Commits for chmalee

v504_base to v505_preview (2026-09-21 to 2026-10-05) v505

1ab5d5566906c050e5bc8ce2bf2a21cf0d08e439 Mon Sep 21 15:23:53 2026 -0700

• Fix hubspace UI race condition on file metadata editing, wait for the hub.txt parse to finish before offering file metadata edit, refs #38398
  • src/hg/js/hgMyData.js - lines changed 20, context: html, text, full: html, text

a3dbceed952bbbfbd67e73148714bb3a828a0ec8 Mon Sep 21 15:24:52 2026 -0700

• Add some uiTests for hubspace, mostly checking that file metadata editing works when a hub.txt is in a batch. This test does not actually test uploading anything, refs #38398
  • src/hg/hgHubConnect/tests/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/hgHubConnect/tests/pages/hgHubConnect.js - lines changed 130, context: html, text, full: html, text
  • src/hg/hgHubConnect/tests/t01-hubTxtGenome.js - lines changed 80, context: html, text, full: html, text

0325ff9542311af737bd2eadd9b105d863c79574 Tue Sep 22 10:58:54 2026 -0700

• Make trackHubSkipHubName not return invalid pointers on bad input names, refs #38414
  • src/hg/lib/trackHub.c - lines changed 4, context: html, text, full: html, text

2cdae04ddc1e46cdfc2e5e8cf479cbbbb616ad10 Tue Sep 22 15:55:10 2026 -0700

• htmlSanitize tooltips before printing them into the page, refs #38226
  • src/hg/hgTracks/imageV2.c - lines changed 30, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 13, context: html, text, full: html, text
  • src/hg/js/hgTracks.js - lines changed 7, context: html, text, full: html, text
  • src/hg/js/utils.js - lines changed 2, context: html, text, full: html, text

3f7bd2d5d5d8c71665acbd21926a2333afe2c674 Wed Sep 23 11:20:20 2026 -0700

• Fix one last tooltip encoding spot after nightly code review, refs #38226
  • src/hg/js/utils.js - lines changed 1, context: html, text, full: html, text

0c48fcbee53684d81c83e92973238ad49d8e1f32 Wed Sep 23 11:46:28 2026 -0700

• Fix the html,css,,javascript, and attribute Encode methods to handle null input strings, refs #38226
  • src/lib/htmshell.c - lines changed 12, context: html, text, full: html, text

31f2090cd11876f61a92260838078077f68a94ee Thu Sep 24 15:32:25 2026 -0700

• Add a test program and wrapper for debugging hung https connections, refs #38366
  • src/lib/tests/httpsFerryLeakTest.c - lines changed 76, context: html, text, full: html, text
  • src/lib/tests/httpsFerryLeakTest.sh - lines changed 60, context: html, text, full: html, text
  • src/lib/tests/makefile - lines changed 5, context: html, text, full: html, text

de6d2d4e5d0106a57d1ada79e9e36005676c260e Fri Sep 25 12:39:18 2026 -0700

• Add trackDb defined filters, coloring, and mouseovers for vcf tracks, using INFO fields or sub INFO fields, like vep.Consequence, refs #37617, #37618
  • src/hg/hgTracks/bigBedTrack.c - lines changed 18, context: html, text, full: html, text
  • src/hg/hgTracks/vcfTrack.c - lines changed 323, context: html, text, full: html, text
  • src/hg/inc/bigBedFilter.h - lines changed 18, context: html, text, full: html, text
  • src/hg/inc/hui.h - lines changed 9, context: html, text, full: html, text
  • src/hg/inc/vcfUi.h - lines changed 62, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 26, context: html, text, full: html, text
  • src/hg/lib/vcfUi.c - lines changed 624, context: html, text, full: html, text

f20626542200362afacab9387842e1f5bb50c87c Fri Sep 25 12:43:42 2026 -0700

• Experimental gnomAD v4.1.1 VCF track for hg38, refs #37617
  • src/hg/makeDb/scripts/gnomadV4.1.1/downloadGnomadV4.1.1.sh - lines changed 50, context: html, text, full: html, text
  • src/hg/makeDb/scripts/gnomadV4.1.1/loadGnomadV4.1.1ChromTables.sh - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gnomad.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gnomadV4.1.1.ra - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 2, context: html, text, full: html, text

bd6026f91fd94fe919fd1b815d27668759021196 Fri Sep 25 13:10:55 2026 -0700

• Fix vcf filter code after merging with master, refs #37617
  • src/hg/lib/hui.c - lines changed 6, context: html, text, full: html, text

280bb44983d29e071e862ede483aececbf22d482 Mon Sep 28 09:53:56 2026 -0700

• Remove vcfPhasedTrio type from colorByInfo tag as it is currently unsupported for now, refs daily code review email
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text

124514ebfd25805353a22085ba5bc02c7bb7c159 Thu Oct 1 11:12:10 2026 -0700

• asmAlias: keep a name that has its own active dbDb row instead of swapping it for an alias, refs #38444 Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
  • src/hg/inc/asmAlias.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/asmAlias.c - lines changed 6, context: html, text, full: html, text