File Changes for braney
switch to commits view, user indexv497_preview to v497_preview2 (2026-04-06 to 2026-04-13) v497
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- src/CLAUDE.md
- lines changed 14, context: html, text, full: html, text
44a5fa24f9a25c1295107787bb6b8f41fc07831c Thu Apr 9 15:48:44 2026 -0700
Add CLAUDE.md for AI assistant guidelines, no redmine
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- lines changed 1, context: html, text, full: html, text
e05d5d771d71b63c84029df3e27266717548eaef Fri Apr 10 10:48:00 2026 -0700
Add CSP inline handler rule to CLAUDE.md, no redmine
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- lines changed 1, context: html, text, full: html, text
f28c94cca4b3080f1957751f998628c95eae9168 Sun Apr 12 12:17:17 2026 -0700
Add rule to deploy static files via make, not manual copy
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 7, context: html, text, full: html, text
8593c40cb74ab6ee9f2318056626305d9d9544d3 Fri Apr 10 12:54:44 2026 -0700
Fix color picker from code review, refs #37329, refs #20460
- Replace Spectrum JS color picker with native HTML5 color input,
matching existing Hi-C picker
- Color saved on form submit, not immediately via AJAX
- Add checkbox to enable/disable color override; auto-checks when
user picks a color
- Gate color picker behind hg.conf showColorPicker=on (off by default)
- Only show picker for non-composite tracks that support it: bed,
bigBed, genePred, bigGenePred, wig, bigWig, rmsk, interact,
bigInteract, bigLolly, vcfTabix, vcf
- Add colorFromCart calls to interact, lolly, vcf phased, and pgSnp
drawing code
- Revert hui.js Spectrum changes from cfeb4d4 (no longer needed)
- Use htmlColorForCode()/htmlColorToRGB() from htmlColor.h instead of
hand-rolled hex parsing in colorFromCart
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/hgTracks/bedTrack.c
- lines changed 8, context: html, text, full: html, text
0c4b26c76ee09cadbe1a444016f2c41df33906f9 Thu Apr 9 15:48:53 2026 -0700
Fix color picker and quickLift issues from code review, refs #37329
Color picker: fix [object Object] bug by calling .toHexString() on spectrum
result, use htmlColor.h instead of hand-rolled hex parsing, show "color
override active" status when override is set. quickLift: remove redundant
quickLiftResolveTable call in genericBedClick, move hFindSplitTable into
else branch where it's needed.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- lines changed 8, context: html, text, full: html, text
4905867d4df06d0c4cfe5769998334eaed96d6d6 Thu Apr 9 16:02:15 2026 -0700
Revert "Fix color picker and quickLift issues from code review, refs #37329"
This reverts commit 0c4b26c76ee09cadbe1a444016f2c41df33906f9.
- lines changed 10, context: html, text, full: html, text
8593c40cb74ab6ee9f2318056626305d9d9544d3 Fri Apr 10 12:54:44 2026 -0700
Fix color picker from code review, refs #37329, refs #20460
- Replace Spectrum JS color picker with native HTML5 color input,
matching existing Hi-C picker
- Color saved on form submit, not immediately via AJAX
- Add checkbox to enable/disable color override; auto-checks when
user picks a color
- Gate color picker behind hg.conf showColorPicker=on (off by default)
- Only show picker for non-composite tracks that support it: bed,
bigBed, genePred, bigGenePred, wig, bigWig, rmsk, interact,
bigInteract, bigLolly, vcfTabix, vcf
- Add colorFromCart calls to interact, lolly, vcf phased, and pgSnp
drawing code
- Revert hui.js Spectrum changes from cfeb4d4 (no longer needed)
- Use htmlColorForCode()/htmlColorToRGB() from htmlColor.h instead of
hand-rolled hex parsing in colorFromCart
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/hgTracks/bigBedTrack.c
- lines changed 14, context: html, text, full: html, text
802ca99f5f06437c32db764bc8e01786ed395c21 Tue Apr 7 14:05:35 2026 -0700
Fix mergeSpannedItems not working with quickLift
For quickLifted tracks, bb->start/bb->end are in the source assembly
coordinates while winStart/winEnd are in the target assembly, so the
span check never matched. Use lf->start/lf->end (lifted coordinates)
when quickLiftFile is set. Also use cloneBed(bedCopy) for building the
merged item instead of re-parsing from source-assembly bedRow, refs #36048
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/hgTracks/hgTracks.c
- lines changed 32, context: html, text, full: html, text
b5cbbe9353e85ec653bb18eee381c6989f529289 Sun Apr 12 12:21:24 2026 -0700
Show alternative chromosome names from chromAlias on hgTracks position line, refs #29201
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/hgTracks/interactTrack.c
- lines changed 1, context: html, text, full: html, text
8593c40cb74ab6ee9f2318056626305d9d9544d3 Fri Apr 10 12:54:44 2026 -0700
Fix color picker from code review, refs #37329, refs #20460
- Replace Spectrum JS color picker with native HTML5 color input,
matching existing Hi-C picker
- Color saved on form submit, not immediately via AJAX
- Add checkbox to enable/disable color override; auto-checks when
user picks a color
- Gate color picker behind hg.conf showColorPicker=on (off by default)
- Only show picker for non-composite tracks that support it: bed,
bigBed, genePred, bigGenePred, wig, bigWig, rmsk, interact,
bigInteract, bigLolly, vcfTabix, vcf
- Add colorFromCart calls to interact, lolly, vcf phased, and pgSnp
drawing code
- Revert hui.js Spectrum changes from cfeb4d4 (no longer needed)
- Use htmlColorForCode()/htmlColorToRGB() from htmlColor.h instead of
hand-rolled hex parsing in colorFromCart
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/hgTracks/lollyTrack.c
- lines changed 2, context: html, text, full: html, text
8593c40cb74ab6ee9f2318056626305d9d9544d3 Fri Apr 10 12:54:44 2026 -0700
Fix color picker from code review, refs #37329, refs #20460
- Replace Spectrum JS color picker with native HTML5 color input,
matching existing Hi-C picker
- Color saved on form submit, not immediately via AJAX
- Add checkbox to enable/disable color override; auto-checks when
user picks a color
- Gate color picker behind hg.conf showColorPicker=on (off by default)
- Only show picker for non-composite tracks that support it: bed,
bigBed, genePred, bigGenePred, wig, bigWig, rmsk, interact,
bigInteract, bigLolly, vcfTabix, vcf
- Add colorFromCart calls to interact, lolly, vcf phased, and pgSnp
drawing code
- Revert hui.js Spectrum changes from cfeb4d4 (no longer needed)
- Use htmlColorForCode()/htmlColorToRGB() from htmlColor.h instead of
hand-rolled hex parsing in colorFromCart
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/hgTracks/simpleTracks.c
- lines changed 1, context: html, text, full: html, text
8593c40cb74ab6ee9f2318056626305d9d9544d3 Fri Apr 10 12:54:44 2026 -0700
Fix color picker from code review, refs #37329, refs #20460
- Replace Spectrum JS color picker with native HTML5 color input,
matching existing Hi-C picker
- Color saved on form submit, not immediately via AJAX
- Add checkbox to enable/disable color override; auto-checks when
user picks a color
- Gate color picker behind hg.conf showColorPicker=on (off by default)
- Only show picker for non-composite tracks that support it: bed,
bigBed, genePred, bigGenePred, wig, bigWig, rmsk, interact,
bigInteract, bigLolly, vcfTabix, vcf
- Add colorFromCart calls to interact, lolly, vcf phased, and pgSnp
drawing code
- Revert hui.js Spectrum changes from cfeb4d4 (no longer needed)
- Use htmlColorForCode()/htmlColorToRGB() from htmlColor.h instead of
hand-rolled hex parsing in colorFromCart
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/hgTracks/vcfTrack.c
- lines changed 1, context: html, text, full: html, text
8593c40cb74ab6ee9f2318056626305d9d9544d3 Fri Apr 10 12:54:44 2026 -0700
Fix color picker from code review, refs #37329, refs #20460
- Replace Spectrum JS color picker with native HTML5 color input,
matching existing Hi-C picker
- Color saved on form submit, not immediately via AJAX
- Add checkbox to enable/disable color override; auto-checks when
user picks a color
- Gate color picker behind hg.conf showColorPicker=on (off by default)
- Only show picker for non-composite tracks that support it: bed,
bigBed, genePred, bigGenePred, wig, bigWig, rmsk, interact,
bigInteract, bigLolly, vcfTabix, vcf
- Add colorFromCart calls to interact, lolly, vcf phased, and pgSnp
drawing code
- Revert hui.js Spectrum changes from cfeb4d4 (no longer needed)
- Use htmlColorForCode()/htmlColorToRGB() from htmlColor.h instead of
hand-rolled hex parsing in colorFromCart
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/hgc/hgc.c
- lines changed 25, context: html, text, full: html, text
b4538b995c8b87f8663861aa9cde4b8c68e83eb1 Tue Apr 7 12:52:56 2026 -0700
Fix Get DNA position text box being ignored when table is specified, and accept single-base positions. refs #10316, #15336, #37325
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- lines changed 6, context: html, text, full: html, text
54352b1c58abe76d6d8ea4404b4ffb9b00d294bf Wed Apr 8 12:23:43 2026 -0700
don't output links to transcript or gene on quickLifted decipher SNV
tracks #36061
- lines changed 6, context: html, text, full: html, text
1103e292ea1e3c3e1ac2daaa19f4752719ac5015 Thu Apr 9 14:52:32 2026 -0700
fix quickLift DECIPHER SNV: add missing space after Transcript, show correct position for lifted assembly, refs #36061
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- lines changed 15, context: html, text, full: html, text
0c4b26c76ee09cadbe1a444016f2c41df33906f9 Thu Apr 9 15:48:53 2026 -0700
Fix color picker and quickLift issues from code review, refs #37329
Color picker: fix [object Object] bug by calling .toHexString() on spectrum
result, use htmlColor.h instead of hand-rolled hex parsing, show "color
override active" status when override is set. quickLift: remove redundant
quickLiftResolveTable call in genericBedClick, move hFindSplitTable into
else branch where it's needed.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- lines changed 15, context: html, text, full: html, text
4905867d4df06d0c4cfe5769998334eaed96d6d6 Thu Apr 9 16:02:15 2026 -0700
Revert "Fix color picker and quickLift issues from code review, refs #37329"
This reverts commit 0c4b26c76ee09cadbe1a444016f2c41df33906f9.
- src/hg/htdocs/goldenPath/help/bigPsl.html
- lines changed 6, context: html, text, full: html, text
ca1f5d4b6f57481b8468c77dc40a65f9eb4ec029 Wed Apr 8 14:57:47 2026 -0700
Fix bigPsl.as documentation: say "other sequence" not "other chromosome", add PSL field names, refs #37155
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/htdocs/style/HGStyle.css
- lines changed 12, context: html, text, full: html, text
b5cbbe9353e85ec653bb18eee381c6989f529289 Sun Apr 12 12:21:24 2026 -0700
Show alternative chromosome names from chromAlias on hgTracks position line, refs #29201
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/inc/bigPsl.h
- lines changed 7, context: html, text, full: html, text
ca1f5d4b6f57481b8468c77dc40a65f9eb4ec029 Wed Apr 8 14:57:47 2026 -0700
Fix bigPsl.as documentation: say "other sequence" not "other chromosome", add PSL field names, refs #37155
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/inc/bigTransMap.h
- lines changed 6, context: html, text, full: html, text
ca1f5d4b6f57481b8468c77dc40a65f9eb4ec029 Wed Apr 8 14:57:47 2026 -0700
Fix bigPsl.as documentation: say "other sequence" not "other chromosome", add PSL field names, refs #37155
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/js/hui.js
- lines changed 9, context: html, text, full: html, text
0c4b26c76ee09cadbe1a444016f2c41df33906f9 Thu Apr 9 15:48:53 2026 -0700
Fix color picker and quickLift issues from code review, refs #37329
Color picker: fix [object Object] bug by calling .toHexString() on spectrum
result, use htmlColor.h instead of hand-rolled hex parsing, show "color
override active" status when override is set. quickLift: remove redundant
quickLiftResolveTable call in genericBedClick, move hFindSplitTable into
else branch where it's needed.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- lines changed 9, context: html, text, full: html, text
4905867d4df06d0c4cfe5769998334eaed96d6d6 Thu Apr 9 16:02:15 2026 -0700
Revert "Fix color picker and quickLift issues from code review, refs #37329"
This reverts commit 0c4b26c76ee09cadbe1a444016f2c41df33906f9.
- lines changed 22, context: html, text, full: html, text
8593c40cb74ab6ee9f2318056626305d9d9544d3 Fri Apr 10 12:54:44 2026 -0700
Fix color picker from code review, refs #37329, refs #20460
- Replace Spectrum JS color picker with native HTML5 color input,
matching existing Hi-C picker
- Color saved on form submit, not immediately via AJAX
- Add checkbox to enable/disable color override; auto-checks when
user picks a color
- Gate color picker behind hg.conf showColorPicker=on (off by default)
- Only show picker for non-composite tracks that support it: bed,
bigBed, genePred, bigGenePred, wig, bigWig, rmsk, interact,
bigInteract, bigLolly, vcfTabix, vcf
- Add colorFromCart calls to interact, lolly, vcf phased, and pgSnp
drawing code
- Revert hui.js Spectrum changes from cfeb4d4 (no longer needed)
- Use htmlColorForCode()/htmlColorToRGB() from htmlColor.h instead of
hand-rolled hex parsing in colorFromCart
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/lib/bigPsl.as
- lines changed 6, context: html, text, full: html, text
ca1f5d4b6f57481b8468c77dc40a65f9eb4ec029 Wed Apr 8 14:57:47 2026 -0700
Fix bigPsl.as documentation: say "other sequence" not "other chromosome", add PSL field names, refs #37155
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/lib/bigTransMap.as
- lines changed 6, context: html, text, full: html, text
ca1f5d4b6f57481b8468c77dc40a65f9eb4ec029 Wed Apr 8 14:57:47 2026 -0700
Fix bigPsl.as documentation: say "other sequence" not "other chromosome", add PSL field names, refs #37155
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/lib/hui.c
- lines changed 16, context: html, text, full: html, text
8593c40cb74ab6ee9f2318056626305d9d9544d3 Fri Apr 10 12:54:44 2026 -0700
Fix color picker from code review, refs #37329, refs #20460
- Replace Spectrum JS color picker with native HTML5 color input,
matching existing Hi-C picker
- Color saved on form submit, not immediately via AJAX
- Add checkbox to enable/disable color override; auto-checks when
user picks a color
- Gate color picker behind hg.conf showColorPicker=on (off by default)
- Only show picker for non-composite tracks that support it: bed,
bigBed, genePred, bigGenePred, wig, bigWig, rmsk, interact,
bigInteract, bigLolly, vcfTabix, vcf
- Add colorFromCart calls to interact, lolly, vcf phased, and pgSnp
drawing code
- Revert hui.js Spectrum changes from cfeb4d4 (no longer needed)
- Use htmlColorForCode()/htmlColorToRGB() from htmlColor.h instead of
hand-rolled hex parsing in colorFromCart
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/utils/otto/lrg/bigPsl+6.as
- lines changed 6, context: html, text, full: html, text
ca1f5d4b6f57481b8468c77dc40a65f9eb4ec029 Wed Apr 8 14:57:47 2026 -0700
Fix bigPsl.as documentation: say "other sequence" not "other chromosome", add PSL field names, refs #37155
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/utils/otto/uniprot/bigPslUniprot.as
- lines changed 6, context: html, text, full: html, text
ca1f5d4b6f57481b8468c77dc40a65f9eb4ec029 Wed Apr 8 14:57:47 2026 -0700
Fix bigPsl.as documentation: say "other sequence" not "other chromosome", add PSL field names, refs #37155
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/utils/redmineCli
- lines changed 187, context: html, text, full: html, text
9745b5b84a513b8fc527081b47f416884a0aad5f Tue Apr 7 14:57:14 2026 -0700
Add relate, watch, and users subcommands to redmineCli, refs #37339
- `relate`: create relations between two or more tickets
- `watch`: add watchers to a ticket by name
- `users`: list project members with short names and IDs
- Expand user ID table from 5 hardcoded MLQ members to all 42 project members
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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