pre> </DIV> <DIV class="style"><span class="types bigBed"></span> <div class="format"><code>style <heatmap></code></div> <P>BigBed tracks can be created with a variety of extra fields. When created according to the <a href="../heatmap.html">heatmap schema</a>, the extra fields include data to support a positional heatmap display. This setting @@ -3436,30 +3436,47 @@ than the stated number of bases.</P> <P><B>Example:</B></P> <pre> intronGap 12</pre> <P>Don't draw exon arrows when the gap between exons is 12 bases or less.</P> </DIV> <DIV class="defaultLinkedTables"><span class="types genePred bigGenePred"></span> <div class="format"><code>defaultLinkedTables <table1>[,table2...]</code></div> <P>In hgTables, when selecting output fields, display these all.joiner-linked tables by default.</P> <P><B>Example:</B></P> <pre> defaultLinkedTables kgXref</pre> </DIV> +<DIV class="pslSequence"><span class="types psl bigPsl"></span> +<div class="format"><code>pslSequence <no/all/different></code></div> + <P><I>Obsolete. The Browser does not read this setting.</I> + It selected how bases were labelled on psl tracks that also have sequence + loaded. The <code>baseColor</code> family replaced it in 2006, and nothing + has read either this spelling or the older + <code>pslSequenceBases</code> since. + <UL> + <LI><code>all</code> is now <code>baseColorDefault itemBases</code>.</LI> + <LI><code>different</code> is now <code>baseColorDefault diffBases</code>.</LI> + <LI><code>no</code> left the choice to the user, which is what happens when + <code>baseColorDefault</code> is not set.</LI> + </UL> + Both replacements need <code>baseColorUseSequence</code> to be set. Remove + <code>pslSequence</code> from a trackDb file; it has no effect.</P> +</DIV> + <DIV class="idXref"><span class="types genePred bigGenePred"></span> <div class="format"><code>idXref <idColumn> <altIdColumn></code></div> <P>By using this setting you can link alternative names to the gene models found in a genePred. This is used by the Table Browser to establish links to other tables.</P> <P><B>Example:</B></P> <pre> track knownGenes idXref kgAlias kgID alias </pre> <P>The ID in the name column of the knownGenes table is related to the alias found in the kgAlias table.</P> </DIV> <DIV class="oldToNew"><span class="types genePred"></span> <div class="format"><code>oldToNew <tableName></code></div>