798b37017a4e1b95f3ccdf7c8b477dfb5446a324
lrnassar
  Fri Jul 24 15:22:34 2026 -0700
lrSv: QA fixes for cardSv/noyvertSv additions - BND filter, makedoc, link targets. refs #37888

Add BND to filterValues.svType on the longReadVariants supertrack and the merged
lrSvAll track (and the lrSvMergeAll.py generator) so the breakend variants that
noyvertSv contributes are filterable. Correct a stale makedoc comment that said
CARD was not in the lrSvAll merge (it is). Add target="_blank" to the API and
hgdownload links in cardSv.html and noyvertSv.html.

diff --git src/hg/makeDb/doc/hg38/lrSv.txt src/hg/makeDb/doc/hg38/lrSv.txt
index df579e947d4..baf41227165 100644
--- src/hg/makeDb/doc/hg38/lrSv.txt
+++ src/hg/makeDb/doc/hg38/lrSv.txt
@@ -659,31 +659,31 @@
 bigBedToBed NIH_CARD_longReadSVs.bb stdin \
   | python3 $HOME/kent/src/hg/makeDb/scripts/lrSv/lrSvCardBbToBed.py /dev/stdin cardSv.bed
 # CARD: 228,855 input records written; by type: DEL=101,570, DUP=1,
 #       INS=126,853, INV=431
 # CARD: 32 records with svLen or insLen > 1 Mb kept (large ONT/assembly calls)
 bedSort cardSv.bed cardSv.sorted.bed
 bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSvCard.as \
     -tab cardSv.sorted.bed /hive/data/genomes/hg38/chrom.sizes cardSv.bb
 
 # All 228,855 provider records are carried through 1:1 (no rows dropped). The
 # provider bigBed itself is a subset of the ~234,905 SVs reported in the paper.
 # A handful of very large calls (INS up to 92 Mb, several multi-Mb INV/DEL) are
 # almost certainly ONT/assembly artifacts but are kept, not silently dropped.
 # svLen is stored as the reference span (1 bp for INS); the inserted-sequence
 # length lives in insLen. AC is the genotyped carrier count (= nabecCount +
-# hbccCount). Not added to the lrSvAll merge for now.
+# hbccCount). Included in the lrSvAll merge (source key CARD).
 
 ##########
 # 2026-07-17 Claude max
 
 # noyvertSv: multi-ancestry long-read SV imputation panel, 888 Oxford Nanopore
 # genomes from the 1000 Genomes Project (164 EUR, 144 AMR, 168 EAS, 171 SAS,
 # 241 AFR), SVs jointly called with Sniffles2 v2.0.7.
 # Paper: Noyvert et al. 2025, eLife reviewed preprint, doi 10.7554/eLife.106115
 #   (no PMID; not indexed in PubMed).
 #
 # The authors shared a per-variant summary table (SV.Noyvert.et.al.tsv.gz) with
 # all 107,445 panel SVs: per-superpopulation allele frequencies, Sniffles2
 # stdev metrics, Hardy-Weinberg p-values, leave-one-out and UK Biobank
 # imputation accuracy, and, where applicable, the significant UK Biobank SV-WAS
 # trait associations. Inserted sequences are not included in the file. There is