File Changes for max
switch to commits view, user indexv495_base to v496_preview (2026-03-09 to 2026-03-16) v496
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- src/hg/js/subCfg.js
- lines changed 46, context: html, text, full: html, text
31a8f798f6eb4466ccb1a7b76e5644b55c369980 Fri Mar 13 06:16:40 2026 -0700
subCfg: auto-show/hide composite vis on subtrack checkbox changes, refs #37182
Move the logic that auto-sets composite visibility to pack/hide when
subtracks are checked/unchecked into a separate onUserCbChange handler
bound via native addEventListener. jQuery .trigger('change') only fires
jQuery handlers, not native ones, so this correctly distinguishes real
user clicks from programmatic triggers during page init. Also bind it
on matCB (matrix) checkboxes and check only visible subCBs to avoid
counting hidden-but-checked subtracks.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/lib/hui.c
- lines changed 1, context: html, text, full: html, text
903fa16639cacdeb96b1cb4eb8ba706d70c93236 Tue Mar 10 14:46:10 2026 -0700
better err msg, refs #37219
- src/hg/makeDb/doc/hg38/gnomadStr.txt
- lines changed 33, context: html, text, full: html, text
f43f1239645183b88a00b3de83f74fd5553e6ce1 Thu Mar 12 07:52:35 2026 -0700
Add gnomAD STR genotype track under gnomadVariants supertrack
87 disease-associated STR loci from gnomAD v3.1.3, aggregated from
~1.4M individual genotypes (18,511 WGS samples, ExpansionHunter v5).
Includes allele frequency distributions and population breakdowns.
Added relatedTracks links to strVar supertrack, refs #35420, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/doc/hg38/mpravardb.txt
- lines changed 22, context: html, text, full: html, text
ce180274fa3ba3db5c10ecbd9ae2479d4816e972 Tue Mar 10 04:00:45 2026 -0700
Add MPRAVarDB track: 239k MPRA-tested regulatory variants from 18 studies
Convert MPRAVarDB CSV (Wang et al. 2024) to bigBed9+ with liftOver of
hg19 variants to hg38. Color by significance (red=FDR<0.05, orange=p<0.05,
grey=not significant). MouseOver shows ref/alt/cell line/log2FC/p/FDR.
Track added to existing MPRAs superTrack, refs #34284
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- lines changed 3, context: html, text, full: html, text
56c1481dcd7988e497207c1a69bda2da42e986d0 Tue Mar 10 04:03:37 2026 -0700
docs change after claude
- src/hg/makeDb/doc/hg38/strchive.txt
- lines changed 32, context: html, text, full: html, text
e82a8101c1aa495e0e6c841f83f4d6c980fddf49 Thu Mar 12 07:28:49 2026 -0700
Add STRchive disease-associated STR loci track to strVar supertrack
75 curated disease-associated tandem repeat expansion loci from
STRchive (Hiatt et al. 2025), with pathogenic thresholds, inheritance
modes, and disease annotations. Colored by inheritance mode, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/doc/hg38/webstr.txt
- lines changed 40, context: html, text, full: html, text
6bb46ba4e8d91ab3670d354ef18d8bf5321ec9ee Thu Mar 12 07:15:29 2026 -0700
Add WebSTR short tandem repeat track under new strVar supertrack
New track with 1.7M STR loci from WebSTR EnsembleTR panel (hg38),
with allele frequency data for 5 populations from 1000 Genomes
(3,550 samples). Includes conversion script, .as schema, trackDb,
and full HTML documentation, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/scripts/gnomadStr/gnomadStr.as
- lines changed 21, context: html, text, full: html, text
f43f1239645183b88a00b3de83f74fd5553e6ce1 Thu Mar 12 07:52:35 2026 -0700
Add gnomAD STR genotype track under gnomadVariants supertrack
87 disease-associated STR loci from gnomAD v3.1.3, aggregated from
~1.4M individual genotypes (18,511 WGS samples, ExpansionHunter v5).
Includes allele frequency distributions and population breakdowns.
Added relatedTracks links to strVar supertrack, refs #35420, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/scripts/gnomadStr/gnomadStrToBed.py
- lines changed 126, context: html, text, full: html, text
f43f1239645183b88a00b3de83f74fd5553e6ce1 Thu Mar 12 07:52:35 2026 -0700
Add gnomAD STR genotype track under gnomadVariants supertrack
87 disease-associated STR loci from gnomAD v3.1.3, aggregated from
~1.4M individual genotypes (18,511 WGS samples, ExpansionHunter v5).
Includes allele frequency distributions and population breakdowns.
Added relatedTracks links to strVar supertrack, refs #35420, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/scripts/mpravardb/mpravardb.as
- lines changed 26, context: html, text, full: html, text
ce180274fa3ba3db5c10ecbd9ae2479d4816e972 Tue Mar 10 04:00:45 2026 -0700
Add MPRAVarDB track: 239k MPRA-tested regulatory variants from 18 studies
Convert MPRAVarDB CSV (Wang et al. 2024) to bigBed9+ with liftOver of
hg19 variants to hg38. Color by significance (red=FDR<0.05, orange=p<0.05,
grey=not significant). MouseOver shows ref/alt/cell line/log2FC/p/FDR.
Track added to existing MPRAs superTrack, refs #34284
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/scripts/mpravardb/mpravardbToBed.py
- lines changed 173, context: html, text, full: html, text
ce180274fa3ba3db5c10ecbd9ae2479d4816e972 Tue Mar 10 04:00:45 2026 -0700
Add MPRAVarDB track: 239k MPRA-tested regulatory variants from 18 studies
Convert MPRAVarDB CSV (Wang et al. 2024) to bigBed9+ with liftOver of
hg19 variants to hg38. Color by significance (red=FDR<0.05, orange=p<0.05,
grey=not significant). MouseOver shows ref/alt/cell line/log2FC/p/FDR.
Track added to existing MPRAs superTrack, refs #34284
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/scripts/strchive/strchive.as
- lines changed 19, context: html, text, full: html, text
e82a8101c1aa495e0e6c841f83f4d6c980fddf49 Thu Mar 12 07:28:49 2026 -0700
Add STRchive disease-associated STR loci track to strVar supertrack
75 curated disease-associated tandem repeat expansion loci from
STRchive (Hiatt et al. 2025), with pathogenic thresholds, inheritance
modes, and disease annotations. Colored by inheritance mode, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/scripts/strchive/strchiveToBed.py
- lines changed 61, context: html, text, full: html, text
e82a8101c1aa495e0e6c841f83f4d6c980fddf49 Thu Mar 12 07:28:49 2026 -0700
Add STRchive disease-associated STR loci track to strVar supertrack
75 curated disease-associated tandem repeat expansion loci from
STRchive (Hiatt et al. 2025), with pathogenic thresholds, inheritance
modes, and disease annotations. Colored by inheritance mode, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/scripts/webstr/webstr.as
- lines changed 31, context: html, text, full: html, text
6bb46ba4e8d91ab3670d354ef18d8bf5321ec9ee Thu Mar 12 07:15:29 2026 -0700
Add WebSTR short tandem repeat track under new strVar supertrack
New track with 1.7M STR loci from WebSTR EnsembleTR panel (hg38),
with allele frequency data for 5 populations from 1000 Genomes
(3,550 samples). Includes conversion script, .as schema, trackDb,
and full HTML documentation, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/scripts/webstr/webstrToBed.py
- lines changed 115, context: html, text, full: html, text
6bb46ba4e8d91ab3670d354ef18d8bf5321ec9ee Thu Mar 12 07:15:29 2026 -0700
Add WebSTR short tandem repeat track under new strVar supertrack
New track with 1.7M STR loci from WebSTR EnsembleTR panel (hg38),
with allele frequency data for 5 populations from 1000 Genomes
(3,550 samples). Includes conversion script, .as schema, trackDb,
and full HTML documentation, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/trackDb/human/hg38/gnomad.ra
- lines changed 14, context: html, text, full: html, text
f43f1239645183b88a00b3de83f74fd5553e6ce1 Thu Mar 12 07:52:35 2026 -0700
Add gnomAD STR genotype track under gnomadVariants supertrack
87 disease-associated STR loci from gnomAD v3.1.3, aggregated from
~1.4M individual genotypes (18,511 WGS samples, ExpansionHunter v5).
Includes allele frequency distributions and population breakdowns.
Added relatedTracks links to strVar supertrack, refs #35420, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- lines changed 2, context: html, text, full: html, text
44a568b95d278dc404a42e24c5877b523aa42e50 Fri Mar 13 07:37:16 2026 -0700
adding a note to gnomad to make it clear that 3.1 should not be used, email from Chris
- lines changed 2, context: html, text, full: html, text
b0c906a6201e5c88b7cb936f9f5e8f87da38b2fc Fri Mar 13 07:43:13 2026 -0700
gnomad track is now much more than variants, so removing the variants name from the shortlabel, no redmine
- src/hg/makeDb/trackDb/human/hg38/gnomadStr.html
- lines changed 125, context: html, text, full: html, text
f43f1239645183b88a00b3de83f74fd5553e6ce1 Thu Mar 12 07:52:35 2026 -0700
Add gnomAD STR genotype track under gnomadVariants supertrack
87 disease-associated STR loci from gnomAD v3.1.3, aggregated from
~1.4M individual genotypes (18,511 WGS samples, ExpansionHunter v5).
Includes allele frequency distributions and population breakdowns.
Added relatedTracks links to strVar supertrack, refs #35420, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/trackDb/human/hg38/gnomadV4.1.html
- lines changed 14, context: html, text, full: html, text
44a568b95d278dc404a42e24c5877b523aa42e50 Fri Mar 13 07:37:16 2026 -0700
adding a note to gnomad to make it clear that 3.1 should not be used, email from Chris
- lines changed 25, context: html, text, full: html, text
7577ca944ad2c81bd75ad35993c8b86dc471fef1 Fri Mar 13 07:48:31 2026 -0700
the gnomad track had no intro at all anymore, so I added one, no redmine
- src/hg/makeDb/trackDb/human/hg38/mpra.html
- lines changed 209, context: html, text, full: html, text
ce180274fa3ba3db5c10ecbd9ae2479d4816e972 Tue Mar 10 04:00:45 2026 -0700
Add MPRAVarDB track: 239k MPRA-tested regulatory variants from 18 studies
Convert MPRAVarDB CSV (Wang et al. 2024) to bigBed9+ with liftOver of
hg19 variants to hg38. Color by significance (red=FDR<0.05, orange=p<0.05,
grey=not significant). MouseOver shows ref/alt/cell line/log2FC/p/FDR.
Track added to existing MPRAs superTrack, refs #34284
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/trackDb/human/hg38/mpra.ra
- lines changed 12, context: html, text, full: html, text
ce180274fa3ba3db5c10ecbd9ae2479d4816e972 Tue Mar 10 04:00:45 2026 -0700
Add MPRAVarDB track: 239k MPRA-tested regulatory variants from 18 studies
Convert MPRAVarDB CSV (Wang et al. 2024) to bigBed9+ with liftOver of
hg19 variants to hg38. Color by significance (red=FDR<0.05, orange=p<0.05,
grey=not significant). MouseOver shows ref/alt/cell line/log2FC/p/FDR.
Track added to existing MPRAs superTrack, refs #34284
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/trackDb/human/hg38/ncOrfs.ra
- lines changed 60, context: html, text, full: html, text
8a818d25a85939496ec2c133bb37c3702921fe43 Fri Mar 13 15:02:19 2026 -0700
commit missing files due to build problems, refs #37036
- src/hg/makeDb/trackDb/human/hg38/strVar.html
- lines changed 27, context: html, text, full: html, text
6bb46ba4e8d91ab3670d354ef18d8bf5321ec9ee Thu Mar 12 07:15:29 2026 -0700
Add WebSTR short tandem repeat track under new strVar supertrack
New track with 1.7M STR loci from WebSTR EnsembleTR panel (hg38),
with allele frequency data for 5 populations from 1000 Genomes
(3,550 samples). Includes conversion script, .as schema, trackDb,
and full HTML documentation, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- lines changed 6, context: html, text, full: html, text
e82a8101c1aa495e0e6c841f83f4d6c980fddf49 Thu Mar 12 07:28:49 2026 -0700
Add STRchive disease-associated STR loci track to strVar supertrack
75 curated disease-associated tandem repeat expansion loci from
STRchive (Hiatt et al. 2025), with pathogenic thresholds, inheritance
modes, and disease annotations. Colored by inheritance mode, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- lines changed 4, context: html, text, full: html, text
8a818d25a85939496ec2c133bb37c3702921fe43 Fri Mar 13 15:02:19 2026 -0700
commit missing files due to build problems, refs #37036
- src/hg/makeDb/trackDb/human/hg38/strVar.ra
- lines changed 5, context: html, text, full: html, text
31a8f798f6eb4466ccb1a7b76e5644b55c369980 Fri Mar 13 06:16:40 2026 -0700
subCfg: auto-show/hide composite vis on subtrack checkbox changes, refs #37182
Move the logic that auto-sets composite visibility to pack/hide when
subtracks are checked/unchecked into a separate onUserCbChange handler
bound via native addEventListener. jQuery .trigger('change') only fires
jQuery handlers, not native ones, so this correctly distinguishes real
user clicks from programmatic triggers during page init. Also bind it
on matCB (matrix) checkboxes and check only visible subCBs to avoid
counting hidden-but-checked subtracks.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/trackDb/human/hg38/strchive.html
- lines changed 98, context: html, text, full: html, text
e82a8101c1aa495e0e6c841f83f4d6c980fddf49 Thu Mar 12 07:28:49 2026 -0700
Add STRchive disease-associated STR loci track to strVar supertrack
75 curated disease-associated tandem repeat expansion loci from
STRchive (Hiatt et al. 2025), with pathogenic thresholds, inheritance
modes, and disease annotations. Colored by inheritance mode, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra
- lines changed 13, context: html, text, full: html, text
6bb46ba4e8d91ab3670d354ef18d8bf5321ec9ee Thu Mar 12 07:15:29 2026 -0700
Add WebSTR short tandem repeat track under new strVar supertrack
New track with 1.7M STR loci from WebSTR EnsembleTR panel (hg38),
with allele frequency data for 5 populations from 1000 Genomes
(3,550 samples). Includes conversion script, .as schema, trackDb,
and full HTML documentation, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- lines changed 1, context: html, text, full: html, text
31a8f798f6eb4466ccb1a7b76e5644b55c369980 Fri Mar 13 06:16:40 2026 -0700
subCfg: auto-show/hide composite vis on subtrack checkbox changes, refs #37182
Move the logic that auto-sets composite visibility to pack/hide when
subtracks are checked/unchecked into a separate onUserCbChange handler
bound via native addEventListener. jQuery .trigger('change') only fires
jQuery handlers, not native ones, so this correctly distinguishes real
user clicks from programmatic triggers during page init. Also bind it
on matCB (matrix) checkboxes and check only visible subCBs to avoid
counting hidden-but-checked subtracks.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/trackDb/human/hg38/webstr.html
- lines changed 115, context: html, text, full: html, text
6bb46ba4e8d91ab3670d354ef18d8bf5321ec9ee Thu Mar 12 07:15:29 2026 -0700
Add WebSTR short tandem repeat track under new strVar supertrack
New track with 1.7M STR loci from WebSTR EnsembleTR panel (hg38),
with allele frequency data for 5 populations from 1000 Genomes
(3,550 samples). Includes conversion script, .as schema, trackDb,
and full HTML documentation, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/trackDb/human/hg38/webstr.ra
- lines changed 21, context: html, text, full: html, text
6bb46ba4e8d91ab3670d354ef18d8bf5321ec9ee Thu Mar 12 07:15:29 2026 -0700
Add WebSTR short tandem repeat track under new strVar supertrack
New track with 1.7M STR loci from WebSTR EnsembleTR panel (hg38),
with allele frequency data for 5 populations from 1000 Genomes
(3,550 samples). Includes conversion script, .as schema, trackDb,
and full HTML documentation, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- lines changed 14, context: html, text, full: html, text
e82a8101c1aa495e0e6c841f83f4d6c980fddf49 Thu Mar 12 07:28:49 2026 -0700
Add STRchive disease-associated STR loci track to strVar supertrack
75 curated disease-associated tandem repeat expansion loci from
STRchive (Hiatt et al. 2025), with pathogenic thresholds, inheritance
modes, and disease annotations. Colored by inheritance mode, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/makeDb/trackDb/relatedTracks.ra
- lines changed 3, context: html, text, full: html, text
f43f1239645183b88a00b3de83f74fd5553e6ce1 Thu Mar 12 07:52:35 2026 -0700
Add gnomAD STR genotype track under gnomadVariants supertrack
87 disease-associated STR loci from gnomAD v3.1.3, aggregated from
~1.4M individual genotypes (18,511 WGS samples, ExpansionHunter v5).
Includes allele frequency distributions and population breakdowns.
Added relatedTracks links to strVar supertrack, refs #35420, refs #36652
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/utils/makefile
- lines changed 1, context: html, text, full: html, text
eef33606ff233b6ce9afd612e89fe80b99744312 Tue Mar 10 05:49:20 2026 -0700
Add redmineDump script to dump Redmine tickets as Markdown, refs #36890
Python script that reads redmine.apiKey from ~/.hg.conf, fetches a
ticket with all journals/attachments via the Redmine API, and outputs
the full discussion in Markdown. Supports --images to download
attachments to a temp directory.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- lines changed 2, context: html, text, full: html, text
c1f42e37c13dab40740b9994daa2040422dd3b30 Tue Mar 10 06:02:12 2026 -0700
cleanup after claude
- lines changed 2, context: html, text, full: html, text
72bb682e10783656300effd6c4d00141907da610 Thu Mar 12 05:35:40 2026 -0700
fixing build error
- src/utils/redmineDump
- lines changed 247, context: html, text, full: html, text
eef33606ff233b6ce9afd612e89fe80b99744312 Tue Mar 10 05:49:20 2026 -0700
Add redmineDump script to dump Redmine tickets as Markdown, refs #36890
Python script that reads redmine.apiKey from ~/.hg.conf, fetches a
ticket with all journals/attachments via the Redmine API, and outputs
the full discussion in Markdown. Supports --images to download
attachments to a temp directory.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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