df22e780c9e8a304b59e6d26bc34e0f729e33e45
galt
  Thu Nov 13 17:07:54 2025 -0800
Adds a checkbox that turns on rearrangement mode automatically for all CTs generated by hgBlat. This is one of the main features of the ticket, but not all desired features. fixes #32857

diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 851a9e5cd96..3604883f573 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -26850,30 +26850,38 @@
 char *extraForMismatch = "indelPolyA=on showDiffBasesAllScales=. baseColorUseSequence=lfExtra baseColorDefault=diffBases";
   
 if (isProt)
     extraForMismatch = "";
 char buffer[4096];
 safef(buffer, sizeof buffer, customTextTemplate, bigBedTn.forCgi, host, extraForMismatch, bigBedTn.forCgi, trackName, trackDescription);
 
 struct customTrack *ctList = getCtList();
 struct customTrack *newCts = customFactoryParse(database, buffer, FALSE, NULL, NULL);
 theCtList = customTrackAddToList(ctList, newCts, NULL, FALSE);
 
 customTracksSaveCart(database, cart, theCtList);
 
 cartSetString(cart, "i", "PrintAllSequences");
 hgCustom(newCts->tdb->track, NULL);
+
+if (sameOk(cartOptionalString(cart, "autoRearr"), "1"))  
+    {
+    char snakeVar[256];
+    safef(snakeVar, sizeof snakeVar, "%s.doSnake", newCts->tdb->track);
+    cartSetString(cart, snakeVar, "1");
+    }
+
 }
 
 void doHPRCTable(struct trackDb *tdb, char *itemName)
 /* Put up a generic bigBed details page, with a table of links to turn on related
  *  * chain tracks with visibility toggles */
 {
 int start = cartInt(cart, "o");
 int end = cartInt(cart, "t");
 genericHeader(tdb, itemName);
 genericBigBedClick(NULL, tdb, itemName, start, end, 0);
 printTrackHtml(tdb);
 // tell the javscript to reorganize the column of assemblies:
 jsIncludeFile("hgc.js", NULL);
 jsInlineF("var doHPRCTable = true;\n");
 }