Commits for max

v499_preview2 to v499_base (2026-05-25 to 2026-06-01) v499

6b0d68657267f1e02c47d4224ea62446bbbb2ba0 Fri May 22 06:55:52 2026 -0700

• small non-AI changes to the html docs pages of the long-read SV tracks
  • src/hg/makeDb/doc/hg38/lrSv.txt - lines changed 42, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/aprSv.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/colorsDbSv.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/cpc1Sv.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/dbVarNr.html - lines changed 175, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hgsvc2Sv.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hgsvc3Sv.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hprc2JasmineSv.html - lines changed 106, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/mei.html - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/meiDeepmei1kg.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/meiHgsvc3.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/tommoJpSv.html - lines changed 1, context: html, text, full: html, text

5603b712f9fe5889953fee5061af23f55fe5e6d1 Fri May 22 07:16:06 2026 -0700

• Prefixing all subtrack longLabels in the Human Methylation Atlas summary and signals tracks with "Methylation Atlas: " so the source of each subtrack is clear in the track list, refs #36826 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
  • src/hg/makeDb/trackDb/human/methylationAtlas.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/methylationAtlasSignals.ra - lines changed 244, context: html, text, full: html, text

081dc1a2de216d74a28252747d593c2b1288f251 Tue May 26 02:06:08 2026 -0700

• hubApi/botDelay: return JSON 500 when bottleneck server is unreachable abortAndExplainConnectFail() previously called exit(0) directly after writing raw HTML, which bypassed every error handler and produced a broken response for JSON API clients. Change it to errAbort() so it can be caught by errCatch. Wrap both hgBotDelayTimeFrac() call sites in hubApi (the global delay in main() and the BLAT-specific extra delay in apiBlat()) in errCatch blocks that call apiErrAbort(500) on failure, giving callers a proper JSON error rather than an HTML fragment or a silent exit. refs #36315 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
  • src/hg/hubApi/blat.c - lines changed 9, context: html, text, full: html, text
  • src/hg/hubApi/hubApi.c - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/botDelay.c - lines changed 16, context: html, text, full: html, text

b5997c3b91cd3dfa56da7de7e21601b333989773 Tue May 26 08:56:05 2026 -0700

• [Claude] add TREDNet enhancer/silencer predictions under new crPred supertrack 512,577 candidate enhancers and 319,322 candidate silencers predicted by the TREDNet deep learning model across 97 ENCODE biosamples (Huang & Ovcharenko 2024, PMID 38978133). Per-sample 1-kb BED files merged with bedtools, annotated with contributing cell types/tissues/cell lines, colored by dominant sample category using the Okabe-Ito palette. Tracks live under the new crPred (Cis-regulatory Predictions) supertrack. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> refs #37631
  • src/hg/makeDb/doc/hg38/crPred.txt - lines changed 53, context: html, text, full: html, text
  • src/hg/makeDb/scripts/tredNet/tredNet.as - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/scripts/tredNet/tredNetBuild.py - lines changed 328, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/crPred.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/crPred.ra - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/tredNet.html - lines changed 75, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/tredNetEnhancer.html - lines changed 116, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/tredNetSilencer.html - lines changed 117, context: html, text, full: html, text

0159c1e515b598e2050935f4f12a2c5a5023a433 Tue May 26 09:22:03 2026 -0700

• hubtools: fix critical runtime crashes and logic errors, refs #36790 - stanzaAddVal/stanzaNew had no body or were undefined; add both - tdbCommentsAppendOneList iterated wrong variable name (tdb vs pairs) - fetchChromSizes: wrap raw bytes in io.BytesIO for gzip.GzipFile - getChromSizesFname: remove reference to undefined variable dataDir - errAbort: bare raise outside except replaced with raise Exception(msg) - httpReqOld: path=url -> path=parsed_url.path in no-params branch - broadPeak conversion: correct type to bigBed 6+3, bedType to bed6+3 - getAsFname: add bigBroadPeak URL to prevent KeyError - httpReq: add raise_for_status() to surface 4xx/5xx errors - Add missing imports: urllib.parse, gzip, csv, io - except: -> except ImportError: for requests import guard - tarfile.extractall: use filter='data' on Python 3.12+ to prevent path traversal - ThreadPoolExecutor: use with-block to ensure shutdown - downloadUrl: HTTPError now re-raised after logging at error level - logging.warn() -> logging.warning() (removed in Python 3.12) - Fix docstring typos: dadta, apend, stray z in comment Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
  • src/utils/hubtools/hubtools - lines changed 35, context: html, text, full: html, text

d8ddf1a6c92e6efeb99481bf4849569abe5f8f5e Tue May 26 09:46:29 2026 -0700

• [Claude] ncOrfs: fix review feedback — mouseOver label, .as description, HTML wording, addIntrons exit check - ncOrfs.ra mouseOver: rename "MANE host" to "Host transcript" so the label is accurate for both MANE and GENCODE fallback transcripts - utrAnnotUorfs.as intronsSource description: mention GENCODE fallback as an alternative source, not just MANE Select/Plus Clinical - gencNcOrfs.html: "only one of those positions" -> "only one of those two positions" for consistency with ncOrfs.html - addIntrons.py load_donors(): check bigBedToBed exit code and call sys.exit() on failure instead of silently continuing with empty data refs #35101 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
  • src/hg/makeDb/scripts/ncOrfs/addIntrons.py - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/scripts/ncOrfs/utrAnnotUorfs.as - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gencNcOrfs.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/ncOrfs.ra - lines changed 1, context: html, text, full: html, text

3b99f4a5047b00898392a53f55d8ab95d38e9b52 Wed May 27 02:34:34 2026 -0700

• [Claude] nuorfdb: fix incorrect Bhatt-lab attribution and author names; utrAnnotUorfs: doc cleanup, refs #35101 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
  • src/hg/makeDb/trackDb/human/hg38/nuorfdb.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/utrAnnotUorfs.html - lines changed 23, context: html, text, full: html, text

06767bdb38bd195d69b84b79499431709e625382 Thu May 28 01:35:36 2026 -0700

• small wording change to hgTrackUi parent link, no redmine yet
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 1, context: html, text, full: html, text

8c1ebdae695b1bb40e45f41aff4a4f9fb9e52491 Thu May 28 05:43:13 2026 -0700

• [Claude] add EVE missense variant effect heatmap track for hg38 #Preview2 week - bugs introduced now will need a build patch to fix Heatmap bigBed track showing EVE scores for all possible missense substitutions in 2,949 disease-associated proteins. One entry per protein; columns = amino acid positions at genomic codon coordinates, rows = 20 standard amino acids. Colors blue (benign) to red (pathogenic). Includes conversion script, autoSql, trackDb, HTML doc, and makedoc. Added to predictionScoresSuper. refs #31804 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
  • src/hg/makeDb/doc/hg38/eve.txt - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/scripts/eve/eve_heatmap.as - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/scripts/eve/vcfToEveHeatmap.py - lines changed 230, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/eve.html - lines changed 122, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/eve.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/predictionScoresSuper.ra - lines changed 1, context: html, text, full: html, text

3180d71425ab40bc022712bb95868bfe80747375 Fri May 29 08:52:38 2026 -0700

• [Claude] varFreqs: split SPARK+SCHEMA by phenotype, add disease + array combined tracks, drop array cohorts from varFreqsAll #Preview2 week - bugs introduced now will need a build patch to fix Split SFARI SPARK WES and WGS by autism status using fill-tags -S with the SPARK individuals_registration TSV (AC_AUT / AN_AUT / AF_AUT plus AC_NON_AUT / AN_NON_AUT / AF_NON_AUT). Added matching SCHEMA case/control sums (AC_CASE etc.). Two new combined bigBed tracks: varFreqsDisease (SPARK, SFARI WGS, TOPMed, SCHEMA, GREGoR, GA4K) and varFreqsArray (TPMI, MexBB, UKBB). TPMI and MexBB are removed from varFreqsAll so the main combined track is purely WGS/WES. Build scripts parameterized so the same code drives all three combined builds: mergeAndAnnotate.sh gains --databases / --tag, vcfToBigBed.py gains --databases-file / --populations-file and a per-track autoSql table name. mergeAndAnnotate.sh now pins /cluster/software/src/bcftools-1.22 in PATH (--unify-chr-names is a 1.22 feature; conda's 1.14 silently fails). refs #36642
  • src/hg/makeDb/doc/hg38/varFreqs.txt - lines changed 103, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/databases.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/databases_array.tsv - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/databases_disease.tsv - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/mergeAndAnnotate.sh - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/populations.tsv - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/schema_addAcAnAf.py - lines changed 56, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/sparkMergeVcfAddCounts.sh - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/vcfToBigBed.py - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/sfariSparkExomes.html - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 178, context: html, text, full: html, text