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 It is obsolete, but deleting the row was the wrong way to say so. 118 psl and 6 bigPsl native tracks set it, and so do three public-hub bigPsl tracks.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 The library blurb is restored too, rewritten to say the setting is obsolete and to map its three values onto baseColorDefault, which replaced it in 8d32ba75938 in 2006.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/trackDbHub.v3.html src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html index fc59ea703fb..b220e727fb4 100755 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html @@ -1086,30 +1086,33 @@ <TR VALIGN=TOP><TD class="baseColorTickColor"><A name="baseColorTickColor"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">baseColorTickColor <lighterShade/contrastingColor></code></div> </TD></TR> <TR VALIGN=TOP><TD class="showDiffBasesAllScales"><A name="showDiffBasesAllScales"></A><IMG class='toggle detail'> <div class="format"><code class="level-full">showDiffBasesAllScales on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="indelDoubleInsert"> <A name="indelDoubleInsert"></A> <A name="indelQueryInsert"></A> <A name="indelPolyA"></A><IMG class='toggle detail'> <div class="format"> <span class="indelDoubleInsert"><code class="level-full">indelDoubleInsert <off/on></code></span><BR> <span class="indelQueryInsert"><code class="level-full">indelQueryInsert <off/on></code></span><BR> <span class="indelPolyA"><code class="level-full">indelPolyA <off/on></code></span></div> </TD></TR> + <TR VALIGN=TOP><TD class="pslSequence"><A name="pslSequence"></A><IMG class='toggle detail'> + <div class="format"><code class="level-deprecated">pslSequence <no/all/different></code></div> + </TD></TR> <TR VALIGN=TOP><TD class="showCdsAllScales"><A name="showCdsAllScales"></A><IMG class='toggle detail'> <div class="format"><code class="level-new">showCdsAllScales on</code></div> </TD></TR> <TR VALIGN=TOP><TD class="showCdsMaxZoom"><A name="showCdsMaxZoom"></A><IMG class='toggle detail'> <div class="format"><code class="level-new">showCdsMaxZoom <basesPerPixel></code></div> </TD></TR> <TR VALIGN=TOP><TD class="showDiffBasesMaxZoom"><A name="showDiffBasesMaxZoom"></A><IMG class='toggle detail'> <div class="format"><code class="level-new">showDiffBasesMaxZoom <basesPerPixel></code></div> </TD></TR> <TR VALIGN=TOP><TD class="labelFields"><IMG class='toggle detail'> <div class="format"><code class="level-full">labelFields <fieldName[,fieldName]></code></div> </TD></TR> <TR VALIGN=TOP><TD class="defaultLabelFields"><IMG class='toggle detail'> <div class="format"><code class="level-full">defaultLabelFields <fieldName[,fieldName]></code></div> </TD></TR>