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 It is obsolete, but deleting the row was the wrong way to say so. 118 psl and 6 bigPsl native tracks set it, and so do three public-hub bigPsl tracks.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 The library blurb is restored too, rewritten to say the setting is obsolete and to map its three values onto baseColorDefault, which replaced it in 8d32ba75938 in 2006.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/trackDbSettings.yaml src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml index 28ce9e1236d..8e7f1b36c9a 100644 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml @@ -1954,54 +1954,56 @@ that contains the decorations. decorator.default.filterValues <specification> Decorators support the same filter options that bigBed tracks do. This includes the filter , filterText , and filterValues settings, as described in the Track Hub Filters Quick Start Guide . decorator.default.mouseOver <specification> Decorators also support the same mouseOver and mouseOverField settings that can be applied to bigBed tracks. There is one more setting that is currently specific to decorators. decorator.default.maxLabelBases <integer> This setting controls a failsafe option for deactivating the drawing of decoration labels when they''re in block mode. There will also be a checkbox on the track configuration page to deactivate labels manually, but even when that is on, a track display can quickly become unintelligible if the window displayed is too large - there will simply be too many track items and too many decoration labels to process visually. maxLabelBases sets a maximum window size (in bases) for which labels will be drawn. If not set, the value will default to 200kb.' format: decorator.default.* examples: [] - name: searchIndex types: - - bed - bigBed + - bigPsl + - bigGenePred + - bigBarChart roles: - leaf category: bigBed - Item or Region Track Settings context: trackDb level: full required: false summary: Specifies the list of field names on which a index has been made. description: '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 HERE 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 ( sort -k1,1 -k2,2n ), where newer versions of the tool bedToBigBed (available here ) are enhanced to catch improper input. Example: searchIndex name' format: searchIndex <str> examples: - searchIndex name - name: searchTrix types: - - bed - bigBed + - bigGenePred roles: - leaf category: bigBed - Item or Region Track Settings context: trackDb level: full required: false summary: 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. description: '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 here for instructions on how to build a TRIX file and a Searchable Track Hub Quick Start Guide here. Example: searchTrix url or relative path' format: searchTrix <url/relativePath> examples: - searchTrix url or relative path - name: labelFields @@ -3117,30 +3119,49 @@ - psl - bigPsl - chain - bigChain - bam roles: - leaf category: bigPsl - Pairwise Alignments context: trackDb level: full required: false summary: Show base differences for all zoom levels. description: Show base differences for all zoom levels. format: showDiffBasesAllScales on examples: [] +- name: pslSequence + types: + - psl + - bigPsl + roles: + - leaf + category: bigPsl - Pairwise Alignments + context: trackDb + level: deprecated + required: false + summary: Obsolete. + description: Obsolete. The Browser does not read this setting. It selected how bases were labelled on + psl tracks that also have sequence loaded. The baseColor family replaced it in 2006, and nothing has + read either this spelling or the older pslSequenceBases since. all is now baseColorDefault itemBases + . different is now baseColorDefault diffBases . no left the choice to the user, which is what happens + when baseColorDefault is not set. Both replacements need baseColorUseSequence to be set. Remove pslSequence + from a trackDb file; it has no effect. + format: pslSequence <no/all/different> + examples: [] - name: showCdsAllScales types: - psl - bigPsl roles: - leaf category: bigPsl - Pairwise Alignments context: trackDb level: new required: false summary: Show CDS for PSL tracks at all zoom levels. description: Show CDS for PSL tracks at all zoom levels. format: showCdsAllScales on examples: [] - name: showCdsMaxZoom