Commits for max

v495_base to v496_preview (2026-03-09 to 2026-03-16) v496

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/doc/hg38/mpravardb.txt - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mpravardb/mpravardb.as - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mpravardb/mpravardbToBed.py - lines changed 173, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/mpra.html - lines changed 209, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/mpra.ra - lines changed 12, context: html, text, full: html, text

56c1481dcd7988e497207c1a69bda2da42e986d0 Tue Mar 10 04:03:37 2026 -0700

• docs change after claude
  • src/hg/makeDb/doc/hg38/mpravardb.txt - lines changed 3, 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>
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/redmineDump - lines changed 247, context: html, text, full: html, text

c1f42e37c13dab40740b9994daa2040422dd3b30 Tue Mar 10 06:02:12 2026 -0700

• cleanup after claude
  • src/utils/makefile - lines changed 2, context: html, text, full: html, text

903fa16639cacdeb96b1cb4eb8ba706d70c93236 Tue Mar 10 14:46:10 2026 -0700

• better err msg, refs #37219
  • src/hg/lib/hui.c - lines changed 1, context: html, text, full: html, text

72bb682e10783656300effd6c4d00141907da610 Thu Mar 12 05:35:40 2026 -0700

• fixing build error
  • src/utils/makefile - lines changed 2, 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/doc/hg38/webstr.txt - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/scripts/webstr/webstr.as - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/scripts/webstr/webstrToBed.py - lines changed 115, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/strVar.html - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/webstr.html - lines changed 115, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/webstr.ra - lines changed 21, 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/strchive.txt - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/scripts/strchive/strchive.as - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/scripts/strchive/strchiveToBed.py - lines changed 61, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/strVar.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/strchive.html - lines changed 98, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/webstr.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>
  • src/hg/makeDb/doc/hg38/gnomadStr.txt - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/scripts/gnomadStr/gnomadStr.as - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/scripts/gnomadStr/gnomadStrToBed.py - lines changed 126, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gnomad.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gnomadStr.html - lines changed 125, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/relatedTracks.ra - lines changed 3, 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/js/subCfg.js - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/strVar.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, 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
  • src/hg/makeDb/trackDb/human/hg38/gnomad.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gnomadV4.1.html - lines changed 14, 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/gnomad.ra - lines changed 2, 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/gnomadV4.1.html - lines changed 25, 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/ncOrfs.ra - lines changed 60, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/strVar.html - lines changed 4, context: html, text, full: html, text