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

diff --git src/hg/makeDb/doc/mm10.encode4.regulation.txt src/hg/makeDb/doc/mm10.encode4.regulation.txt
index 8bef0206757..7877b320ccb 100644
--- src/hg/makeDb/doc/mm10.encode4.regulation.txt
+++ src/hg/makeDb/doc/mm10.encode4.regulation.txt
@@ -251,30 +251,52 @@
 ##############################################################################
 # Step 11: 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.
 #
 # mm10: Deleted 2,594 files (0.7 TB freed)
 
 ##############################################################################
 # Track hierarchy summary
 ##############################################################################
 
+##############################################################################
+# Step 9: 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 and TF ChIP
+# metadata TSVs.
+#
+# Composites updated:
+#   encode4RegEpigenetics: 589 peak/signal pairs, 0 singletons
+#   encode4RegTfChip:      167 peak/signal pairs, 0 singletons
+# RNA-seq not changed (signal only, no peak/signal pairing).
+
+##############################################################################
+# Track hierarchy and disk usage summary
+##############################################################################
+
 # Regulation group priority order: cCREs (0.4) > encode4Reg (0.5) > tabulaMuris (1)
 #
 # encode4Reg (superTrack, priority 0.5, group=regulation)
 # ├── encode4RegMarkH3k27ac (multiWig, full)                         priority 1.4
 # ├── encode4RegDnase       (multiWig, hide)                         priority 1.1
 # ├── encode4RegAtac        (multiWig, hide)                         priority 1.2
 # ├── encode4RegMarkH3k4me3 (multiWig, hide)                         priority 1.3
 # ├── encode4RegMarkCtcf    (multiWig, hide)                         priority 1.5
 # ├── encode4RegTxn         (multiWig, hide)                         priority 1.6
 # ├── encode4RegEpigenetics (bigComposite faceted, 1,178, 30 ON)     priority 2.0
 # ├── encode4RegRnaSeq      (bigComposite faceted, 1,054, 6 ON)      priority 2.1
 # └── encode4RegTfChip      (bigComposite faceted, 334, 10 ON)       priority 2.2
 
 # Disk usage (/gbdb/mm10/encode4/regulation/):
 #   organAve:          1.5 TB (122 files)