7e87cadb469b4e0eb4fb7f973154357cfe7fc345
lrnassar
  Mon Sep 21 15:56:18 2026 -0700
QA fixes for the mei (Mobile Insertions) track collection. refs #37524

Fix two data bugs found during QA and rebuild the affected bigBeds.
meiEul1dbToBed.py looked up samples and individuals by name, but euL1db
joins on 1-based row numbers, so neither join ever matched and the
individual count, tissues, clinical conditions and populations were empty
on all 8,991 insertions while the contributing-samples table printed row
numbers. Both loaders now key on the row number, the table prints the
sample name, and the adjacent population filter is case-insensitive so it
actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every
record, which dropped the first base of the element on the 96 GRCh38 and
111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no
anchor base; it now prefers INFO SEQ, which always matches SVLEN.

Correct seven statements on the description pages against their sources:
the HGSVC3 single-caller split was attributed to PALMER rather than
L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db
was credited with aligning the L1HS consensus when the paper says it was
processed from our RepeatMasker track, DeepMEI's network was described as
a classifier rather than a genotyper and given the wrong training set,
euL1db listed two detection methods absent from the data, and HMEID
contradicted itself on the MELT ASSESS cutoff.

Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted
callset is kept off the download server; the container page no longer
claims the whole collection is long-read, lists the two euL1db subtracks,
scopes its display conventions to the subtracks they describe, and cites
all six papers; dead and wrong track links are repointed and pinned to a
db; $db replaces hardcoded hg38 in paths on pages that serve three
assemblies; the euL1db labels no longer carry hg38 counts and a lift note
that made no sense on hg19; all six subtracks gain a dataVersion; the
euL1db filter ranges match the data; and five autoSql field descriptions
match what the files contain.

Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct
the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19
carries the two euL1db subtracks.

diff --git src/hg/makeDb/scripts/mei/meiEul1dbRef.as src/hg/makeDb/scripts/mei/meiEul1dbRef.as
index 7569ab67e94..fee0e8b946d 100644
--- src/hg/makeDb/scripts/mei/meiEul1dbRef.as
+++ src/hg/makeDb/scripts/mei/meiEul1dbRef.as
@@ -1,19 +1,19 @@
 table meiEul1dbRef
 "euL1db: L1-HS copies present in the human reference genome"
 (
 string  chrom;        "Reference chromosome"
 uint    chromStart;   "0-based start of reference L1HS element"
 uint    chromEnd;     "Half-open end of reference L1HS element"
-string  name;         "Subgroup label (L1HS-Ta, L1HS-PreTa, L1HS-Hybrid)"
+string  name;         "Subgroup label (L1HS-Ta, L1HS-PreTa, L1HS-undef)"
 uint    score;        "Score (unused, 0)"
 char[1] strand;       "Strand"
 uint    thickStart;   "Start of thick drawing region"
 uint    thickEnd;     "End of thick drawing region"
 uint    itemRgb;      "RGB color, by L1HS subgroup"
 string  family;       "Family|Always L1HS"
-string  subGroup;     "Sub-group|L1HS-Ta, L1HS-PreTa, L1HS-Hybrid"
-string  integrity;    "Integrity|full-length or 5prime-truncated"
+string  subGroup;     "Sub-group|L1HS-Ta, L1HS-PreTa or L1HS-undef if euL1db assigned no sub-group"
+string  integrity;    "Integrity|full-length, 5prime-truncated, 3prime-truncated or internal_fragment"
 uint    refStart;     "Position on L1HS consensus|5' start in L1HS consensus sequence"
 uint    refStop;      "Position on L1HS consensus|3' stop in L1HS consensus sequence"
 uint    elementLen;   "Element length (bp)"
 )