04456b0be37a7d7b57551e0d9596e3ef0b8f0393
max
  Thu Jul 16 00:34:37 2026 -0700
Add HPRC Release 2 hg38 native tracks (alignments, coverage, breaks, rearrangements, chains), refs #35415

#Preview2 week - bugs introduced now will need a build patch to fix
New pan-genome track container (group hprc) derived from the HPRC Release 2
per-assembly chains to GRCh38 (462 haplotypes), running in parallel to the
existing HPRC release 1 tracks:
- hprc2Coverage: fraction of assemblies aligning across GRCh38
- hprc2Breaks:   alignment breaks, colored by prevalence
- hprc2Rearr:    insertions/deletions/inversions/duplications/complex indels,
lrSv color palette, numeric size field, 50 bp default filter
- hprc2Chains:   per-haplotype bigChain composite, grouped by superpopulation
Container hidden by default. Scripts, autoSql, and makeDoc included.

diff --git src/hg/makeDb/scripts/hprc2/hprc2Arrange.as src/hg/makeDb/scripts/hprc2/hprc2Arrange.as
new file mode 100644
index 00000000000..8169c559da8
--- /dev/null
+++ src/hg/makeDb/scripts/hprc2/hprc2Arrange.as
@@ -0,0 +1,18 @@
+table hprc2Arrange
+"HPRC2 assembly rearrangements and indels relative to GRCh38"
+    (
+    string chrom;       "Chromosome (or contig, scaffold, etc.)"
+    uint   chromStart;  "Start position in chromosome"
+    uint   chromEnd;    "End position in chromosome"
+    string name;        "Name of item"
+    uint   score;       "Number of HPRC2 assemblies with this event"
+    char[1] strand;     "+ or -"
+    uint thickStart;    "Start of where display should be thick"
+    uint thickEnd;      "End of where display should be thick"
+    uint itemRgb;       "Color"
+    lstring source;     "List of assemblies with this event"
+    uint querySize;     "Size of item on assembly (query) side"
+    string label;       "Label for item"
+    uint size;          "Event size (bp)|Deletion/inversion/duplication: span on GRCh38. Insertion: bases inserted from the assembly."
+    lstring _mouseover; "mouseOver for item"
+    )