Commits for mspeir

v504_preview to v504_preview2 (2026-09-07 to 2026-09-14) v504

6a29bc1077e1bd2926fa1508c6fdde383397f4a4 Tue Sep 8 16:14:56 2026 -0700

• relatedTracks.ra: drop 20 entries naming tracks that are not on the RR An audit of the table against the public trackDb found 77 relationship rows pointing at a track the RR does not have. Most are fine and stay: the track is either gated behind an alpha include and still in development (LCRs, gerp, imprinting, mei, srSv, t2tChain, tads, TOGAv2, clinvarMapped, colorsDbLegacy, hg38Patch11, singleCellSignalsPeaks, cancerMutations), or the family is already public on other assemblies and only this version or assembly has yet to be pushed (transMapV6, crispr10K, tanDups, ukbDepletion). Those entries start working on their own when the track ships. The 20 lines removed here name tracks with no public counterpart under any name on any assembly, so they could never render for a reader on the RR: ucscRetroAli8, superseded by the V9 track that is public wgRnaOld and cancerMutations, both release alpha transMapV4, absent from the RR entirely, so the source page does not exist ensGene on hg38 and mm10, where Ensembl Genes was retired sibAltEvents, public on no assembly chainNetHs1, which is assembly-hub machinery rather than a native hg38 track cloneEndUcsc, a mapping that only ever existed on hgwdev The three crispr lines came out for a different reason. On hgwdev crispr is a superTrack over crisprRanges and crisprTargets while the RR carries only the standalone crisprAllTargets, so the entries looked like they wanted repointing. The file already relates crisprAllTargets and crispr10K reciprocally further down, on all three assemblies, which made them redundant instead. Every name still in the file resolves in the hgwdev trackDb, and no duplicate assembly and track pair remains. Rebuilt with make update on hg38, hg19 and mm10: 24 rows dropped, none added, nothing else changed. The original audit checked names against alpha, which is why these got in. refs #38016 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/trackDb/relatedTracks.ra - lines changed 20, context: html, text, full: html, text

e5759993329b6e609e9ab825991a90283e714088 Wed Sep 9 11:17:57 2026 -0700

• Help pages: fix broken internal links and restore anchors people still cite, refs #38062 Three groups of anchor problems on the help and FAQ pages. Broken internal links, five pages: posters.html listed a 2022 section that does not exist (no 2022 posters), api.html listed REST and JSON separately after the two sections were merged, docker.html pointed at a #UsrAcct section that is not on that page, FAQgenes.html had a capitalized #ncbiRefSeq where the anchor is #ncbiRefseq, and the genomes.txt settings rows in trackDbHub.v3.html carried no anchors so its own "genome" link missed. Retired anchors that are still cited in twenty years of answers on the genome list. Content moved to its own page and the old anchor was deleted rather than left behind, so the citations land at the top of the page. Reattached seven numeric FAQformat anchors to the Topics entry linking to each format's page. BED, PSL, GFF and GTF were removed from the custom track page in 2012 and never added back to its list of supported formats; added them with the old anchors, which fixes customTrack.html and hgTracksHelp.html together since both include customTrackText.html. Also restored #lines there, and #Session on hgTrackHubHelp.html and #link4 on FAQlink.html. Section anchors on six pages that had none, so a support answer can link to one part of them: bam.html, hic.html, bedgraph.html, ftp.html, net.html and trackDbIndexBb.html. Skipped quickLiftChain.html, oligoMatch.html and cutters.html, which are track description fragments included into the details page rather than standalone pages. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • src/hg/htdocs/FAQ/FAQformat.html - lines changed 7, context: html, text, full: html, text
  • src/hg/htdocs/FAQ/FAQgenes.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/FAQ/FAQlink.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/api.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/bam.html - lines changed 4, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/bedgraph.html - lines changed 4, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/customTrackText.html - lines changed 5, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/docker.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/ftp.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hic.html - lines changed 5, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/net.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/posters.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDbIndexBb.html - lines changed 3, context: html, text, full: html, text

bc030946a04b1f5c4c0a1501e0eb385747238b1b Wed Sep 9 11:43:51 2026 -0700

• trackDb docs: send a library cross-link to the current spec when the host page has no such anchor, refs #38062 trackDbLibrary.shtml is shared by trackDbDoc.html and all four trackDbHub version pages. Its setting blurbs cross-reference other settings with a bare fragment, but the anchor is written by each host page's own table of contents, so a blurb that mentions a setting newer than a frozen hub spec has no target on that page. trackDbHub.v0, v1 and v2 therefore carry dangling links to filterLabel, detailsDynamicTable, filterBy, faceted_composite, onlyVisibility and detailsStaticTable, and the library is regenerated while those snapshots stay put, so the set grows with every new setting. Rather than edit the frozen snapshots or hard-code a page into the library, check at the moment a blurb is moved out of the hidden library into the document and repoint the link to trackDbHub.html, which always serves the current spec, when the anchor is not on the page. Links whose target is present are untouched, so this changes nothing on trackDbDoc.html or on the current spec, and it keeps working as settings are added. Only the visibility blurb's link to faceted_composite is reachable by a reader today; the rest sit in blurbs those pages do not display. Verified in a browser on all five pages. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js - lines changed 19, context: html, text, full: html, text

160d10a30597d7435c30409878e2ba11c3e7c660 Wed Sep 9 14:19:40 2026 -0700

• trackDb docs: stop the shared script from aborting on the pages without a search box, refs #38062 Two JavaScript faults on the trackDb doc pages, both of which trackDbHub.v3.html had already avoided while the other pages drifted. trackDbDoc.html, changes.html and trackDbHub.v0/v1/v2.html load /js/utils.js in their head, and the hgMenubar include further down brings in the same file by a different path, so it ran twice. utils.js declares mouseoverContainer with let at top level, so the second run threw a redeclaration error. v3 does not load utils.js in the head, and the menubar copy is in place well before anything needs it, so drop the head copy from the other five. documentLoad() then called addEventListener on the result of getElementById("tdbSearch") with no null check, and only v3 has that input, so the function threw partway through on the other four pages and never reached its end. The search box and jump-to-top button do not exist on those pages, so nothing visible was lost, but the exception aborted the rest of documentLoad and would have swallowed anything added after it. Guard the two listeners. All six pages now load with no console errors, checked in a browser. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • src/hg/htdocs/goldenPath/help/trackDb/changes.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js - lines changed 5, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v0.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v1.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html - lines changed 1, context: html, text, full: html, text

eebe031af9dfcecc8f5d0c1a5cd6a13b4d3e8865 Wed Sep 9 14:43:26 2026 -0700

• VCF help: explain which display modes draw the haplotype view, and add the settings that were missing, refs #38010 Neither VCF help page said that the haplotype sorting display depends on the track's display mode. vcfTrack.c reaches vcfHapClusterOverloadMethods only when the visibility is pack or squish and the file has genotypes for more than one sample; every other case falls through to vcfFileToPgSnp. So full draws one row per variant, dense collapses them onto a single row, and in both of those the "Enable Haplotype sorting display" checkbox and everything conditional on it do nothing. Multi-region view and the density graph option disable it as well. Say so on hgVcfTrackHelp.html, above the settings it governs, and on vcf.html next to the visibility parameter. vcf.html also listed only hapCluster{Enabled,ColorBy,TreeAngle,Height}, applyMinQual, minQual and minFreq. Add hapClusterMethod, sampleColorFile, minAc and the four vcfDo* switches that hide filter controls, in a block of their own since they are mostly used by hubs. sampleMetadataFile and showHardyWeinberg are defined in vcfUi.h but nothing in the tree reads them, so they are left out. Checked all four modes on the HGDP phased variants track, chr21:33,000,000- 33,010,000: dense 566 px, squish 617, pack 681, full 9574. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html - lines changed 10, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/vcf.html - lines changed 19, context: html, text, full: html, text

6d02024d6f5b80437784b274ff2ccf6940dde976 Wed Sep 9 15:08:26 2026 -0700

• VCF help: document geneTrack, the function coloring scheme, and vcfPhasedColorBy, refs #38010 The rest of the settings vcfUi.c reads from trackDb but neither help page mentioned. geneTrack (vcfUi.c:269 and :681) is the gate for the functional-effect coloring in both the haplotype display and the trio display: the radio button is only printed when the setting is non-empty. Nothing on either page said so, so the scheme was undiscoverable and its absence looked like a bug. hapClusterColorBy therefore has four values, not the three both pages listed -- hgVcfTrackHelp.html went as far as saying "There are three ways that reference and alternate alleles can be colored" above three bullets. Add the fourth, in the order vcfCfgHapClusterColor prints the buttons, and add function to the value lists in vcf.html. vcfPhasedColorBy (mendelDiff|deNovo|function|noColor) was documented nowhere at all, not even in trackDbLibrary.shtml, though vcf.html already described what it does in the alt text of the trio screenshot. Add it to the trio settings. Both settings tables needed a wider value column to fit, so those rows are repadded; no wording in them changed. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html - lines changed 6, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/vcf.html - lines changed 5, context: html, text, full: html, text

9d9210bb7b34131505ab50b5e62bb88680dc6129 Wed Sep 9 15:14:09 2026 -0700

• trackDb docs: add vcfPhasedColorBy, refs #38010 vcfPhasedColorBy has been read by vcfUi.c since the trio display went in, but it was documented nowhere: not on the VCF help pages, not in trackDbLibrary, and tdbQuery -check would have rejected it because tagTypes.tab did not list it either. So a hub author had no way to find the setting and no way to use it without tripping the checker. Add the library blurb, the rows in trackDbDoc.html and trackDbHub.v3.html, a changes.html entry, and the tagTypes.tab registration. The blurb spells out that mendelDiff needs vcfParentSamples and that function is only offered when geneTrack is set, since both conditions are enforced in vcfUi.c and neither is obvious from the value name. Companion to the two commits documenting the same settings on vcf.html and hgVcfTrackHelp.html. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • src/hg/htdocs/goldenPath/help/trackDb/changes.html - lines changed 11, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text

a8377d52dc28dbd8a424bf1536009d72359c8cb1 Wed Sep 9 15:25:08 2026 -0700

• trackDb: register minAc and vcfDoMinAc in tagTypes.tab, refs #38010 Both are read from trackDb but neither was listed, so tdbQuery -check would reject a stanza that used them. minAc is not just a UI default: vcfTrack.c:98 reads it, minAcFail() at :190 drops records whose INFO AC is below it, and filterRecords applies that on all three code paths, vcfPhasedLoadItems included. vcfDoMinAc gates the matching control in vcfCfgUi the same way its three siblings do. Registered for vcf, vcfTabix and vcfPhasedTrio, since filterRecords runs for the trio type too (vcfTrack.c:2344). Note minFreq and minQual are still listed as vcf and vcfTabix only, although filterRecords treats them the same way; left alone rather than widened here. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 2, context: html, text, full: html, text

37adfded75ec133c1fd2b4cb86e4757e76a54de5 Wed Sep 9 15:29:55 2026 -0700

• trackDb docs: describe minAc and vcfDoMinAc, and fix two mislabelled vcfDoMaf rows, refs #38010 The last two VCF settings with no description anywhere. Both were absent from trackDbLibrary, trackDbDoc and trackDbHub.v3, so registering them in tagTypes.tab last commit made them legal but still undiscoverable. minAc is a real filter, not just a UI default: minAcFail() in vcfTrack.c takes the largest alternate allele count from the AC field of the INFO column and drops the record when it is below the setting. Records whose INFO has no usable AC are never dropped, which is worth saying since it is the surprising half. vcfDoMinAc gates the matching control, like its three siblings. Rows follow the placement the sibling settings already use: minAc beside minFreq in the vcfTabix table, vcfDoMinAc beside vcfDoMaf in both the vcfTabix and vcfPhasedTrio tables. While adding those, trackDbDoc.html turned out to carry two rows with class="vcfDoMaf" whose anchor and format line both read vcfDoQual, so the page listed vcfDoQual twice and never showed vcfDoMaf's syntax. Copy-paste, present in both the vcfTabix and vcfPhasedTrio tables. Corrected. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • src/hg/htdocs/goldenPath/help/trackDb/changes.html - lines changed 11, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 13, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html - lines changed 9, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 15, context: html, text, full: html, text