Commits for max

v500_preview to v500_preview2 (2026-06-08 to 2026-06-15) v500

ef61e73fc416622d8557ec2439df2344a1cc80c3 Tue Jun 9 15:10:01 2026 -0700

• lrSv: replace HPRC v2.0 pangenome SV track with v2.1 (hprc2v21Sv) Drop the v2.0 wave-decomposed hprc2Sv track and add hprc2v21Sv built from the HPRC v2.1 minigraph-cactus raw vg deconstruct VCFs (gref95.ro), on both hg38 (GRCh38 path, 596,063 SVs) and hs1 (T2T-CHM13 path, 608,435 SVs). The v2.1 files lack per-allele TYPE/LEN, so the new converter classifies INS/DEL by parsimony-trimming REF/ALT and the net length change. The v2.0 build recipe, converter and schema are kept but commented out in the makeDocs in case wave-decomposed VCFs are released again, refs #36258
  • src/hg/makeDb/doc/hg38/lrSv.txt - lines changed 66, context: html, text, full: html, text
  • src/hg/makeDb/doc/hs1/lrSv.txt - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvHprc2Ro.as - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvHprc2RoVcfToBed.py - lines changed 217, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hprc2Sv.html - lines changed 118, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hprc2v21Sv.html - lines changed 108, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.html - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 8, context: html, text, full: html, text

644eae7700eb62343b142a44258ee91a944f4853 Tue Jun 9 15:17:03 2026 -0700

• lrSv: rebuild merged lrSvAll track with HPRC v2.1 data Repoint the HPRC entry in databases.tsv from the removed v2.0 hprc2.bb to the new hprc2v21.bb and re-run the merge. The combined track now holds 2,359,011 variants (was 2,694,871); the drop is the smaller v2.1 HPRC callset. Regenerated lrSvAll.ra and updated the overview table on the container page. The HPRC Jasmine track is intentionally not part of the merge, refs #36258
  • src/hg/makeDb/scripts/lrSv/databases.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSvAll.ra - lines changed 1, context: html, text, full: html, text

cd4cf386f217a028a89e351a736e1310f0d2a5d1 Wed Jun 10 06:04:14 2026 -0700

• lrSv: document the lrSvAll merge build in the makeDoc Add a section explaining how the combined lrSvAll track is built: the databases.tsv config that lists the source bigBeds, how to run lrSvMergeAll.py, that it auto-generates lrSvAll.ra, and that the HPRC row uses the v2.1 file while the Jasmine callset is excluded, refs #36258
  • src/hg/makeDb/doc/hg38/lrSv.txt - lines changed 30, context: html, text, full: html, text

325cbfe133124a17017edda28f0789217e86c61f Wed Jun 10 06:17:25 2026 -0700

• just a few comments
  • src/hg/lib/cart.c - lines changed 3, context: html, text, full: html, text

d4951d6de0335238ce124b3fb9703d82d329b1ab Sat Jun 13 06:35:27 2026 -0700

• html updates to varFreqs, refs #36642
  • src/hg/makeDb/trackDb/human/varFreqs.html - lines changed 111, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/relatedTracks.ra - lines changed 6, context: html, text, full: html, text

9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700

• lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
  • src/hg/makeDb/doc/hg38/lrSv.txt - lines changed 52, context: html, text, full: html, text
  • src/hg/makeDb/doc/hs1/lrSv.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/databases.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSv1kgOntVcfToBed.py - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvAou1kCsvToBed.py - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvAprVcfToBed.py - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvChirmade101TsvToBed.py - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvColorsDbSvVcfToBed.py - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvCommon.py - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvCpc1VcfToBed.py - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvDecode.as - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvDecodeVcfToBed.py - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvGustafsonVcfToBed.py - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvHprc2RoVcfToBed.py - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvVcfToBed.py - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSvAll.ra - lines changed 3, context: html, text, full: html, text

4a1651999514d41b9ed33cbd8ee7ceee08df21eb Sat Jun 13 23:28:59 2026 -0700

• removing kim
  • src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 55, context: html, text, full: html, text

d08b94fcff0787dd853676e631364945c4986bfe Sun Jun 14 09:21:03 2026 -0700

• ading p. notation to mouseover, no redmine yet
  • src/hg/hgTracks/simpleTracks.c - lines changed 14, context: html, text, full: html, text