Commits for lrnassar

v504_base to v505_preview (2026-09-21 to 2026-10-05) v505

7e87cadb469b4e0eb4fb7f973154357cfe7fc345 Mon Sep 21 15:56:18 2026 -0700

• QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks.
  • src/hg/makeDb/doc/hg19.txt - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/mei.txt - lines changed 60, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mei/meiDeepmei1kg.as - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mei/meiEul1db.as - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mei/meiEul1dbRef.as - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mei/meiEul1dbToBed.py - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mei/meiHgsvc3.as - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mei/meiHgsvc3CsvToBed.py - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mei/meiHmeid.as - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/mei.html - lines changed 101, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/mei.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/meiDeepmei1kg.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/meiEul1db.html - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/meiEul1dbRef.html - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/meiHgsvc3.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/meiHmeid.html - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/meiSwegen.html - lines changed 14, context: html, text, full: html, text

e461209cf1fd3758d63641915cd91ca9c8ab3020 Thu Sep 24 17:00:10 2026 -0700

• Remove tool output accidentally left in the mei description page, per CR. refs #37524 getTrackReferences writes its diagnostics to stdout rather than stderr, so six "Failed to fetch complete links from NCBI" lines ended up in the References section of mei.html and rendered as visible text on the track description page. NCBI is still not answering, so rather than rerun the tool the references are now assembled from the citation blocks already present on the six subtrack pages. That also restores the publisher links for every paper, which the failed lookups had degraded to bare PubMed URLs. Also make the INFO SEQ guard in meiHgsvc3CsvToBed.py require a usable string, so an empty SEQ= value would fall back to the ALT-derived sequence instead of silently producing an empty one. No record in either callset carries an empty SEQ today and the rebuilt output is byte-identical.
  • src/hg/makeDb/scripts/mei/meiHgsvc3CsvToBed.py - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/mei.html - lines changed 14, context: html, text, full: html, text

79b493d56edd2ffdafebdd20bc69528b3bdfee0a Mon Sep 28 15:54:54 2026 -0700

• News announcement for the redesigned BLAT search and results pages, with the matching indexNews.html item. The entry carries two anchors: #100726 for the usual date form and #newBLAT, which the blatNewFormNewsUrl hg.conf setting on the BLAT banner points at. The banner announces the switch to the new pages on October 28. refs #37996
  • src/hg/htdocs/goldenPath/newsarch.html - lines changed 58, context: html, text, full: html, text
  • src/hg/htdocs/indexNews.html - lines changed 11, context: html, text, full: html, text

10f0f6d5160a96867ecf534e1b9d138df7d9b796 Mon Sep 28 16:17:46 2026 -0700

• Fiber-seq: hide the container by default, and split the five GM lines out into a Rare disease sample class. Max asked for superTrack on rather than on show, since the track covers much the same ground as ENCODE DNase and does not earn a slot in everyone's default hg38 view. The five lymphoblastoid lines GM25455, GM25456, GM27730, GM28570 and GM28572 had been filed as Common Cell Line; Andrew Stergachis says they are rare disease cases consented to broad genomic data sharing and the first of a batch the lab intends to keep adding, so SAMPLE_CLASS_COLORS gains a third entry and the facet now reads 20 HPRC, 16 Common Cell Line, 5 Rare disease sample. refs #36210
  • src/hg/makeDb/doc/hg38/fiberSeq.txt - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/scripts/fiberSeq/fiberSeqSamples.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/scripts/fiberSeq/fiberSeqTrackDb.py - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/fiberSeq.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/fiberSeq.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/fiberSeqCompendium.html - lines changed 11, context: html, text, full: html, text

e1d9e18ef2ac6813136d012f9817ddc50ca5bad9 Mon Sep 28 16:27:37 2026 -0700

• Fiber-seq: spell out the accessibility track's shortLabel as "Fiber-seq Accessible" rather than "Fiber-seq Acc". Twenty characters, which is exactly leftLabelWidthDefaultChars, so it fills the left label without clipping; checked in a render at ACTB. refs #36210
  • src/hg/makeDb/scripts/fiberSeq/fiberSeqTrackDb.py - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/fiberSeq.ra - lines changed 1, context: html, text, full: html, text

0b41a0f1e7f66e0bce33b879275a93ccb9d8f976 Mon Sep 28 16:33:18 2026 -0700

• Fiber-seq description pages: bold the six data type names in the Compendium Description, and drop three passages that explained our own rendering rather than the data. The sample table no longer opens by justifying itself with how many checkboxes 41 samples times six data types would need; the difference track now says each position is colored by the most stringent threshold it meets, instead of describing the order the four signals are painted in; and the peak paragraph no longer explains that dense mode has no per-item hover. "Container name" and "subtracks" become "collection name" and "FIRE peaks", per the rule against exposing internal container terms, and the API paragraph points at the Table Browser for the peaks rather than only saying they are unavailable. Per Lou's review. refs #36210
  • src/hg/makeDb/trackDb/human/hg38/fiberSeqAcc.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/fiberSeqCompendium.html - lines changed 27, context: html, text, full: html, text

0ba660768822e93ed43e9a717f580c525094caf8 Mon Sep 28 16:42:18 2026 -0700

• Fiber-seq: sentence case for the Common cell line sample class, which was Title Cased because that is how Mitchell wrote it in the mail that gave us the classification rule. The other two values were already right, and tadsEncode's organ facet is the precedent (Adrenal gland, Bone marrow). The swatch table on the description page had been saying "Common cell line" in its prose all along, so the filter label and the text explaining it now agree. fiberSeq.ra is untouched: the class only lives in the metadata TSV and the colors JSON, both read at runtime, so no trackDb reload is needed. Caught by Lou. refs #36210
  • src/hg/makeDb/doc/hg38/fiberSeq.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/fiberSeq/fiberSeqSamples.tsv - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/scripts/fiberSeq/fiberSeqTrackDb.py - lines changed 1, context: html, text, full: html, text

54f465e316441236c128491e53c0e5464c0e672c Tue Sep 29 11:40:49 2026 -0700

• Fiber-seq: bring the fiberSeqTrackDb.py docstrings back in line with the three-value sampleClass, and stop the Compendium intro from keeping a running tally of where the lymphoblastoid lines came from. readSamples still said the five GM lines were common cell lines and writeMetadata still said there were two classes, both a few lines from the SAMPLE_CLASS_COLORS entry that added the third. writeMetadata also still had "Common Cell Line" in the old Title Case, which yesterday's rename missed because the string is wrapped across two source lines and a line oriented sed cannot see it; worth remembering for the next rename. The intro sentence had grown a breakdown that did not add up, 20 HPRC plus 5 rare disease against 27 lymphoblastoid lines, leaving GM12878 and HG002 unaccounted; it now points at the Sample class filter instead of counting, since the lab has said more rare disease samples are coming and the tally would go stale again. While in there, the claim that accession order keeps each class together is softened to what the data actually does: the common cell lines fall in two runs either side of the HPRC block. Generated output is unchanged; the .ra, the metadata TSV and the colors JSON all regenerate byte identical. Caught by Claude review of 10f0f6d516. refs #36210
  • src/hg/makeDb/scripts/fiberSeq/fiberSeqTrackDb.py - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/fiberSeqCompendium.html - lines changed 3, context: html, text, full: html, text

de9c4a994c80701abb407a64634cfc4f419a4e67 Tue Sep 29 13:13:27 2026 -0700

• New Genome Browser favicon designs for dev, beta and RR, now 16x16 plus 32x32 instead of 16x16 only. Each host still serves a hand-placed copy of its own faviconDev/Beta/RR.ico as favicon.ico, which is not in the tree. Also adds apple-touch-icon.png, which iOS already requests and was getting a 404 for; it is the same on every host, so it is committed under its real name. refs #36625
  • src/hg/htdocs/apple-touch-icon.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/faviconBeta.ico - 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/faviconDev.ico - 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/faviconRR.ico - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

b6447cadc83582018d1241b1d3336e844b8b086e Tue Sep 29 13:26:29 2026 -0700

• Lighten the new dev favicon from #B54A4A to #DA7C25, halfway to the old helix's yellow-orange strand. refs #36625
  • src/hg/htdocs/faviconDev.ico - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

360607541994aa88b49fc241c34bd964a1db7b50 Tue Sep 29 15:07:07 2026 -0700

• Rebuild the hs1 sgdpCopyNumber track as a faceted composite, so its 319 samples are picked from a searchable metadata table rather than 319 checkboxes; the same bigBeds are pointed at by the same /gbdb paths, so no data changed. Subtracks are renamed from <region>_<population>_<libId>_wssd to sgdpCopyNumber_<libId> because a faceted composite requires the parent name plus the primaryKey value, and dataTypes is deliberately unset: with it hgTrackUi parses the data element only as far as the first underscore and would truncate LP6005441-DNA_A01 to LP6005441-DNA. The per-subtrack 'visibility dense' lines are gone because a faceted composite honors a child's own display mode where a classic composite ignores it, so keeping them would pin every sample to dense and remove the per-item click that the copy number is read from. Sample attributes come from the Reich lab SGDP tables and 317 of the 319 join; sgdpCopyNumberBuild.py takes its sample list from the checked-in sgdpCopyNumberSamples.tsv rather than from trackDb, because at release the generated stanzas replace sgdpCopyNumber.trackDb.ra and the legacy region prefix that the two unmatched samples depend on disappears with them. Alpha gets the new file and beta/public keep the old one until the metadata and color files are on the RR, without which the picker renders empty. sgdpCopyNumber_subset, which turns out to be the first 29 samples in plate order rather than any curated set, is not in the alpha version; whether it is retired for good is still open on the ticket. Faceted composite suggested by Gerardo, and the cross-sandbox metadata fetch that this track turned up was fixed by Max in b3a26a6aff3. refs #29344
  • src/hg/makeDb/doc/hs1/t2t-supplied.txt - lines changed 103, context: html, text, full: html, text
  • src/hg/makeDb/scripts/sgdpCopyNumber/sgdpCopyNumberBuild.py - lines changed 408, context: html, text, full: html, text
  • src/hg/makeDb/scripts/sgdpCopyNumber/sgdpCopyNumberFetchMeta.sh - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/scripts/sgdpCopyNumber/sgdpCopyNumberSamples.tsv - lines changed 325, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/sgdpCopyNumber.html - lines changed 466, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/sgdpCopyNumber.alpha.trackDb.ra - lines changed 2895, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/t2t-supplied.trackDb.ra - lines changed 2, context: html, text, full: html, text

32eec44ad3147d1c9912002e586662d199f78974 Tue Sep 29 15:33:05 2026 -0700

• labelTrackAsDensityWindowSize fires on winTooBigDoWiggle, which compares the window width against maxWindowCoverage and never looks at a count, so "too many items" named the wrong cause: evaSnp sets maxWindowCoverage 250000 alongside maxItems 1000000, so a 400 kb window holding a single variant claimed there were too many items to draw. Say "window too large" instead. Caught in code review of 07f0635. refs #38407
  • src/hg/hgTracks/hgTracks.c - lines changed 1, context: html, text, full: html, text

d19b85083618569a8b3400a8d17a3d2028ef223d Tue Sep 29 15:38:31 2026 -0700

• The itemRgb doc said a color setting "in the same stanza" loses to an explicit itemRgb on, which is narrower than bedItemRgb() behaves: both settings go through trackDbSetting(), which walks the parent chain, and the two lookups are independent, so a parent's itemRgb on beats a color set on the child itself. Reworded that and the matching colorFields sentence, and added the changes.html row this should have had. Caught by CR of 64adf565f28. refs #36212
  • src/hg/htdocs/goldenPath/help/trackDb/changes.html - lines changed 14, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 9, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml - lines changed 7, context: html, text, full: html, text

38fc33c4bbf6c8b960af709cb17a2467d6b6cac2 Tue Sep 29 15:40:59 2026 -0700

• The description page variables section claimed shell and awk examples were safe from substitution, which is wrong twice over: parseVarNameMaybe accepts a bare $db as readily as ${db}, so an example using $db or $track as its own shell variable gets the value put in, and $$ still collapses to a single $. Say that instead, and document $$ as the way to write a literal dollar. The section also renders on trackDbDoc.html, which is the native trackDb doc, where "other trackDb settings are not available" is false, so it is now scoped to a hub's description page. Caught in code review of 8d05f42. refs #38283
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 11, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml - lines changed 28, context: html, text, full: html, text

824df26b6320b692d629566c5a10b15004da82ce Tue Sep 29 16:09:00 2026 -0700

• addProteinSequence in mavemdLib translates each transcript's CDS from hg38.2bit so makeMaveMdVariants can check every projected codon against the reference residue its own HGVS term asserts; the existing comparison against MaveDB's genomic mapping only reaches the 3% of projected items that carry both terms, because 18 of the 40 protein accessions have no genomic-route variants at all. 39 of 40 accessions match at 0.000%; NP_689629.2 (FKRP) has 99 nonsense terms numbered one codon downstream of their own reference residue, which still reach mavemdVar through MaveDB's genomic mapping but are dropped from mavemdMap, which places columns from the protein term and has no fallback. The haplotype test now also reads hgvs_nt, since PTEN 00000054-a-1 states 1,236 haplotypes as c.[1207G>T;1209C>T] with no protein term and they were counted as rejected submissions, making both figures in the makeDoc wrong. assayLine runs the heatmap legend through asciiText because bedField turns the en dash in three MaveDB titles into &#8211; and the legend is drawn as raster text; clinGenId links to by_canonicalid rather than /allele, which serves JSON to a browser, matching human/civic.ra; the generated filter fragment no longer emits the blank line after each group that the makeDoc itself warns ends a stanza; and runBuild.sh tails the log on failure instead of dying silently under set -e. Also reworded the grey legend entry, which said no threshold was reached in either direction but covers 6,656 normal and 145 abnormal items, alphabetized the references, and fixed stale counts in the makeDoc. Caught by Claude review of 29af14b, fcf788d and 97c7de5. refs #38407 refs #37800
  • src/hg/makeDb/doc/hg38/mavemd.txt - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mavemd/makeMaveMdHeatmap.py - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mavemd/makeMaveMdVariants.py - lines changed 69, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mavemd/mavemdLib.py - lines changed 113, context: html, text, full: html, text
  • src/hg/makeDb/scripts/mavemd/runBuild.sh - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/mavemd.html - lines changed 42, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/mavemd.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/mavemdMap.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/mavemdVar.html - lines changed 45, context: html, text, full: html, text

ab234fe62907c81b702a63f5a73d40500a40916f Tue Sep 29 16:12:28 2026 -0700

• Fiber-seq: give the FIRE peak subtracks "visibility dense" instead of "onlyVisibility dense", so their mouseOver can actually be seen. onlyVisibility pins a faceted child rather than defaulting it: tdbVisLimitedByAncestors() in hg/lib/hui.c overwrites the computed visibility with the pinned mode, so a request for pack or full was discarded even from the URL, and the dropdown offered only hide and dense. Since no bigBed-like track draws per-item map boxes in dense, the mouseOver on all 41 peak stanzas was dead config and fiberSeqCompendium.html was promising a hover nobody could reach. Measured at ACTB with the map_data image map: pinned, a forced pack still computed to dense with 0 FIRE tooltips; defaulted, pack and full compute correctly and carry 8. Peaks still come up dense, which is what Andrew asked for in July. The signal types keep onlyVisibility, where pinning to full costs nothing because a bigWig draws the same at pack and full, and that is verified here too: acc, cpg and hap stay at full whatever is requested, and the container stays hidden on a fresh cart. Also fixes two makeDoc slips, the facet notes naming the script's dict keys rather than the column headings writeMetadata() emits, and the opening summary still saying accessibility and CpG "both became faceted composites" when they were merged into one 235 lines later. Caught by Claude review of 156d289 and 5179d7f. refs #38407
  • src/hg/makeDb/doc/hg38/fiberSeq.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/scripts/fiberSeq/fiberSeqTrackDb.py - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/fiberSeq.ra - lines changed 41, context: html, text, full: html, text

dbc8dc013509561c1a9612491c0c84358c1db182 Tue Sep 29 17:26:25 2026 -0700

• Home page and contacts page search box did nothing when the text matched a position regex (chr1:1000000-1001000, BED-style, single base): searchBarClick only navigated in the non-position branch, after the hgSearch getChromName lookup. Now a position goes straight to hgTracks, as hgSearch.js already does. Broken since 258a0a679dd. refs #38449
  • src/hg/htdocs/contacts.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/index.html - lines changed 2, context: html, text, full: html, text

f4d967492fedb59d2e528cf196e35c1da248ae96 Fri Oct 2 07:15:47 2026 -0700

• Quarterly pennant cleanup: removing New/Updated pennantIcons released before July 2026 (strVar, nmd, promoterAi, primateAi, mpra, varaico). No RM.
  • src/hg/makeDb/trackDb/human/hg38/mpra.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/nmd.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/strVar.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/primateAi.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/promoterAi.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/strVarNew.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 3, context: html, text, full: html, text

53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700

• Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
  • src/hg/makeDb/doc/ce11/gpnStar.txt - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/doc/dm6/gpnStar.txt - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/doc/galGal6/gpnStar.txt - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/gpnStar.txt - lines changed 71, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm39/gpnStar.txt - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/scripts/gpnStar/gpnStarCheckSections.py - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/scripts/gpnStar/gpnStarCoordCheck.py - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/scripts/gpnStar/gpnStarMirror.py - lines changed 84, context: html, text, full: html, text
  • src/hg/makeDb/scripts/gpnStar/gpnStarRebuild.sh - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/scripts/gpnStar/gpnStarVerify.sh - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal6/gpnStar.html - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal6/gpnStar.ra - lines changed 125, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal6/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dm6/gpnStar.html - lines changed 150, context: html, text, full: html, text
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116aaf68aa340197a2a63856a90f533909e15f92 Fri Oct 2 14:25:53 2026 -0700

• BRCAmlaZanti.py: match ENIGMA PP4/BP5 variants by normalized genomic allele instead of HGVS name, so the 297 variants the source papers spell differently (c.4574_4575del vs Li's c.4574_4575delAA, Zanti's ins for a dup, del15) become one item with their LRs multiplied, as Finja Hennig asked. Every item is now drawn the way the ClinVar track draws it (deleted bases shifted left, 2 bp flank for ins/dup), names drop spelled-out bases, LRs are written with 5 significant figures, and the Zanti <CNV> row is dropped. Zanti rows are keyed from their own VCF columns because hgvsToVcf mis-converts intronic insertions (#38469), and the pre-Zanti input now comes from archive/v1.1 since /gbdb BRCAmfa.bb is this script's own output. The hgvsToVcf FILTER and del/dup count checks were added after a Claude review. refs #38467
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