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v497_base to v498_preview (2026-04-20 to 2026-04-27) v498
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f4d6633d6a724d7b682f9f49ed983e22a5e0975d Mon Apr 20 14:41:07 2026 -0700
- updating a few lrSv subtracks, and moving the colorsDbSnv track under
the varFreqs track. refs #36642
- src/hg/makeDb/trackDb/human/colorsDb.html - lines changed 126, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/han945Sv.html - lines changed 10, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/lrSv.html - lines changed 143, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 21, context: html, text, full: html, text
a1f009b6019876a1bc845c6f0892b7bc942e368e Mon Apr 20 14:43:29 2026 -0700
- Hiding regeneron subtracks of varFreqs track again, no permission to distribute these.
- src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 21, context: html, text, full: html, text
366afa4a74c46ec6fb2b667a2902a873feec40cf Mon Apr 20 23:00:05 2026 -0700
- varFreqsAll: rebuild combined bigBed to include GA4K and CoLoRSdb
Regenerate the All Databases Combined track with the two long-read
PacBio subtracks (GA4K 552 samples and CoLoRSdb v1.2.0 1,027 samples)
that were added to varFreqs since the March build. Source count rises
from 21 to 23 databases; final bigBed is 37.7 GB with 1.17B records
and 113 fields. Updates varFreqs.ra filterValues.sources and per-
database AF/AC filters for the two new sources, and databases.tsv
+ varFreqs.txt (build notes).
refs #36642
- src/hg/makeDb/doc/hg38/varFreqs.txt - lines changed 25, context: html, text, full: html, text
- src/hg/makeDb/scripts/varFreqs/databases.tsv - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 9, context: html, text, full: html, text
65091fe6f6487c23d650a144e947fc1c582d3f40 Tue Apr 21 02:16:16 2026 -0700
- abelSv: move under lrSv supertrack as short-read comparison subtrack
Move the Abel et al. 2020 CCDG 17,795-genome SV callset from a
top-level hg38 track to a subtrack of the lrSv supertrack (parallel
to onekg3202Sr) and relabel shortLabel/longLabel to flag Illumina
short-read provenance. The same bigBed is now visible on hg38 in
the long-read SV browsing context. Also:
- Clarify abelSv.html variant counts: 738,624 upstream unique SVs
across both callsets, 737,998 after B37->hg38 liftOver (626
unmapped). B38=458,106, B37lift=279,892.
- lrSv.html: fix triple-slash https:/// in the Ebert et al. Science
reference URL.
- bigBed.html: add closing </li> on the extra-fields pipe-separator
bullet and tighten a comma in the same sentence.
refs #36258, refs #37376
- src/hg/htdocs/goldenPath/help/bigBed.html - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/abelSv.html - lines changed 12, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/abelSv.ra - lines changed 37, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/lrSv.html - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 39, context: html, text, full: html, text
8faeb3cba60c7cb842bc17c17a57c9b53ef1b478 Tue Apr 21 02:51:32 2026 -0700
- ncbiCloneEndsCH1073: add NCBI CH1073 BAC library clone end placements track on danRer11, refs #35059
210,777 unique-concordant clone-insert placements from NCBI's CH1073
(RZPD-1073 / DanioKey) library clone report. Separate from the existing
bacEndPairsLift (danRer4 -> danRer11 UCSC-BLAT lift), which is left in place.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/doc/danRer11/ncbiCloneEndsCH1073.txt - lines changed 34, context: html, text, full: html, text
- src/hg/makeDb/scripts/ncbiCloneEndsCH1073/cloneEnds.as - lines changed 17, context: html, text, full: html, text
- src/hg/makeDb/scripts/ncbiCloneEndsCH1073/makeBed.py - lines changed 125, context: html, text, full: html, text
- src/hg/makeDb/scripts/ncbiCloneEndsCH1073/refSeqNames.py - lines changed 33, context: html, text, full: html, text
- src/hg/makeDb/trackDb/zebrafish/danRer11/ncbiCloneEndsCH1073.html - lines changed 123, context: html, text, full: html, text
- src/hg/makeDb/trackDb/zebrafish/danRer11/ncbiCloneEndsCH1073.ra - lines changed 20, context: html, text, full: html, text
- src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra - lines changed 2, context: html, text, full: html, text
07c109ea4fe627879544dddf222650ab8c29eaf8 Tue Apr 21 02:55:53 2026 -0700
- redmineCli: add --file-list-add PATH option to append paths idempotently, refs #35059
Existing --file-list overwrites the custom field. The new --file-list-add
reads the current value, appends each path that isn't already listed, and
writes the combined value back with CRLF separators (matching Redmine's
internal format).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
989d891c0c0a500e584d55f2f368b52f2abe5f1d Tue Apr 21 06:25:48 2026 -0700
- kwanhoSv: flag as preliminary, ask users to contact authors
Mark the Kim et al. 2026 PD brain long-read SV subtrack as
preliminary in its shortLabel and longLabel, and add a prominent
warning banner at the top of the description page telling users to
contact the authors (ASAP / Kim lab) before using the data, since
the callset will be updated before publication.
refs #36258
- src/hg/makeDb/trackDb/human/kwanhoSv.html - lines changed 9, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 2, context: html, text, full: html, text
8e279300b1726f355767b467bc699685e90d487b Tue Apr 21 06:27:16 2026 -0700
- composite hgTrackUi: fix btn_minus_all to hide parent, remember last vis, refs #37182
Two fixes around composite visibility on hgTrackUi:
1) The global [-] button (btn_minus_all) unchecked all subtracks but left
the composite visibility dropdown unchanged. The earlier fix in
814472876ea covered only the matrix-corner [-] (_matSetMatrixCheckBoxes);
the global button goes through matSubCBsCheck, which is now updated to
the same pattern.
2) [-] / [+] and individual subCB clicks now remember the prior visibility
via a data-last-viz attribute on the dropdown. Hiding stashes the
current value; re-showing restores it (falling back to pack/dense if
nothing saved) instead of always jumping to pack.
Factored into two helpers in hui.js: hideCompositeSaveVis() and an
extended exposeAll(). subCfg.onUserCbChange (individual subCB/matCB
path) delegates to the same helpers so behavior is uniform.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
5e4ca58df1b5bfe554fe5cc3309a39736ca256ee Tue Apr 21 08:08:52 2026 -0700
- cpc1Sv: restrict to the 58 CPC samples, drop HPRC-specific SVs
Rewrite lrSvCpc1VcfToBed.py to identify the 58 CPC sample columns by
name prefix (HIFI032* or RY*), recompute AC/AN/NS from those GT
columns only, and skip any snarl that no CPC sample carries. The
HPRC portion is already represented elsewhere in lrSv, so this keeps
the track population-consistent with its label.
Rebuild results: 46,092 snarl sites on hs1 (down from 97,205 when
combined with HPRC), 36,030 lifted to hg38 (down from 81,261;
10,062 unmapped). Updates cpc1Sv.html, lrSv.ra labels, and the
makeDoc.
refs #36258
- src/hg/makeDb/doc/hg38/lrSv.txt - lines changed 20, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvCpc1VcfToBed.py - lines changed 95, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/cpc1Sv.html - lines changed 23, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 3, context: html, text, full: html, text
9a11061ca6b40fe16bdfd09b1af53192f6c7c85b Tue Apr 21 08:13:02 2026 -0700
- lrSv: add HTML doc pages and conversion scripts for recent subtracks, + hs1 HGSVC3
Subtrack stanzas for these SV callsets landed in earlier commits but
the conversion scripts and per-track HTML description pages were
never added; trackDb therefore had no doc to serve. This commit
catches up.
Docs (new):
- colorsDbSv.html CoLoRSdb 1,427-sample long-read SVs
- gustafsonSv.html 1KG ONT 100 (Gustafson 2024, PMID 39358015)
- hgsvc2Sv.html HGSVC2 (Ebert 2021, PMID 33632895)
- hprc2Sv.html HPRC release-2 pangenome SVs (no PMID yet;
see humanpangenome.org/hprc-data-release-2/)
- onekg3202Sr.html 1KG 3202 Illumina SHORT-READ GATK-SV
(Byrska-Bishop 2022, PMID 36055201)
Scripts (new):
- lrSvGustafson.as / lrSvGustafsonVcfToBed.py
- lrSvHgsvc2.as / lrSvHgsvc2TsvToBed.py (merges insdel + inv tables)
- lrSvHprc2.as / lrSvHprc2VcfToBed.py (streams wave-decomposed VCF,
explodes multi-allelic rows,
filters to SV-sized or INV)
- lrSv1kg3202Sr.as / lrSv1kg3202SrVcfToBed.py
HGSVC3 also on hs1:
- hgsvc3Sv.html: note that the hs1 build is native (not lifted):
HGSVC3 aligned all assemblies to both GRCh38 and T2T-CHM13 and
released separate annotation tables per reference. Added the
T2T-CHM13 source URL to the Methods section and the hs1 hgsvc3.bb
download link to Data Access.
- doc/hs1/lrSv.txt (new): hs1-specific wget + build steps; refers
back to doc/hg38/lrSv.txt for the full process.
refs #36258
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/doc/hs1/lrSv.txt - lines changed 30, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSv1kg3202Sr.as - lines changed 30, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSv1kg3202SrVcfToBed.py - lines changed 126, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvGustafson.as - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvGustafsonVcfToBed.py - lines changed 114, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvHgsvc2.as - lines changed 40, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvHgsvc2TsvToBed.py - lines changed 163, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvHprc2.as - lines changed 20, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvHprc2VcfToBed.py - lines changed 180, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/colorsDbSv.html - lines changed 104, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/gustafsonSv.html - lines changed 96, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hgsvc2Sv.html - lines changed 122, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hgsvc3Sv.html - lines changed 27, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hprc2Sv.html - lines changed 96, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/onekg3202Sr.html - lines changed 112, context: html, text, full: html, text
b132fa0f0ba226c056f5408a2c02c3d945ccc9c1 Tue Apr 21 08:17:52 2026 -0700
- han945Sv: fix OMIX download link
Replace the broken ngdc.cncb.ac.cn/omix/release/OMIX005649 URL in the
Data Access section with the correct biosino.org analysis page for
this dataset.
refs #36258
- src/hg/makeDb/trackDb/human/han945Sv.html - lines changed 1, context: html, text, full: html, text
40c7b6fb506ddde686cd56a976b8a07e46db775b Tue Apr 21 08:19:46 2026 -0700
- hprc2Sv: highlight alignments_v2.0.csv as authoritative file list
Reframe the existing link to HPRC's alignments_v2.0.csv in the
Methods section so it is clear that this CSV points to both the
GRCh38 and CHM13 pangenome VCFs used for the track (not just the
list of underlying assemblies). Existing S3 download links preserved.
refs #36258
- src/hg/makeDb/trackDb/human/hprc2Sv.html - lines changed 37, context: html, text, full: html, text
aaa2d4e074608d3e07ecf7d7a7e35cfa96b0a06d Tue Apr 21 08:29:35 2026 -0700
- tommoJpSv: fix broken jMorp download link
The previous dataset-specific URL (tommo-jsv1-20211208-af) returned an
error. Point to the general jMorp downloads page instead, where users
can find the current ToMMo SV callset.
refs #36258
- src/hg/makeDb/trackDb/human/tommoJpSv.html - lines changed 2, context: html, text, full: html, text
8a5a466f5e13a020954014cdefc81400072db516 Tue Apr 21 08:29:55 2026 -0700
- lrSv: add hprc2 hs1 subtrack using T2T-CHM13 wave VCF, refs #36258
The HPRC release-2 pangenome publishes a wave-decomposed VCF against
both GRCh38 and T2T-CHM13. We already had the GRCh38 version as the
hprc2Sv subtrack on hg38; this adds the parallel T2T-CHM13 build under
/gbdb/hs1/lrSv/hprc2.bb. The existing trackDb stanza (bigDataUrl
/gbdb/$D/lrSv/hprc2.bb) picks it up on hs1 without changes.
1,451,269 SV rows kept (937,425 INS, 360,960 DEL, 147,898 COMPLEX,
4,986 INV) using the existing lrSvHprc2VcfToBed.py converter.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/doc/hg38/lrSv.txt - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/doc/hs1/lrSv.txt - lines changed 21, context: html, text, full: html, text
d93c426ef1ad5fbb32b754408599eaf380a199e5 Tue Apr 21 13:34:58 2026 -0700
- choriCloneEnds: reorganize danRer11 CHORI BAC clone end placements as a superTrack, refs #35059
- Rename ncbiCloneEndsCH1073 to choriCloneEnds throughout (trackDb, HTML,
makeDoc, scripts dir, /hive and /gbdb layout). User-visible label is
now "CHORI Clones" since all three libraries (CH1073, CH73, CH211) are
CHORI/BACPAC BAC libraries; data source (NCBI Clone DB) is cited in
Methods.
- Wrap the existing CH1073 track in a choriCloneEnds superTrack and
add two new subtracks built from the parallel unique_concordant GFFs
at ftp.ncbi.nih.gov/repository/clone/reports/Danio_rerio/ :
CH73 (99,141 placements, 23 oversize)
CH211 (70,231 placements, 46 oversize)
CH1073 is rebuilt with the same pipeline (210,777 placements).
- Build all three bigBeds with -extraIndex=name and register
searchTable / searchType bigBed stanzas with searchIndex name on each
subtrack, so clone names (CH1073-100A1, CH73-1A1, CH211-1A1, ...)
resolve from the Genome Browser position box.
- Single shared HTML description page; Methods now links to the NCBI
FTP source and to the UCSC makeDoc and scripts dir on GitHub.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/doc/danRer11/choriCloneEnds.txt - lines changed 36, context: html, text, full: html, text
- src/hg/makeDb/doc/danRer11/ncbiCloneEndsCH1073.txt - lines changed 34, context: html, text, full: html, text
- src/hg/makeDb/scripts/choriCloneEnds/cloneEnds.as - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/scripts/choriCloneEnds/makeBed.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/makeDb/scripts/choriCloneEnds/refSeqNames.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/makeDb/trackDb/zebrafish/danRer11/choriCloneEnds.html - lines changed 142, context: html, text, full: html, text
- src/hg/makeDb/trackDb/zebrafish/danRer11/choriCloneEnds.ra - lines changed 87, context: html, text, full: html, text
- src/hg/makeDb/trackDb/zebrafish/danRer11/ncbiCloneEndsCH1073.html - lines changed 123, context: html, text, full: html, text
- src/hg/makeDb/trackDb/zebrafish/danRer11/ncbiCloneEndsCH1073.ra - lines changed 20, context: html, text, full: html, text
- src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra - lines changed 1, context: html, text, full: html, text
06a482a2120d4d85c7c34fb5038213e07f595554 Tue Apr 21 15:00:21 2026 -0700
- lrSv: add tommoJpCnv short-read CNV comparator (multiWig)
ToMMo 48KJPN-CNV Frequency Panel: copy-number variation frequencies
from short-read whole-genome sequencing of 48,874 Japanese individuals
(jMorp 20230828 release, GATK CNV germline workflow at 1 kb
resolution). Published as a companion short-read comparator to the
long-read tommoJpSv track.
Rendered as a multiWig container with two bigWig subtracks (transparent
overlay): tommoJpCnvLoss.bw counts samples at CN<2 per bin (red) and
tommoJpCnvGain.bw counts samples at CN>2 per bin (green). Values are
absolute carrier counts out of 48,874. 2,006,905 bins with at least one
CNV carrier; bins that are wholly CN=2 are omitted.
Files:
- trackDb/human/lrSv.ra: new tommoJpCnv multiWig container
- trackDb/human/tommoJpCnv.html: new doc page
- trackDb/human/lrSv.html: summary-table row + per-track blurb
- scripts/lrSv/lrSvTommoJpCnvVcfToBedGraph.py: VCF -> two bedGraphs
- doc/hg38/lrSv.txt: wget, converter invocation, bigWig build steps
refs #36258
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/doc/hg38/lrSv.txt - lines changed 26, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvTommoJpCnvVcfToBedGraph.py - lines changed 95, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/lrSv.html - lines changed 21, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 33, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/tommoJpCnv.html - lines changed 110, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/tommoJpSv.html - lines changed 29, context: html, text, full: html, text
695f40f9d6139a4df393522c067f1702aff8d3bd Wed Apr 22 03:13:39 2026 -0700
- varFreqs: add SVatalog 101 short-read SNV frequencies subtrack
SNV/indel allele frequencies from the 101-sample GWAS SVatalog cohort
(Chirmade et al. 2026, Heredity, PMID 41203876), called from 10X
Genomics linked short-read WGS with GATK HaplotypeCaller v4.0.0.0 and
phased with SHAPEIT v4.2.0. Sibling of the lrSv chirmade101Sv
structural-variant track, which is built from the same 101 samples.
8,814,835 autosomal + chrX sites. Source release ships only AF; AC and
AN are synthesized in the emitted VCF as AC=round(AF*202) and AN=202
(2*101 diploid), with the gnomAD v3.1 non-Finnish European AF and dbSNP
rsID passed through as GNOMAD_NFE_AF and RSID info fields. VCF is
bgzipped + tabix-indexed (172 MB + 1.6 MB .tbi).
Files:
- scripts/varFreqs/svatalogFreqToVcf.py (new): per-chrom allele-freq
TSV -> single VCF with hg38 ##contig header
- trackDb/human/varFreqs.ra: new svatalogSnv vcfTabix subtrack
- trackDb/human/svatalogSnv.html (new): doc page
- trackDb/human/varFreqs.html: new row in Available Datasets table
- doc/hg38/varFreqs.txt: wget-free build block (input files were
downloaded manually from Zenodo 13367574)
Note: the All Databases Combined varFreqs bigBed has NOT been rebuilt
to include this new source yet; a subsequent merge pass will add it.
refs #36258
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/doc/hg38/varFreqs.txt - lines changed 23, context: html, text, full: html, text
- src/hg/makeDb/scripts/varFreqs/svatalogFreqToVcf.py - lines changed 137, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/svatalogSnv.html - lines changed 95, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/varFreqs.html - lines changed 9, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 9, context: html, text, full: html, text
1732661494ece5e645a9522f15a0f5922b035d1a Wed Apr 22 08:57:11 2026 -0700
- colorsDbSv: rebuild from pbsv+Jasmine source VCFs with richer AS
Rebuild the CoLoRSdb SV bigBeds for hg38 and hs1 from the upstream
pbsv+Jasmine VCFs that the CoLoRSdb project distributes directly.
The previous bigBed stored AF as a string (breaking the numeric
filter) and lacked insLen (causing a "filter on field insLen not in
AS file" error under the supertrack-level filter). The new build:
- stores AF as a float
- adds a derived insLen column (alt-ref length delta for INS, 0
otherwise) so the shared lrSv insLen filter applies
- keeps every INFO field from the source (SVTYPE, SVLEN, END, AC,
AN, NS, AC_Hom, AC_Het, AC_Hemi, AF, HWE, ExcHet, nhomalt) plus
REF/ALT
- uses the canonical svName(TYPE, featLen, AC) label via lrSvCommon
Record counts match the source VCFs: 426,239 on hg38 (59 MB) and
839,714 on hs1 (87 MB). /gbdb symlinks unchanged. The trackDb
colorsDbSv stanza is updated to reference the new AS field names
(acHom/acHet/acHemi, AF, AN) and to add the insLen filter. Also
fixes a nearby `version 1.1` -> `dataVersion 1.1` typo in
lrSv1kgOnt that was failing the tagTypes check.
refs #36258
- src/hg/makeDb/doc/hg38/lrSv.txt - lines changed 21, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvColorsDbSv.as - lines changed 28, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvColorsDbSvBuild.sh - lines changed 37, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvColorsDbSvVcfToBed.py - lines changed 174, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 161, context: html, text, full: html, text
151410cc48b9b1f8b1cb9bee89b7004eca871c61 Wed Apr 22 09:03:35 2026 -0700
- lrSv: harmonize long-read shortLabels, add aprSv/cpc1Sv/abelSv to overview
Normalize the shortLabel text of every long-read subtrack to the pattern
"<Cohort> <N> SVs" (no commas in N): CoLoRSdb 1427, AoU 1027, ToMMo 333,
GA4K 502, deCODE 3622, HPRC v2 233, Kim PD 100 prelim. Short-read
comparators (abelSv, onekg3202Sr, tommoJpCnv) are left alone per user
instruction.
Also add three rows that were missing from lrSv.html's overview table:
aprSv (Arab APR 53), cpc1Sv (CPC 58, HPRC-specific SVs removed) and
abelSv (CCDG 17,795 Illumina short-read comparator). Updates the
comparator footnote to mention both short-read rows.
refs #36258
- src/hg/makeDb/trackDb/human/lrSv.html - lines changed 33, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 7, context: html, text, full: html, text
f058c8fe4601b223ff47468eb3525c05ccd03850 Wed Apr 22 09:17:17 2026 -0700
- srSv: new short-read SV supertrack, split out of lrSv
Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr,
tommoJpCnv) out of the Long-read SV supertrack into a new sibling
supertrack srSv (Short-read SVs), so the lrSv collection contains
only long-read callsets. Filter fields (svType, svLen, insLen, AC)
are mirrored at the srSv supertrack level to keep the UX parallel
to lrSv.
- trackDb: new human/srSv.ra with the three subtrack stanzas and
updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas
removed from human/lrSv.ra. human/trackDb.ra now includes
srSv.ra. Also a new human/srSv.html overview page; the SR rows
and SR-specific paragraphs removed from human/lrSv.html.
- Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/
{lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to
scripts/srSv/ with git mv (history preserved) and renamed to
drop the "lrSv" prefix. Internal path references in abelSvBuild.sh
and abelSvVcfToBed.py updated.
- makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and
extended with the onekg3202Sr and tommoJpCnv sections moved from
lrSv.txt. lrSv.txt leaves a pointer.
- Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr,
lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*.
/gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and
/gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/.
refs #36258
- src/hg/makeDb/doc/hg38/abelSv.txt - lines changed 37, context: html, text, full: html, text
- src/hg/makeDb/doc/hg38/lrSv.txt - lines changed 48, context: html, text, full: html, text
- src/hg/makeDb/doc/hg38/srSv.txt - lines changed 99, context: html, text, full: html, text
- src/hg/makeDb/scripts/srSv/abelSv.as - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/makeDb/scripts/srSv/abelSvBuild.sh - lines changed 7, context: html, text, full: html, text
- src/hg/makeDb/scripts/srSv/abelSvVcfToBed.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/makeDb/scripts/srSv/onekg3202Sr.as - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/makeDb/scripts/srSv/onekg3202SrVcfToBed.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/makeDb/scripts/srSv/tommoJpCnvVcfToBedGraph.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/makeDb/trackDb/human/lrSv.html - lines changed 50, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 114, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/srSv.html - lines changed 105, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/srSv.ra - lines changed 137, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 1, context: html, text, full: html, text
66ea6cb4eaf2036e464be55b295765ed5105a0fb Wed Apr 22 09:42:25 2026 -0700
- hgTrackUi/hui: render filter UI on supertrack configuration pages
Supertracks (group of tracks with superTrack on, no data of their own)
previously had no way to expose a shared filter: their trackDb stanza
can declare filter.* / filterByRange.* / filterValues.*, but those
settings were never drawn on the supertrack's hgTrackUi page. So users
had to open each subtrack's own configuration page and set the same
filter there, and the "lrSv.filter.svLen" cart namespace went unused.
This change wires that up:
- hgTrackUi.c (superTrackUi): after listing the subtracks, if the
supertrack tdb declares any filter.* settings call scoreCfgUi() to
render the standard filter UI. Cart variables land under the
supertrack's own name (e.g. "lrSv.filter.svLen.min"), and subtracks
already inherit them through cartOptionalStringClosestToHome()
walking tdb->parent. Subtrack-level values continue to override.
- hui.c:
- buildFilterBy() / filterByValues(): tolerate a NULL autoSql object,
so supertracks (which have no data table) don't errAbort when they
declare filterValues.* of virtual aggregated fields. Missing-field
errAbort still fires in the normal subtrack case.
- scoreCfgUi() / cfgByCfgType(): when called with title == NULL (the
supertrack filter path), suppress the default "<p>" separator and
the "<BR>" between the title bar and the filter block; the caller
renders its own section heading.
- asForTdb(): handle conn == NULL by returning NULL rather than
crashing, since supertrack filter rendering has no associated
sqlConnection.
refs #37426
- src/hg/hgTrackUi/hgTrackUi.c - lines changed 21, context: html, text, full: html, text
bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
- lrSv/srSv: human-readable SV type filter labels, script cleanups
Add human-readable labels to the supertrack-level svType filter on
both the lrSv and srSv supertracks using the "CODE|CODE (Long name)"
filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)",
etc. Labels keep the short code up front so users can match what
hgTracks shows next to each feature.
Also sweep in the in-progress converter/as-file cleanups under
scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py
helpers, consistent insLen / svLen / AC column naming, tightened
field-description text) that had been piling up as an unstaged
working tree.
refs #36258
- src/hg/makeDb/scripts/lrSv/lrSv.as - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSv1kgOnt.as - lines changed 5, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSv1kgOntVcfToBed.py - lines changed 42, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvAou1k.as - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvAou1kCsvToBed.py - lines changed 30, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvApr.as - lines changed 5, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvAprVcfToBed.py - lines changed 28, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvChirmade101.as - lines changed 4, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvChirmade101TsvToBed.py - lines changed 27, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvCommon.py - lines changed 138, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvCpc1.as - lines changed 5, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvCpc1VcfToBed.py - lines changed 23, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvDecode.as - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvDecodeVcfToBed.py - lines changed 23, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvGa4kSv.as - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvGa4kSvVcfToBed.py - lines changed 24, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvGustafson.as - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvGustafsonVcfToBed.py - lines changed 27, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvHgsvc2.as - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvHgsvc2TsvToBed.py - lines changed 18, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvHgsvc3.as - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvHgsvc3TsvToBed.py - lines changed 22, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvHprc2.as - lines changed 4, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvHprc2VcfToBed.py - lines changed 33, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvKwanho.as - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvKwanhoTsvToBed.py - lines changed 42, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvTommoJp.as - lines changed 4, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvTommoJpVcfToBed.py - lines changed 20, context: html, text, full: html, text
- src/hg/makeDb/scripts/lrSv/lrSvVcfToBed.py - lines changed 29, context: html, text, full: html, text
- src/hg/makeDb/scripts/srSv/abelSv.as - lines changed 4, context: html, text, full: html, text
- src/hg/makeDb/scripts/srSv/abelSvVcfToBed.py - lines changed 34, context: html, text, full: html, text
- src/hg/makeDb/scripts/srSv/onekg3202Sr.as - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/scripts/srSv/onekg3202SrVcfToBed.py - lines changed 23, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/abelSv.html - lines changed 28, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/aou1kSv.html - lines changed 30, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/aprSv.html - lines changed 36, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/chirmade101Sv.html - lines changed 32, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/colorsDbSv.html - lines changed 4, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/cpc1Sv.html - lines changed 36, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/decodeSv.html - lines changed 26, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/ga4kSv.html - lines changed 29, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/gustafsonSv.html - lines changed 30, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/han945Sv.html - lines changed 26, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hgsvc2Sv.html - lines changed 29, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hgsvc3Sv.html - lines changed 38, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hprc2Sv.html - lines changed 31, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/kwanhoSv.html - lines changed 36, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/lrSv1kgOnt.html - lines changed 38, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/onekg3202Sr.html - lines changed 36, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/srSv.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/tommoJpSv.html - lines changed 33, context: html, text, full: html, text
f30798ae5d11e88e0ab7eb2bcab634e253fd0675 Thu Apr 23 10:36:40 2026 -0700
- Add gnomAD MPC v4.1.1 track to hg38.
New composite track under the gnomAD container showing per-variant
MPC (Missense deleteriousness Prediction by Constraint) scores from
gnomAD v4.1.1. Four bigWigs provide per-base scores (one per ALT
nucleotide); a companion bigBed carries the ~250K multi-transcript
variants with a per-transcript breakdown. Included via 'alpha' for
QA review. refs #37434
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/doc/hg38/gnomadMpc.txt - lines changed 46, context: html, text, full: html, text
- src/hg/makeDb/scripts/gnomadMpc/gnomadMpc.as - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/scripts/gnomadMpc/gnomadMpcToBed.py - lines changed 97, context: html, text, full: html, text
- src/hg/makeDb/scripts/gnomadMpc/gnomadMpcToWig.py - lines changed 86, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/gnomadMpc.html - lines changed 175, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/gnomadMpc.ra - lines changed 79, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text
5fa73cd9b411b3147227a4a31f6df7b24638dd00 Fri Apr 24 05:37:11 2026 -0700
- adding exon length to mouseover, refs #37439
- src/hg/hgTracks/simpleTracks.c - lines changed 4, context: html, text, full: html, text
875dc5de11d5e0eb51e94cb37d5b74da447a6c7b Fri Apr 24 06:17:18 2026 -0700
- removing old nmdEscape track from tdb, no redmine
- src/hg/makeDb/trackDb/human/nmdEscape.ra - lines changed 22, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 1, context: html, text, full: html, text
0151d00a4a1d73a78c35f6158c6c936ff338faeb Fri Apr 24 10:37:34 2026 -0700
- NMD Escape: MANE subtrack, Rule 1 bug fix, transcript filter. refs #33737
- Add nmdEscMane subtrack (MANE Select Plus Clinical 1.5), built from
/gbdb/hg38/mane/mane.bb. Reuses nmdEscTranscripts.html.
- Fix Rule 1: measure 50 bp upstream of the transcript's last splice
junction (including 3'UTR introns) rather than stripping 3'UTR from
the exon list first. The old logic painted the entire last CDS exon
as NMD-escape whenever the transcript had only one CDS exon, even
when a 3'UTR intron sat far past the stop codon (e.g. NBDY: 207 bp
of CDS over-painted for a junction 2.6 kb past the stop).
- Add --rule1-mode {cds,mrna} (default cds): cds counts only CDS bp
on the walk-back (paints up to 50 bp of CDS matching the rule label
literally); mrna counts mRNA bp and clips to CDS (tracks the 55 bp
rule literature). Documented in makeDoc.
- Rule 4: when a 3'UTR intron exists, the last CDS-containing exon
has a downstream EJC and is now eligible for the long-exon rule.
- Mouseover lists contributing transcript accessions when 1-3 items
collapse into a region; falls back to a count above that.
- Add filterText/filterType/filterLabel on all three escape subtracks
so a user can narrow the display to one transcript.
- genePredNmdEsc: --gene-sym-field (default 17 for Gencode; pass 18
for MANE, whose HGNC symbol lives in bigGenePred geneName2).
- Add findShortTxLongUtrIntron.py helper for finding MANE transcripts
with long UTR introns (used to pick NMD edge-case test cases).
Post-fix collapsed-region counts (--rule1-mode=cds):
MANE 1.5: 67,752
Gencode V49: 233,375
RefSeq Curated: 112,356
- src/hg/makeDb/doc/hg38/nmd.txt - lines changed 51, context: html, text, full: html, text
- src/hg/makeDb/scripts/nmd/findShortTxLongUtrIntron.py - lines changed 98, context: html, text, full: html, text
- src/hg/makeDb/scripts/nmd/genePredNmdEsc - lines changed 139, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/nmd.ra - lines changed 21, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/nmdEscTranscripts.html - lines changed 18, context: html, text, full: html, text
3a62ea7e9a8cb3503586a0a78570331308c9bc58 Mon Apr 27 02:23:00 2026 -0700
- NMD Escape MANE: expose NM_ accession via labelFields. refs #33737
Per QA, the MANE subtrack now shows the NCBI RefSeq accession by default
instead of the HGNC gene symbol, with the ENST and gene symbol still
selectable via labelFields.
- genePredNmdEsc: new --ncbi-id-field N option (default -1 = unused).
When set, the named bigGenePred column is captured per-transcript and
written into a new ncbiIds output column. For MANE pass 21.
- genePredNmdEsc: new --no-collapse option. By default, regions with
identical (chrom, start, end, rule) from multiple transcripts collapse
into one row with comma-separated lists. With --no-collapse the script
emits one row per (transcript, region). Used for MANE so each
label-field column holds a single value: the 74 MANE Plus Clinical
genes (e.g. LMNA) get two rows per region instead of one row with a
two-element list.
- nmdEscCollapsed.as: add lstring ncbiIds column. Schema is now bed9+3.
- nmd.ra (nmdEscMane only): labelFields ncbiIds,name,transcripts;
defaultLabelFields ncbiIds; labelSeparator " / ". Gencode and RefSeq
subtracks unchanged - they default to the gene symbol (name column)
and have an empty ncbiIds column.
- doc/hg38/nmd.txt: bump all three bedToBigBed invocations to bed9+3
and document the --ncbi-id-field 21 + --no-collapse invocation for
MANE.
Counts: MANE 68,028 (--no-collapse); Gencode 233,375; RefSeq 112,356.
- src/hg/makeDb/doc/hg38/nmd.txt - lines changed 12, context: html, text, full: html, text
- src/hg/makeDb/scripts/nmd/genePredNmdEsc - lines changed 29, context: html, text, full: html, text
- src/hg/makeDb/scripts/nmd/nmdEscCollapsed.as - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/nmd.ra - lines changed 7, context: html, text, full: html, text
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