9f5a3871b95f595b5a218f0d05395a8c72d58844 braney Tue Aug 25 12:57:10 2026 -0700 remove the bigBedOnePath fallback, leaving a single bigBed load path, refs #36940 bigBedOnePath has defaulted to on since v492 and the setting has been removed from the hg.conf of the RR, Euro, Asia and hgwbeta. Drop the check and the code it guarded at all four sites: the field-count default in bigBedAddLinkedFeaturesFromExt, the method setup in commonBigBedMethods, the bedSize default in bigBedClick, and the bigBed case in hgc. The two branches in the hgc case differed only in a minimum the surviving path does not want. complexBedMethods lost its only isBigBed=TRUE caller with that branch, so drop the parameter. Retire the setting from the hg.conf catalog and its gate backlog, and repair the two hgc.c citations whose line numbers this commit shifted, refs #37925. Verified pixel-identical: 14 scenarios rendered before and after, covering the four QA sessions on the ticket plus mm10 knownGene, dbSnp155, rmsk, encRegTfbsClustered, clinvar and tandemDups. All AE=0. diff --git src/hg/utils/hgConfCatalog/hgConfCatalog.py src/hg/utils/hgConfCatalog/hgConfCatalog.py index 55981dcd176..0b666eb494b 100755 --- src/hg/utils/hgConfCatalog/hgConfCatalog.py +++ src/hg/utils/hgConfCatalog/hgConfCatalog.py @@ -244,31 +244,31 @@ note="Expose the hub API key UI. Shares its call site with " "storeUserFiles, so the two should be retired together."), h("autoBlatBigPsl", "flag", "hg/hgBlat/hgBlat.c:3377", default="FALSE", role="gate", verified=True, ticket="32751", note="Always create a custom track from BLAT results, so a result " "page can be reopened and shared. The read at hgBlat.c:2972 " "overrides the file-scope autoBigPsl, which is initialised " "FALSE at hgBlat.c:60 under the comment \"DEFAULT VALUE change " "to TRUE in future\", and eleven branches downstream test it. " "Filed as a knob until that was read, on the strength of the " "default being an identifier the harvester could not resolve; " "a flag whose own source says to flip it later is a gate."), h("blatShowLocus", "flag", "hg/hgBlat/hgBlat.c:1165", default="FALSE", role="gate", verified=True, note="Show the genomic locus alongside BLAT results."), - h("modernAlignPage", "flag", "hg/hgc/hgc.c:9390", default="FALSE", + h("modernAlignPage", "flag", "hg/hgc/hgc.c:9377", default="FALSE", role="gate", verified=True, ticket="37893", note="Use the modern single-page base-by-base alignment view (the one " "hgBlat's new results page uses) for ordinary alignment clicks too " "- mRNA/EST, PSL and similar hgc details - instead of the classic " "two-frame <frameset>. Off during QA; flip to TRUE once released."), h("blatNewPageBanner", "flag", "hg/hgBlat/hgBlat.c:845", default="FALSE", role="gate", verified=True, note="The banner on the classic BLAT results page that offers a " "one-click switch to the new sortable table display. Guards " "the advertisement, not the feature: turning it on makes the " "browser recommend the new page without releasing new CGIs, " "and users who already opted in or follow a direct link get " "the new page either way. Goes away with the banner, once the " "new page is the default. Born TRUE at c683ecb63d7 and put " "back to FALSE at 81d7cff6cb6 while the new page is still " @@ -353,35 +353,30 @@ default="TRUE", role="gate", verified=True, note="Merge behaviour for recommended track sets. Public since " "v467."), h("svgBarChart", "flag", "hg/hgc/barChartClick.c:588", default="TRUE", role="gate", verified=True, note="SVG rather than raster bar charts on the details page. " "Public since v428, the longest-shipped gate still in place."), h("canDoHgcInPopUp", "flag", "hg/hgTracks/config.c:837", default="TRUE", role="gate", verified=True, note="Details pages in a popup instead of a page load. Public " "since v492. Three call sites."), h("greyBarIcons", "flag", "hg/hgTracks/hgTracks.c:10479", default="TRUE", role="gate", verified=True, note="The grey side-bar icons on track images. Public since v492. " "Four call sites in hgTracks.c and imageV2.c."), - h("bigBedOnePath", "flag", "hg/hgTracks/bigBedTrack.c:1122", - default="TRUE", role="gate", verified=True, - note="Single code path for bigBed fetching, replacing the older " - "split. Public since v492. Four call sites, and deleting it " - "removes a whole alternative path rather than just a branch."), h("trackHubsCanAddGroups", "flag", "hg/lib/hubConnect.c:41", default="TRUE", role="gate", verified=True, note="Let hubs declare their own track groups. Public since v492."), h("newBotDelay", "flag", "hg/lib/botDelay.c:215", default="TRUE", role="gate", verified=True, note="The reworked bot-delay logic. Public since v492."), h("gcOnTheFly", "flag", "hg/hgTracks/hgTracks.c:7576", default="TRUE", role="gate", verified=True, note="Calculate the GC percent track at draw time instead of " "reading a stored table. Public since v496, so it is inside " "its grace period."), h("useBlatBigPsl", "flag", "hg/hgBlat/hgBlat.c:859", default="TRUE", role="gate", verified=True, note="bigPsl output from BLAT. Public since v348."), h("alwaysItemRgb", "flag", "hg/cgilib/bedCart.c:34", default="TRUE", @@ -617,31 +612,31 @@ "reads use it through MULTI_REGION_CFG_BUTTON_TOP: the top-bar " "button at hgTracks.c:9166 and the \"Show all\" checkbox in the " "multi-region dialog at config.c:1024. They disagreed about " "the compiled-in default for four years, because e1f7896a08f " "turned the flag on by default in 2022 and changed only the " "hgTracks.c read, so on a machine that did not set the flag the " "button was in the top bar while the checkbox was hidden. " "config.c now defaults TRUE as well."), h("ignoreDefaultKnown", "flag", "hg/lib/hdb.c:6146", default="FALSE", role="knob", verified=True, note="In hdbDefaultKnownDb, ignore the defaultKnown table and treat " "the requested db as its own known-genes db. A property of a " "machine whose gene tables are not laid out the way the RR's " "are, so a knob; it gates no feature and there is nothing to " "flip."), - h("blatOldTracks", "internal", "hg/hgc/hgc.c:27582", default="keep", + h("blatOldTracks", "internal", "hg/hgc/hgc.c:27569", default="keep", verified=True, note="What happens to the custom tracks left behind by a user's " "earlier BLAT searches when a new search makes another one. " "Three values: keep (the default) leaves every one of them " "alone, hide leaves them in the session but sets them to hide, " "delete drops them from the session and lets their trash files " "age out. Only tracks tagged blatResult=on are touched, and " "the track the current search just made is always left alone. " "A string rather than a flag, so it carries no gate/knob role, " "but it is a knob in spirit: which of the three a site wants " "depends on whether its users run many searches in a session " "and get confused about which results are current, and that " "does not stop being a question after a release. When set to " "delete, the BLAT search form shows a Keep results checkbox so " "a user can opt out for one search (cart variable "