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/meiEul1db.as src/hg/makeDb/scripts/mei/meiEul1db.as
index 4ce4f20c3f9..2ae66f891eb 100644
--- src/hg/makeDb/scripts/mei/meiEul1db.as
+++ src/hg/makeDb/scripts/mei/meiEul1db.as
@@ -3,30 +3,30 @@
 (
 string  chrom;            "Reference chromosome"
 uint    chromStart;       "0-based start of MRIP region"
 uint    chromEnd;         "Half-open end of MRIP region"
 string  name;             "MRIP accession (mripN)"
 uint    score;            "Score (pseudo-allele-frequency * 1000)"
 char[1] strand;           "Strand"
 uint    thickStart;       "Start of thick drawing region"
 uint    thickEnd;         "End of thick drawing region"
 uint    itemRgb;          "RGB color, by lineage (germline/somatic/mixed)"
 float   pseudoAlleleFreq; "Pseudo-allele frequency|Aggregated frequency reported by euL1db"
 int     sripCount;        "Sample observations (SRIPs)|Number of sample-level SRIP entries merged into this MRIP"
 int     sampleCount;      "Distinct samples|Number of unique samples contributing"
 int     individualCount;  "Distinct individuals|Number of unique individuals contributing"
 int     studyCount;       "Distinct studies|Number of studies reporting this insertion"
-string  subGroups;        "L1HS sub-group(s)|Comma-separated set (L1-Ta, L1-pre-Ta, L1-Hybrid, unknown)"
-string  integrity;        "Integrity|Comma-separated set (full-length, 5prime-truncated, unknown)"
+string  subGroups;        "L1HS sub-group(s)|Comma-separated set (L1-Ta, L1-pre-Ta, Ta-0, Ta-1, unknown)"
+string  integrity;        "Integrity|Comma-separated set (full-length, 5prime-truncated, 3prime-truncated, internal_fragment, unknown)"
 string  lineage;          "Lineage|germline, somatic, or both"
 string  pcrValidated;     "PCR validated|yes if any contributing SRIP has PCR evidence"
 string  gene;             "Overlapping gene|Reported in euL1db MRIP table"
 string  inReferenceL1HS;  "In reference L1HS|yes if euL1db marks this MRIP as present in reference"
 string  warning;          "Warning|euL1db curation warning, if any"
 lstring studies;          "Study list|Comma-separated study IDs"
 lstring pmids;            "PubMed IDs|Comma-separated PMIDs"
 lstring methods;          "Detection methods|Comma-separated method names"
 lstring tissues;          "Tissues|Comma-separated unique tissues"
 lstring diseases;         "Clinical conditions|Comma-separated unique disease/clinical states"
 lstring populations;      "Populations|Comma-separated unique populations"
-lstring sampleTable;      "Contributing samples|HTML table (sample, individual, study, lineage, integrity, subgroup, PCR)"
+lstring sampleTable;      "Contributing samples|HTML table (SRIP, sample, study, lineage, integrity, sub-group, PCR)"
 )