7dae59171ebf9d462438202cc85ae434e8080fe8
max
  Tue Apr 28 06:30:43 2026 -0700
NMD Escape MANE: dedicated .as for cleaner labelFields dropdown. refs #33737

The MANE bigBed now ships with its own autoSql, so the labelFields
dropdown in the track config shows "Gene Symbol", "Gencode Accession
(ENST)" and "RefSeq Accession (NM_/NR_)" - the descriptions QA asked
for. The shared nmdEscCollapsed.as keeps its generic wording for the
Gencode and RefSeq subtracks, where the "transcripts" column holds
different accession families and a single hard-coded label would not
fit both.

diff --git src/hg/makeDb/doc/hg38/nmd.txt src/hg/makeDb/doc/hg38/nmd.txt
index 691e42ca0f7..f7f5d65e39c 100644
--- src/hg/makeDb/doc/hg38/nmd.txt
+++ src/hg/makeDb/doc/hg38/nmd.txt
@@ -83,32 +83,36 @@
 mkdir -p /hive/data/genomes/hg38/bed/nmd/mane && cd /hive/data/genomes/hg38/bed/nmd/mane
 
 # --ncbi-id-field 21 puts the NCBI RefSeq accession (NM_/NR_) into the
 # collapsed bigBed's ncbiIds column so the trackDb stanza can offer NM_ as
 # the default label via labelFields/defaultLabelFields.
 # --no-collapse emits one row per (transcript, region). MANE Select gives
 # one transcript per gene; MANE Plus Clinical adds a second transcript for
 # 74 genes (e.g. LMNA). Keeping rows per-transcript means each label-field
 # column holds a single value, which renders cleaner than a comma list.
 ~/kent/src/hg/makeDb/scripts/nmd/genePredNmdEsc -f bigGenePred --gene-sym-field 18 \
     --ncbi-id-field 21 --no-collapse \
     /gbdb/hg38/mane/mane.bb \
     nmdManeDeco.bed nmdEscMane.bed
 
 bedSort nmdEscMane.bed nmdEscMane.bed
+# MANE uses its own .as so the labelFields dropdown shows clean column
+# labels ("Gene Symbol" / "Gencode Accession (ENST)" / "RefSeq Accession
+# (NM_/NR_)") that wouldn't fit the Gencode/RefSeq tracks (whose
+# "transcripts" column holds different accession types).
 bedToBigBed nmdEscMane.bed ../../../chrom.sizes nmdEscMane.bb \
-    -tab -type=bed9+3 -as=${HOME}/kent/src/hg/makeDb/scripts/nmd/nmdEscCollapsed.as
+    -tab -type=bed9+3 -as=${HOME}/kent/src/hg/makeDb/scripts/nmd/nmdEscManeCollapsed.as
 
 ln -sf /hive/data/genomes/hg38/bed/nmd/mane/nmdEscMane.bb /gbdb/hg38/nmd/nmdEscMane.bb
 
 # Collapsed-region counts (current script, no Rule 1/4 algorithmic fix):
 #   MANE 1.5:        68,345
 #   Gencode V49:    233,929
 #   RefSeq Curated: 112,903
 
 # 2026-04-24 max: Fixed Rule 1 to measure 50 bp upstream of the last splice
 # junction of the transcript (including 3'UTR introns), not the last CDS-CDS
 # junction; output regions are clipped to CDS. The old logic stripped 3'UTR
 # from the exon list before computing the "last coding junction", which
 # over-painted the last CDS exon as NMD-escape whenever there was only one
 # CDS exon, even when a 3'UTR intron sat far downstream (e.g. NBDY: the
 # entire 207 bp CDS was painted Rule 1 despite the last junction being