af291f82582af89f7c623eb4d13b8141d28e9862
lrnassar
  Mon Apr 13 10:19:16 2026 -0700
Update ENCODE4 makedocs with defaultSortField step. refs #34923

diff --git src/hg/makeDb/doc/hg38/encode4.regulation.txt src/hg/makeDb/doc/hg38/encode4.regulation.txt
index 0d43025038c..f7eb3e10839 100644
--- src/hg/makeDb/doc/hg38/encode4.regulation.txt
+++ src/hg/makeDb/doc/hg38/encode4.regulation.txt
@@ -291,31 +291,48 @@
 # Dev (hgwdev):
 make alpha DBS=hg38
 
 ##############################################################################
 # Step 10: Cleanup — delete local ENCFF files (now S3-served)
 ##############################################################################
 
 # Individual experiment files (ENCFF*.bigWig, ENCFF*.bigBed) and ?proxy=TRUE
 # download artifacts were deleted from the source hub directory, since they
 # are now served via S3 URLs. Only the organ-averaged multiWig files
 # (referenced by gbdb symlinks) and hub.txt/HTML docs were preserved.
 #
 # hg38: Deleted 7,598 files (3.6 TB freed)
 
 ##############################################################################
-# Track hierarchy summary
+# Step 10: Default sort by experiment to group peak/signal pairs (2026-04-13)
+##############################################################################
+
+# The Epigenetics and TF ChIP bigComposite tracks each contain both peak and
+# signal subtracks for the same experiments. To group these pairs adjacent in
+# the configure page, added an _Experiment column to the metadata TSVs
+# containing the ENCSR experiment accession (extracted from shortLabel in the
+# .ra stanzas). The underscore prefix hides it from facet filters.
+# Added defaultSortField _Experiment to the 2 composite stanzas.
+# Also fixed pre-existing CRLF line endings in the Epigenetics metadata TSV.
+#
+# Composites updated:
+#   wgEncodeReg4Epigenetics: 3,152 peak/signal pairs + 49 singletons
+#   wgEncodeReg4TfChip:      2,461 peak/signal pairs + 42 singletons
+# RNA-seq not changed (signal only, no peak/signal pairing).
+
+##############################################################################
+# Track hierarchy and disk usage summary
 ##############################################################################
 
 # Regulation group priority order: cCREs (0.8) > wgEncodeReg4 (0.9) > wgEncodeReg (1)
 #
 # wgEncodeReg4 (superTrack, priority 0.9, group=regulation)
 # ├── wgEncodeReg4MarkH3k27ac (multiWig, full)                     priority 1.4
 # ├── wgEncodeReg4Dnase       (multiWig, hide)                     priority 1.1
 # ├── wgEncodeReg4Atac        (multiWig, hide)                     priority 1.2
 # ├── wgEncodeReg4MarkH3k4me3 (multiWig, hide)                     priority 1.3
 # ├── wgEncodeReg4MarkCtcf    (multiWig, hide)                     priority 1.5
 # ├── wgEncodeReg4Txn         (multiWig, hide)                     priority 1.6
 # ├── wgEncodeReg4TfPeaks     (bigBed 12+ with decorator, hide)    priority 1.7
 # ├── wgEncodeReg4Epigenetics (bigComposite faceted, 6,353, 28 ON) priority 2.0
 # ├── wgEncodeReg4RnaSeq      (bigComposite faceted, 1,046, 6 ON)  priority 2.1
 # └── wgEncodeReg4TfChip      (bigComposite faceted, 4,964, 8 ON)  priority 2.2