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 It is obsolete, but deleting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rewritten to say the setting is obsolete and to map its three values onto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.json src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.json
index cc5c25ea2c7..4cd7823d864 100644
--- src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.json
+++ src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.json
@@ -1464,47 +1464,49 @@
     "psl",
     "bigPsl"
    ],
    "level": "new",
    "fmt": "decorator.default.*",
    "ex": "",
    "desc": "Decorators allow annotation to be placed on top of BED 12+, bigBed, PSL, and bigGenePred tracks by highlighting regions and adding glyphs on top of them."
   },
   {
    "key": "searchIndex",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
-    "bed",
-    "bigBed"
+    "bigBed",
+    "bigPsl",
+    "bigGenePred",
+    "bigBarChart"
    ],
    "level": "full",
    "fmt": "searchIndex <str>",
    "ex": "searchIndex name",
    "desc": "Specifies the list of field names on which a index has been made."
   },
   {
    "key": "searchTrix",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
-    "bed",
-    "bigBed"
+    "bigBed",
+    "bigGenePred"
    ],
    "level": "full",
    "fmt": "searchTrix <url/relativePath>",
    "ex": "searchTrix url or relative path",
    "desc": "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."
   },
   {
    "key": "labelFields",
    "category": "bigBed - Item or Region Track Settings",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigBarChart",
     "bigBed",
@@ -2333,30 +2335,45 @@
    "types": [
     "bed",
     "bigBed",
     "genePred",
     "psl",
     "bigPsl",
     "chain",
     "bigChain",
     "bam"
    ],
    "level": "full",
    "fmt": "showDiffBasesAllScales on",
    "ex": "",
    "desc": "Show base differences for all zoom levels."
   },
+  {
+   "key": "pslSequence",
+   "category": "bigPsl - Pairwise Alignments",
+   "roles": [
+    "leaf"
+   ],
+   "types": [
+    "psl",
+    "bigPsl"
+   ],
+   "level": "deprecated",
+   "fmt": "pslSequence <no/all/different>",
+   "ex": "",
+   "desc": "Obsolete."
+  },
   {
    "key": "showCdsAllScales",
    "category": "bigPsl - Pairwise Alignments",
    "roles": [
     "leaf"
    ],
    "types": [
     "psl",
     "bigPsl"
    ],
    "level": "new",
    "fmt": "showCdsAllScales on",
    "ex": "",
    "desc": "Show CDS for PSL tracks at all zoom levels."
   },