File Changes for max

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

• src/hg/hgTracks/simpleTracks.c
  • lines changed 14, 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/lib/cart.c
  • lines changed 3, context: html, text, full: html, text
    325cbfe133124a17017edda28f0789217e86c61f Wed Jun 10 06:17:25 2026 -0700
    just a few comments
• src/hg/makeDb/doc/hg38/lrSv.txt
  • lines changed 66, context: html, text, full: html, text
    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
  • lines changed 30, 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
  • lines changed 52, 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/hs1/lrSv.txt
  • lines changed 48, context: html, text, full: html, text
    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
  • lines changed 12, 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/scripts/lrSv/databases.tsv
  • lines changed 1, 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
  • lines changed 2, 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/scripts/lrSv/lrSv1kgOntVcfToBed.py
  • lines changed 9, 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/scripts/lrSv/lrSvAou1kCsvToBed.py
  • lines changed 26, 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/scripts/lrSv/lrSvAprVcfToBed.py
  • lines changed 9, 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/scripts/lrSv/lrSvChirmade101TsvToBed.py
  • lines changed 23, 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/scripts/lrSv/lrSvColorsDbSvVcfToBed.py
  • lines changed 10, 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/scripts/lrSv/lrSvCommon.py
  • lines changed 35, 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/scripts/lrSv/lrSvCpc1VcfToBed.py
  • lines changed 10, 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/scripts/lrSv/lrSvDecode.as
  • lines changed 1, 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/scripts/lrSv/lrSvDecodeVcfToBed.py
  • lines changed 32, 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/scripts/lrSv/lrSvGustafsonVcfToBed.py
  • lines changed 22, 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/scripts/lrSv/lrSvHprc2Ro.as
  • lines changed 21, context: html, text, full: html, text
    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/scripts/lrSv/lrSvHprc2RoVcfToBed.py
  • lines changed 217, context: html, text, full: html, text
    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
  • lines changed 28, 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/scripts/lrSv/lrSvMergeAll.py
  • lines changed 30, 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/scripts/lrSv/lrSvVcfToBed.py
  • lines changed 11, 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/trackDb/human/hprc2Sv.html
  • lines changed 118, context: html, text, full: html, text
    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/trackDb/human/hprc2v21Sv.html
  • lines changed 108, context: html, text, full: html, text
    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/trackDb/human/lrSv.html
  • lines changed 8, context: html, text, full: html, text
    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
  • lines changed 3, 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/trackDb/human/lrSv.ra
  • lines changed 8, context: html, text, full: html, text
    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
  • lines changed 10, 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
  • lines changed 55, context: html, text, full: html, text
    4a1651999514d41b9ed33cbd8ee7ceee08df21eb Sat Jun 13 23:28:59 2026 -0700
    removing kim
• src/hg/makeDb/trackDb/human/lrSvAll.ra
  • lines changed 1, 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
  • lines changed 3, 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/trackDb/human/varFreqs.html
  • lines changed 111, 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/relatedTracks.ra
  • lines changed 6, context: html, text, full: html, text
    d4951d6de0335238ce124b3fb9703d82d329b1ab Sat Jun 13 06:35:27 2026 -0700
    html updates to varFreqs, refs #36642