3df73adf84cf0ecfbe9310c21682034c5e6ad7cc
max
  Sat Mar 7 09:47:33 2026 -0800
Default polyA tail detection to off for BAM/CRAM tracks. The polyA detection was designed for mRNA/EST alignments and produces misleading asymmetric coloring on BAM reads due to strand-dependent checks in baseColorOverdrawQInsert. Users who need it for long-read cDNA/RNA sequencing can still enable it via the checkbox in hgTrackUi. refs #37133

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

diff --git src/hg/lib/hui.c src/hg/lib/hui.c
index 44a26fd24b7..673443e7f36 100644
--- src/hg/lib/hui.c
+++ src/hg/lib/hui.c
@@ -1606,31 +1606,31 @@
 void bamAddBaseAndIndelSettings(struct trackDb *tdb)
 /* Unless already set in tdb, add settings to enable base-level differences and indel display. */
 {
 struct hash *settings = tdb->settingsHash;
 if (!hashLookup(settings, BASE_COLOR_USE_SEQUENCE))
     hashAdd(settings, BASE_COLOR_USE_SEQUENCE, cloneString("lfExtra"));
 if (!hashLookup(settings, BASE_COLOR_DEFAULT))
     hashAdd(settings, BASE_COLOR_DEFAULT, cloneString(BASE_COLOR_DRAW_DIFF_BASES));
 if (!hashLookup(settings, SHOW_DIFF_BASES_ALL_SCALES))
     hashAdd(settings, SHOW_DIFF_BASES_ALL_SCALES, cloneString("."));
 if (!hashLookup(settings, INDEL_DOUBLE_INSERT))
     hashAdd(settings, INDEL_DOUBLE_INSERT, cloneString("on"));
 if (!hashLookup(settings, INDEL_QUERY_INSERT))
     hashAdd(settings, INDEL_QUERY_INSERT, cloneString("on"));
 if (!hashLookup(settings, INDEL_POLY_A))
-    hashAdd(settings, INDEL_POLY_A, cloneString("on"));
+    hashAdd(settings, INDEL_POLY_A, cloneString("off"));
 if (!hashLookup(settings, "showDiffBasesMaxZoom"))
     hashAdd(settings, "showDiffBasesMaxZoom", cloneString(BAM_DEFAULT_SHOW_DIFF_BASES_MAX_ZOOM));
 }
 
 /****** base position (ruler) controls *******/
 
 static char *zoomOptions[] = 
     {
     ZOOM_1PT5X,
     ZOOM_3X,
     ZOOM_10X,
     ZOOM_100X,
     ZOOM_BASE
     };