fe73446acf43f70e385dadbbb281634adf3cac9e
lrnassar
  Tue Apr 21 16:44:16 2026 -0700
NMD Escape QA tweaks: hide Gencode subtrack by default, bold rule numbers in mouseovers. refs #33737

- nmdEscGencode default visibility changed from on/dense to off/hide so
only the RefSeq Curated subtrack is on by default. Per Lou's request.
- RULE_DESCRIPTIONS mouseover strings wrap the rule number in <b>...</b>
so the rule shows bold in the tooltip. Both bigBeds rebuilt.

diff --git src/hg/makeDb/scripts/nmd/genePredNmdEsc src/hg/makeDb/scripts/nmd/genePredNmdEsc
index 6c2ea4f891b..a0015502a90 100755
--- src/hg/makeDb/scripts/nmd/genePredNmdEsc
+++ src/hg/makeDb/scripts/nmd/genePredNmdEsc
@@ -3,34 +3,34 @@
 import logging, sys, optparse, gzip, subprocess
 from collections import defaultdict
 from os.path import join, basename, dirname, isfile
 
 # ==== functions =====
 
 # Colors by rule
 RULE_COLORS = {
     1: "255,0,0",       # red - last 50bp of last coding junction
     2: "255,140,0",     # orange - intronless transcript
     3: "139,0,0",       # dark red - first 100bp of coding nucleotides
     4: "255,215,0",     # gold - long coding exon (>400 nt)
 }
 
 RULE_DESCRIPTIONS = {
-    1: "Rule 1 - last 50bp of last coding exon junction",
-    2: "Rule 2 - single coding exon, no 3'UTR intron",
-    3: "Rule 3 - first 100bp of coding nucleotides",
-    4: "Rule 4 - PTC in long exon (>400 nt)",
+    1: "<b>Rule 1</b> - last 50bp of last coding exon junction",
+    2: "<b>Rule 2</b> - single coding exon, no 3'UTR intron",
+    3: "<b>Rule 3</b> - first 100bp of coding nucleotides",
+    4: "<b>Rule 4</b> - PTC in long exon (>400 nt)",
 }
 
 # Lindeboom et al. 2016: reduced NMD efficiency for PTCs in exons longer than this
 LONG_EXON_THRESHOLD = 400
 
 def parseArgs():
     " setup logging, parse command line arguments and options. -h shows auto-generated help page "
     parser = optparse.OptionParser("usage: %prog [options] inFname outDecoFname outCollapsedFname - "
         "Output BEDs with NMD escape regions. First output is decorator format, "
         "second is collapsed bigGenePred with gene symbols and transcript lists.")
 
     parser.add_option("-d", "--debug", dest="debug", action="store_true",
         help="show debug messages")
     parser.add_option("-f", "--format", dest="format", action="store", default="genePredExt",
         help="Input format: 'genePredExt' (with bin column, e.g. ncbiRefSeq) or "