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)" )