Commits for lrnassar
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v501_preview2 to v501_base (2026-07-13 to 2026-07-20) v501
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9f9a96ab068a76799311c09a2813b0b28f8e7712 Mon Jul 13 12:52:41 2026 -0700
- Order EVE heatmap amino acid rows by class to match the MaveDB track. refs #37763
Change the heatmap row order from alphabetical to physicochemical-amino-acid-class order
(A V L I M F Y W R H K D E S T N Q G C P), matching the MaveDB Experiments heatmap so the
tracks can be compared row-for-row. Rebuilds eve.bb; updates the makedoc, the AutoSql row
label comment, and the description page.
- src/hg/makeDb/doc/hg38/eve.txt - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/scripts/eve/eve_heatmap.as - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/scripts/eve/vcfToEveHeatmap.py - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/eve.html - lines changed 2, context: html, text, full: html, text
3d194de4d74f67c1a453035e20c4769d88bec4c4 Mon Jul 13 12:52:57 2026 -0700
- Order popEVE heatmap amino acid rows by class to match the MaveDB track. refs #37791
Change the heatmap row order from alphabetical to physicochemical-amino-acid-class order
(A V L I M F Y W R H K D E S T N Q G C P), matching the MaveDB Experiments heatmap so the
tracks can be compared row-for-row. Rebuilds popEve.bb; updates the makedoc, the AutoSql
row label comment, and the description page.
- src/hg/makeDb/doc/hg38/popEve.txt - lines changed 4, context: html, text, full: html, text
- src/hg/makeDb/scripts/popEve/popEve_heatmap.as - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/scripts/popEve/vcfToPopEveHeatmap.py - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/popEve.html - lines changed 2, context: html, text, full: html, text
15bdf707a4bde0a281109bb810499a2fa98ef6ac Tue Jul 14 07:48:05 2026 -0700
- Fix stale "row Y" reference in popEVE trailingFix comment per CR feedback. refs #37791
The amino acid row reorder made P the last row, not Y, but the trailingFix explanation in
the converter comment and the makedoc still said "row Y, last column". Reworded both to be
order-agnostic ("last row, last column"). Documentation only; the code already operates
positionally on labelParts[-1].
- src/hg/makeDb/doc/hg38/popEve.txt - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/scripts/popEve/vcfToPopEveHeatmap.py - lines changed 3, context: html, text, full: html, text
3a5f01ff264521fd46312b8ada68f3b9c7708d64 Tue Jul 14 07:57:07 2026 -0700
- Add --since/--until window options to codeReviewAi.py --daily mode. refs #36890
Let --daily review an explicit date window instead of only the last N hours, so
a missed period can be backfilled in digestible chunks (e.g. one week at a time)
rather than one large bundle. --since (with optional --until) is passed straight
to git log; --hours behavior is unchanged when --since is absent, so the cron is
unaffected. The window is reflected in the review prompt, progress output, and
the failure-alert email, and is included in saved review filenames so same-day
backfill runs do not overwrite each other.
- src/utils/codeReviewAi.py - lines changed 58, context: html, text, full: html, text
8b1cdafd019d4adcad11a6712f48549b0460f1fa Tue Jul 14 10:31:16 2026 -0700
- Fix codeReviewAi.py false auth-failure on reviews that quote error strings. refs #36890
detect_cli_failure scanned the whole CLI response for auth-error markers before
validating, so a well-formed review whose text legitimately quotes strings like
"authentication_error" or "API Error: 401" (e.g. a review of the auth-handling
code itself) was misflagged as a Claude CLI authentication failure - skipping
the author email and firing a spurious alert. Validate the response first and
only scan for auth markers when it is not a valid review.
- src/utils/codeReviewAi.py - lines changed 10, context: html, text, full: html, text
6577d5ee1319bbea85988c1c89179436b4a94edf Tue Jul 14 11:27:59 2026 -0700
- Address code-review feedback on the Cardiomyopathy VCEP build scripts. refs #37446
- cmpVCEPCardioBoost.py: add the standard --db/--output-dir CLI. It previously
hardcoded the working directory for both its input TSV and its output (unlike
the 11 sibling scripts, and contrary to the makedoc's documented interface);
the build loop's flags were silently ignored. Output is unchanged (31,236
variants per assembly).
- Decode leftover HTML entities (arrows, >=, <=, +/-, x) in print/stderr
diagnostics, comments, and docstrings across all scripts so build logs read
cleanly. The mouseOver / bigBed display strings intentionally keep their
entities.
- cmpVCEPWalsh2019.py: fix the stale docstring that described the
ClinVar-unmatched entries as "deferred" (they are mapped via the hgvsToVcf
fallback, item L) and drop the unverified "163 rows" count.
Per code-review feedback on commit aa5669fe64. No track data changed.
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAFfrequencies.py - lines changed 13, context: html, text, full: html, text
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAnnotate.py - lines changed 4, context: html, text, full: html, text
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAtlasEF.py - lines changed 14, context: html, text, full: html, text
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPCardioBoost.py - lines changed 23, context: html, text, full: html, text
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPClinDomains.py - lines changed 10, context: html, text, full: html, text
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPClinVar506161.py - lines changed 8, context: html, text, full: html, text
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPEvRepo.py - lines changed 10, context: html, text, full: html, text
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPPVS1.py - lines changed 10, context: html, text, full: html, text
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPProvisionalClass.py - lines changed 14, context: html, text, full: html, text
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPRevel.py - lines changed 4, context: html, text, full: html, text
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPWalsh2019.py - lines changed 13, context: html, text, full: html, text
- src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPWalshOR.py - lines changed 4, context: html, text, full: html, text
9dc380d3c6aada6b12cbcd7a95d1d426b47ce86c Tue Jul 14 17:11:11 2026 -0700
- Add Long-read Structural Variants announcement (news archive + gateway news) and track pennantIcon. refs #36258
Add a July 16, 2026 news-archive entry announcing the Long-read Structural
Variants container track on hg38 and hs1, with a UGT2B17 example image, and add
the matching gateway indexNews item (dropping the oldest to keep six). Add a
"New" pennantIcon on the longReadVariants supertrack linking to the post. Also
move the still-unreleased ENCODE4 draft entry to July 22 and keep it commented
out.
- src/hg/htdocs/goldenPath/newsarch.html - lines changed 100, context: html, text, full: html, text
- src/hg/htdocs/images/longReadSVsAnnouncementImage.png - 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/htdocs/indexNews.html - lines changed 11, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 1, context: html, text, full: html, text
74385a9fce53d9b5c48e101f3a0fc89f899d4a47 Thu Jul 16 14:44:36 2026 -0700
- Add Eichler, Lin, Kim, Levin, and ASAP to Long-read SVs announcement acknowledgments per Max. refs #36258
- src/hg/htdocs/goldenPath/newsarch.html - lines changed 4, context: html, text, full: html, text
008dba8f4169e0de018a6e102caf07193e4ad33c Thu Jul 16 14:56:03 2026 -0700
- Point hs1 linkouts in Long-read SVs announcement to hgTracks without g= (hs1 served as file/hub assembly). refs #36258
- src/hg/htdocs/goldenPath/newsarch.html - lines changed 2, context: html, text, full: html, text
e24258cb9af339295d713ab060cadcb284d2cb20 Thu Jul 16 18:05:51 2026 -0700
- Add db= to three more link builders found in QA follow-up. refs #37840
QA (Gerardo) found the "Go to <track> track controls" link on hgc feature
pages still lacked db=; a completeness sweep of every hTrackUiForTrack caller
turned up two more of the same idiom. Add the current-assembly db= to:
hgc.c printTrackUiLink() (rendered via printTrackHtml on most hgc detail
pages), lib/hui.c the related-tracks link, and lib/barChartUi.c the second
isPopup "Change" link in barChartCfgUiSelectEachBar (twin of the one already
fixed in barChartFacetedUi).
- src/hg/lib/barChartUi.c - lines changed 2, context: html, text, full: html, text
29c3c9a501f6cdefcc8e155f075523eb73e15ec9 Thu Jul 16 18:25:15 2026 -0700
- Uncommenting the staged ENCODE4 announcement now that long-read SVs is released, refs #37845
- src/hg/htdocs/goldenPath/newsarch.html - lines changed 3, context: html, text, full: html, text
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