Commits for lrnassar
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v496_preview2 to v496_base (2026-03-23 to 2026-03-30) v496
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6f00f33a31c1cec74f33b7e408165005f8b87e37 Wed Mar 25 13:45:08 2026 -0700
- Fix inaccurate alt text in sessions.html per QA feedback. refs #37254
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/htdocs/goldenPath/help/sessions.html - lines changed 3, context: html, text, full: html, text
c2d63f068433c6f321c57b380733ace4bbec12b7 Thu Mar 26 13:21:13 2026 -0700
- Fix UnboundLocalError in buildPublicSessionThumbnailsIndexPage.py when sessions have
unusual names that cause the trash line parsing to fail. Skip sessions where sessionUrl
was not set instead of crashing. No RM.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/utils/qa/buildPublicSessionThumbnailsIndexPage.py - lines changed 8, context: html, text, full: html, text
2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
- Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10
(encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks
(H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite
faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq)
using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks
track. ENCODE3 regulation tracks are release-tagged to show a snowflake
deprecation notice on alpha while remaining unchanged on beta/public. Includes
generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata
TSVs. refs #34923
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/doc/hg38/encode4.regulation.txt - lines changed 249, context: html, text, full: html, text
- src/hg/makeDb/doc/mm10.encode4.regulation.txt - lines changed 208, context: html, text, full: html, text
- src/hg/makeDb/scripts/encode4regulation/convert_to_bigcomposite.py - lines changed 427, context: html, text, full: html, text
- src/hg/makeDb/scripts/encode4regulation/generate_composites.py - lines changed 438, context: html, text, full: html, text
- src/hg/makeDb/scripts/encode4regulation/generate_multiwig_ra.py - lines changed 269, context: html, text, full: html, text
- src/hg/makeDb/scripts/encode4regulation/validate_encode_urls.py - lines changed 268, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.alpha.ra - lines changed 407, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.html - lines changed 148, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.ra - lines changed 3327, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Atac.html - lines changed 84, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Dnase.html - lines changed 83, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.html - lines changed 65, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra - lines changed 35202, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkCtcf.html - lines changed 86, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k27ac.html - lines changed 85, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k4me3.html - lines changed 85, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.html - lines changed 58, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.ra - lines changed 12042, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.html - lines changed 59, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra - lines changed 25033, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html - lines changed 140, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Txn.html - lines changed 81, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.html - lines changed 135, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.ra - lines changed 1230, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegAtac.html - lines changed 84, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegDnase.html - lines changed 83, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.html - lines changed 65, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra - lines changed 11793, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkCtcf.html - lines changed 86, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k27ac.html - lines changed 85, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k4me3.html - lines changed 85, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.html - lines changed 58, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.ra - lines changed 12130, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.html - lines changed 58, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra - lines changed 3353, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegTxn.html - lines changed 81, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.alpha.ra - lines changed 10, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/relatedTracks.ra - lines changed 11, context: html, text, full: html, text
95860982a496454aec2aab3df0e6cb2c4b7760b4 Thu Mar 26 17:47:15 2026 -0700
- Adjusting track priorities in regulation group for hg38 and mm10. hg38: cCREs
0.8, wgEncodeReg4 0.9, wgEncodeReg 1. mm10: cCREs 0.4, encode4Reg 0.5,
tabulaMuris 1. refs #34923
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/trackDb/human/hg38/encode.cCREs.override.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode.cCREs.override.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.ra - lines changed 1, context: html, text, full: html, text
c082365b4bc8445dfa4decc7e8569fd82d995115 Thu Mar 26 17:53:13 2026 -0700
- Moving individual experiment composites (Indiv.) to end of supertrack container
by setting priority 2.0/2.1/2.2 for Epigenetics/RnaSeq/TfChip on both hg38 and
mm10. refs #34923
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra - lines changed 1, context: html, text, full: html, text
8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
- Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10.
Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count
from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue
availability tables to all layered track descriptions, updates production lab
credits to match original hub per assembly, removes UCSC staff mentions from
credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed
signal+peak Data Type facet in mm10 Epi and TF composite descriptions.
refs #34923
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Atac.html - lines changed 38, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Dnase.html - lines changed 53, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.html - lines changed 6, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkCtcf.html - lines changed 44, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k27ac.html - lines changed 48, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k4me3.html - lines changed 49, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.html - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.html - lines changed 6, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html - lines changed 9, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Txn.html - lines changed 63, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.html - lines changed 11, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegAtac.html - lines changed 26, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegDnase.html - lines changed 39, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.html - lines changed 8, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkCtcf.html - lines changed 30, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k27ac.html - lines changed 33, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k4me3.html - lines changed 34, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.html - lines changed 8, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegTxn.html - lines changed 23, context: html, text, full: html, text
197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
- Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel
912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in
mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark")
in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in
supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics,
and TF ChIP individual track HTML for both assemblies. refs #34923
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.html - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.html - lines changed 8, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.html - lines changed 7, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.html - lines changed 7, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.html - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.ra - lines changed 18, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.html - lines changed 8, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.html - lines changed 7, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.html - lines changed 7, context: html, text, full: html, text
7c4f2e656763f789dafcabae4c2c82f5b581d43f Fri Mar 27 10:15:45 2026 -0700
- Replacing underscores with spaces in all 6,747 hg38 bigComposite subtrack
longLabels for readability. Converts e.g. "Homo_sapiens_K562_stably_expressing"
to "Homo sapiens K562 stably expressing". mm10 labels were already correct.
refs #34923
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra - lines changed 3199, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.ra - lines changed 1046, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra - lines changed 2502, context: html, text, full: html, text
46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
- Darkening too-light track colors for better contrast against white background,
adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay,
RnaSeq by organ, TfChip none since score-colored), and updating all Data Access
sections to mitomap-style format with bigWigToWig/bigBedToBed examples and
representative file URLs. refs #34923
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.html - lines changed 10, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.ra - lines changed 209, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Atac.html - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Dnase.html - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.html - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra - lines changed 563, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkCtcf.html - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k27ac.html - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k4me3.html - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.html - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.ra - lines changed 563, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.html - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html - lines changed 23, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Txn.html - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.html - lines changed 10, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.ra - lines changed 76, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegAtac.html - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegDnase.html - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.html - lines changed 22, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra - lines changed 187, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkCtcf.html - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k27ac.html - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k4me3.html - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.html - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.ra - lines changed 825, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.html - lines changed 22, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegTxn.html - lines changed 19, context: html, text, full: html, text
7e9cf9d7dace5cd9a0519bee134364b87b86d832 Fri Mar 27 12:01:25 2026 -0700
- Updating makedocs for hg38 and mm10 ENCODE4 Regulation tracks to reflect all
changes from 2026-03-27: priorities, symlink renaming, color darkening,
colorSettingsUrl, longLabel cleanup, Data Access sections, HTML audit fixes,
code review fixes, and local ENCFF file cleanup (4.3 TB freed). refs #34923
- src/hg/makeDb/doc/hg38/encode4.regulation.txt - lines changed 79, context: html, text, full: html, text
- src/hg/makeDb/doc/mm10.encode4.regulation.txt - lines changed 76, context: html, text, full: html, text
bc70099d05e549ea2cd85689d7eaeac3d62bef3e Fri Mar 27 15:05:41 2026 -0700
- Fix mlqAutomate quote stripping for Apple Mail/Outlook Mac format. refs #37297
The From:/Date:/To: multi-line quote header used by Apple Mail and Outlook
for Mac was not being detected, only From:/Sent:/To: (Windows Outlook).
This caused quoted thread history to remain in the email body, triggering
false-positive duplicate detection and skipping legitimate new replies.
- src/utils/qa/mlqAutomate.py - lines changed 4, context: html, text, full: html, text
41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
- Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
- src/hg/htdocs/ENCODE/analysis.html - lines changed 2, context: html, text, full: html, text
- src/hg/htdocs/ENCODE/fileFormats.html - lines changed 2, context: html, text, full: html, text
- src/hg/htdocs/ENCODE/usageResources.html - lines changed 2, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/hgGeneGraph.html - lines changed 12, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html - lines changed 2, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/hubQuickStart.html - lines changed 2, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/hubQuickStartFilter.html - lines changed 18, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/hubQuickStartSearch.html - lines changed 4, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/newsarch.html - lines changed 16, context: html, text, full: html, text
- src/hg/htdocs/inc/hgCollectionHelpInclude.html - lines changed 10, context: html, text, full: html, text
- src/hg/htdocs/inc/hgMyData.html - lines changed 2, context: html, text, full: html, text
- src/hg/htdocs/staff.html - lines changed 2, context: html, text, full: html, text
944fa6bbf93daeaac9d5223930696cccccfa5197 Fri Mar 27 17:25:06 2026 -0700
- Updating the page to improve the flow, structure, be clear that the file names need to be identical, and include a new example hub, refs #36957
- src/hg/htdocs/contribTracks.html - lines changed 173, context: html, text, full: html, text
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