Commits for lrnassar

v498_base to v499_preview (2026-05-11 to 2026-05-18) v499

d1fb9d605d77792dff66878cf1a8990320861049 Tue May 12 12:57:38 2026 -0700

• Make the OMIM otto fetch surface its wget log on failure and retry patiently. Previously, "set -e" killed the script after a partial wget failure before the "if [ $? -ne 0 ]" branch could run, so the build email showed only "fetching files ..." with no hint that the public omim.org mim2gene.txt URL had returned 403 (Cloudflare). The fetch now retries on 403/408/429/5xx with linear backoff (up to ~13 min of attempts) and prints wget.log into the email when it still gives up. No RM.
  • src/hg/utils/otto/omim/checkOmim.sh - lines changed 12, context: html, text, full: html, text

d069df7855eb648b5b53c51ef5218fe2e4a1d087 Wed May 13 12:48:53 2026 -0700

• mpraVarDb script rebuild: standardize NA, fix upstream typos, add pvalue note. refs #37359 Build-script changes (mpravardbToBed.py + mpravardb.as): - sanitize_text() now normalizes "None"/"NA"/"N/A"/"null"/"NULL"/"nan" to empty string. Removes 55,108 stale sentinels: 53,144 disease= "None" eQTL rows, 1,964 disease="NA" Kircher rows, 44 ref/alt=NA Myint rows. - Literal-replacement table for three upstream typos: "30 UTR" -> "3'UTR" (26,546 Schuster description rows), "Familial hypercholesterol emia" -> "Familial hypercholesterolemia" (2,176 Kircher disease rows), "Alchol use disorder" -> "Alcohol use disorder" (88 Rao disease rows). - fmt_mo() renders NaN floats as "NA" in mouseOver helper fields; 30,921 rows that previously showed literal "nan" now read "NA". - Tightened name+rsid handling: treat a value as an rsID only if it starts with "rs". 2,088 hg19-coord-style names like "1_1403972_CG" are reformatted to "chr<X>:<hg38pos>:<ref>><alt>" and the rsid field cleared to "" so the dbSNP linkout doesn't fire on a bogus value. - Removed the 250-char truncation that cut Griesemer descriptions mid-sentence; mpravardb.as switched description and mpraStudy from "string" to "lstring" to admit the full upstream text. Description page (mpraVarDb.html): - Added a "Note (pending upstream fix)" paragraph in Methods explaining the 5,092 rows with pvalue > 1 (test statistic mislabeled in the pvalue field by upstream curators for Mouri 2022 and Tewhey 2016). Bracketed by an HTML comment "TEMP: remove once Tao Wang fixes..." for future cleanup when the next snapshot lands. bigBed rebuilt; itemCount 239,028 preserved. Pre-rebuild backup: /hive/data/genomes/hg38/bed/mpra/mpravardb/mpravardb.bb.pre-2026-05-14-backup Makedoc updated with the QA-2 build-script rebuild section.
  • src/hg/makeDb/doc/hg38/mpra.txt - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mpravardb/mpravardb.as - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mpravardb/mpravardbToBed.py - lines changed 50, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/mpraVarDb.html - lines changed 15, context: html, text, full: html, text

2f44ab096235810d5d621b7356bc64fbebe82494 Wed May 13 13:02:57 2026 -0700

• varFreqs: fix numeric-claim discrepancies on indigenomes.html and sgdpFreq.html. indigenomes.html: clarify that the deployed VCF is the public release subset (18,016,257 records) of the larger Jain 2021 callset (55.8M variants), and note that the public release is sites-only with a VRT variant-type INFO field and no AC/AF. sgdpFreq.html: update Methods to reflect the deployed file (44,756,737 SNV records, 601,775 multiallelic decomposed); drop the "34.4M SNPs + 2.1M indels" claim; clarify that the Mallick 2016 FermiKit indel callset is not carried in this track. refs #36642
  • src/hg/makeDb/trackDb/human/indigenomes.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/sgdpFreq.html - lines changed 9, context: html, text, full: html, text

459736686ba7726d2e9bfe63757183b4e8153e53 Wed May 13 13:09:18 2026 -0700

• varFreqs: set default visibility to hide on all 26 non-summary subtracks. Leaves varFreqsAll on pack (the summary combined-track stays the default view) and the supertrack on hide. Users opt into individual cohorts via the combined-track filter; enabling the supertrack no longer tries to render 25+ vcfTabix tracks at once. Confirmed by Max. refs #36642
  • src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 26, context: html, text, full: html, text

7bec995472122739bf0f076de2603708059c65ce Wed May 13 17:23:37 2026 -0700

• Adding NMDetective-AI subtracks (bigWig + bigBed) under the NMD Escape superTrack. refs #33737 Two new subtracks slotted between NMD Escape RefSeq and NMDetective-A (priorities 1.7 and 1.8): - nmdDetectiveAi - position-averaged predictions (bigWig) - nmdDetectiveAiBed - per-stop-gain predictions, one item per (transcript, codon, mutant codon), with diverging Okabe-Ito coloring and a pre-rendered mouseover Predictions are from Veiner et al. (bioRxiv 10.64898/2026.03.24.714003), covering MANE Select transcripts at Gencode v46. Verdict bins in the bigBed mouseover use the GMM-derived thresholds reported in the paper's Methods (-0.17 / +0.43), not symmetric +/- 0.3. Description page covers the +0.5 / -0.5 anchor convention, threshold derivation, and the pre-print status.
  • src/hg/makeDb/doc/hg38/nmd.txt - lines changed 42, context: html, text, full: html, text
  • src/hg/makeDb/scripts/nmd/nmdDetectAi/makeBigBed.py - lines changed 94, context: html, text, full: html, text
  • src/hg/makeDb/scripts/nmd/nmdDetectAi/nmdDetectAi.as - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/nmd.html - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/nmd.ra - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/nmdDetectiveAi.html - lines changed 141, context: html, text, full: html, text

be4ae656ffd6994f4d5de689ffe4117861441181 Wed May 13 19:18:41 2026 -0700

• Note pre-existing hg19-pos-in-name observation in mpravardb makedoc. refs #37359 Surfaced during sandbox validation of the 2026-05-14 script rebuild. For ~73k non-rs rows the chr:pos:ref>alt name carries the original hg19 pos because csv_to_bed builds the name before liftOver runs. Display is unaffected; only relevant if a user copies the name field expecting hg38 coordinates. Documented for whenever a future rebuild gets the post-Step-2 name-rewrite fix folded in.
  • src/hg/makeDb/doc/hg38/mpra.txt - lines changed 12, context: html, text, full: html, text

47519c28b9a21f1ca7ad8881ccd375ff40d7b206 Thu May 14 14:46:13 2026 -0700

• Fix hg38 H3K27ac peak color and strip species prefix from ENCODE4 Regulation bigComposite longLabels. refs #34923 Two QA cleanups from #34923 note 141: - hg38 H3K27ac peak subtracks were colored 255,205,0 (bright #FFCD00, the cCRE classification yellow) while the matching signal subtracks used 181,145,0 (mustard #B59100, the contrast-darkened assay color from /gbdb/hg38/encode4/regulation/epi_colors.json). Changed all 554 peak stanzas in wgEncodeReg4Epigenetics.ra to 181,145,0 so peak + signal match each other and the description-page color legend. mm10 H3K27ac already used 181,145,0 throughout. - Stripped the redundant "Homo sapiens " / "Mus musculus " prefix from the longLabel of every subtrack in the six bigComposite .ra files. 100% of subtracks had the prefix (14,929 total: 6,353 hg38 Epi + 4,964 hg38 TfChip + 1,046 hg38 RnaSeq + 1,178 mm10 Epi + 334 mm10 TfChip + 1,054 mm10 RnaSeq). The species is implicit on a specific assembly and the prefix was pushing biosample descriptions off the visible label width. shortLabels and track names untouched.
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra - lines changed 6907, 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 4964, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra - lines changed 1178, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.ra - lines changed 1054, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra - lines changed 334, context: html, text, full: html, text

9c0f52be6be34a120bd16008b57fc60728bd63bd Thu May 14 14:48:03 2026 -0700

• Update ENCODE4 Regulation makedocs with note 141 QA follow-ups (H3K27ac color, metadata Organ casing, longLabel species prefix). refs #34923
  • src/hg/makeDb/doc/hg38/encode4.regulation.txt - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.encode4.regulation.txt - lines changed 22, context: html, text, full: html, text

5cdfbadbb31400fffdef53c04a3285a63e4fc2cb Fri May 15 10:03:21 2026 -0700

• Silent release of MPRA track, refs #37359
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

705b694649940189cdb66af57560c97a0cd606f7 Fri May 15 14:42:52 2026 -0700

• Three small rtsUpdate fixes uncovered during first live test on Non_Coding_SNVs_hg38: line-buffer stdout so git diff output interleaves correctly with surrounding prints, replace deprecated datetime.utcnow() with timezone-aware datetime.now(datetime.timezone.utc), and print a trailing newline after confirm() so the post-prompt status message doesn't land on the same line as the prompt. refs #32768
  • src/hg/utils/rts/rtsUpdate - lines changed 10, context: html, text, full: html, text

3c24a0d5ece77c493f9def39d135aae37dfbb226 Fri May 15 14:43:02 2026 -0700

• Updating RTS Non_Coding_SNVs_hg38 from abenet's source session via rtsUpdate. Cart version 2 -> 10 with substantial track refresh: clinGen* additions, dbSnp155 family, gnomadStructuralVariants, gnomadConstraint, spliceAI, jaspar2026, gnomadCopyNumberVariants; older entries retired (crispr*, knownGeneV36/V38, rmskHmmer, transMapV4/V6, etc.). refs #32768
  • src/hg/utils/rts/hg38/Non_Coding_SNVs_hg38 - lines changed 335, context: html, text, full: html, text

87eb0adf61763660f65ec29bacf3d8f138c4b56d Fri May 15 15:11:59 2026 -0700

• Move rtsUpdate's audit log out of the kent tree to ~/.rtsUpdate.log, so it stays as a local audit trail without producing an untracked file (or merge-conflict-prone tracked file) in src/hg/utils/rts/. refs #32768
  • src/hg/utils/rts/rtsUpdate - lines changed 1, context: html, text, full: html, text