All File Changes

v497_base to v498_preview (2026-04-20 to 2026-04-27) v498

• confs/hgwbeta.hg.conf
  • lines changed 6, context: html, text, full: html, text
    27d5efcd5e56f195907b370dbd8b2e151c700a64 Sun Apr 26 01:11:17 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 9, context: html, text, full: html, text
    27d5efcd5e56f195907b370dbd8b2e151c700a64 Sun Apr 26 01:11:17 2026 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgGene/hgGene.c
  • lines changed 9, context: html, text, full: html, text
    3670b9f2a58342dcc0629bad9d221a9d5e4ae5ff Thu Apr 23 14:39:37 2026 -0700
    hgGene: render all sections and the Methods page for QuickLift knownGene clicks. refs #36370 - synonym.c: wrap the coord-qualified kgProteinID lookup in emptyForNull. After quickLiftGenePred() rewrites curGeneChrom/Start/End to destination coords, the same-transaction lookup against the source assembly's knownGene table misses and sqlGetField returns NULL; strstr(NULL, "-") on the next line segfaulted, truncating the page at <B>Protein: </B> so GeneReviews, Methods, and any later sections never rendered. - hgGene.c doKgMethod: when the track is quickLifted and the hub trackDb has no html, refetch the trackDb from quickLiftDb using trackHubSkipHubName(tableName). The Methods "Click here" link was landing on a page whose entire body was printf("%s", NULL) => "(null)". Verified on hgwdev-braney with Gerardo's repro (hg38 -> hs1 QuickLift, chr7:156982676-156996015 window, MNX1 / ENST00000469500.5): all 13 sections now render and Methods serves the full GENCODE description. No change on the native hg38 path.
• src/hg/hgGene/synonym.c
  • lines changed 1, context: html, text, full: html, text
    3670b9f2a58342dcc0629bad9d221a9d5e4ae5ff Thu Apr 23 14:39:37 2026 -0700
    hgGene: render all sections and the Methods page for QuickLift knownGene clicks. refs #36370 - synonym.c: wrap the coord-qualified kgProteinID lookup in emptyForNull. After quickLiftGenePred() rewrites curGeneChrom/Start/End to destination coords, the same-transaction lookup against the source assembly's knownGene table misses and sqlGetField returns NULL; strstr(NULL, "-") on the next line segfaulted, truncating the page at <B>Protein: </B> so GeneReviews, Methods, and any later sections never rendered. - hgGene.c doKgMethod: when the track is quickLifted and the hub trackDb has no html, refetch the trackDb from quickLiftDb using trackHubSkipHubName(tableName). The Methods "Click here" link was landing on a page whose entire body was printf("%s", NULL) => "(null)". Verified on hgwdev-braney with Gerardo's repro (hg38 -> hs1 QuickLift, chr7:156982676-156996015 window, MNX1 / ENST00000469500.5): all 13 sections now render and Methods serves the full GENCODE description. No change on the native hg38 path.
• src/hg/hgHubConnect/hooks/pre-finish.c
  • lines changed 50, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgHubConnect/trackHubWizard.c
  • lines changed 1, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 17, context: html, text, full: html, text
    689349fca5a4865a1891db8cd39d392657b2b09b Wed Apr 22 02:54:09 2026 -0700
    Replacing the subtrackUrl setting for faceted composites with subtrackUrls, which supports outlinks in multiple fields. refs #36320
  • lines changed 21, context: html, text, full: html, text
    66ea6cb4eaf2036e464be55b295765ed5105a0fb Wed Apr 22 09:42:25 2026 -0700
    hgTrackUi/hui: render filter UI on supertrack configuration pages Supertracks (group of tracks with superTrack on, no data of their own) previously had no way to expose a shared filter: their trackDb stanza can declare filter.* / filterByRange.* / filterValues.*, but those settings were never drawn on the supertrack's hgTrackUi page. So users had to open each subtrack's own configuration page and set the same filter there, and the "lrSv.filter.svLen" cart namespace went unused. This change wires that up: - hgTrackUi.c (superTrackUi): after listing the subtracks, if the supertrack tdb declares any filter.* settings call scoreCfgUi() to render the standard filter UI. Cart variables land under the supertrack's own name (e.g. "lrSv.filter.svLen.min"), and subtracks already inherit them through cartOptionalStringClosestToHome() walking tdb->parent. Subtrack-level values continue to override. - hui.c: - buildFilterBy() / filterByValues(): tolerate a NULL autoSql object, so supertracks (which have no data table) don't errAbort when they declare filterValues.* of virtual aggregated fields. Missing-field errAbort still fires in the normal subtrack case. - scoreCfgUi() / cfgByCfgType(): when called with title == NULL (the supertrack filter path), suppress the default "<p>" separator and the "<BR>" between the title bar and the filter block; the caller renders its own section heading. - asForTdb(): handle conn == NULL by returning NULL rather than crashing, since supertrack filter rendering has no associated sqlConnection. refs #37426
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    8c8823d9a87b6046094577a808dda4ed4172b416 Thu Apr 23 11:09:48 2026 -0700
    Make quickLifted GENCODE tracks usable: click details, position links, coloring. refs #36059 - Re-vet wgEncodeGencode* in trackHub.c:isVetted() so the quickLift hub no longer emits `avoidHandler on` for GENCODE children. Without this, hgc bypasses findNameBasedHandler and doGencodeGene is never reached, so the details page falls through to the generic showGenePos output. - In gencodeClick.c doGencodeGene/helpers, use quickLiftDb for the MySQL connection (the attrs/tag/pubMed/refSeq/uniProt tables live in the source assembly), use trackHubSkipHubName(tdb->track) for the genePred table name and the Basic/Comp/PseudoGene/PolyA prefix dispatch checks, and teach isGrcHuman/isGrcH37Native to consult the source db — otherwise the page errAborted with "BUG: gencodeClick on wrong database: hub_NNNNN_hs1". - Lift the Position values (transcript + gene bounds, 2-way pseudo, PolyA) through the quickLift chain before printing, so the details page shows destination-assembly coords and the Position link lands at a window that actually contains the gene. - htcDnaNearGene (hgc.c): when quickLifted, lift seqName/winStart/winEnd back to source coords before hgSeqItemsInRange. The prior code pointed the query at the source-assembly table but still passed the destination window, so the "Genomic Sequence from assembly" flow returned "No results returned from query." No longer reachable from the GENCODE details page (doGencodeGene writes its own Sequences table) but still hit by other quickLifted genePred tracks. - simpleTracks.c genePredItemClassColor: the hTableExists() guard was checking `database` (the destination hub db like hub_NNNNN_hs1) even though the MySQL conn was already routed to liftDb; the lookup was skipped and every item fell back to tg->ixColor, rendering all black. Check `db` instead so the gClass_* palette (coding / nonCoding / pseudo / problem) is applied. Verified end-to-end on hgwdev-braney: Gerardo's SHH test case (ENST00000297261.7) and Basic/Comp/PseudoGene/PolyA subtracks; no regression on the non-quickLifted hg38 click.
  • lines changed 4, context: html, text, full: html, text
    5fa73cd9b411b3147227a4a31f6df7b24638dd00 Fri Apr 24 05:37:11 2026 -0700
    adding exon length to mouseover, refs #37439
• src/hg/hgc/bigBedClick.c
  • lines changed 1, context: html, text, full: html, text
    c13d7b1af23d1e1a6f015953536e2d74a467fb16 Wed Apr 22 17:25:40 2026 -0700
    hgc bigBed click: skip intervals that fail to quickLift remap instead of errAborting with an out-of-bounds read. The errAbort message printed fields[3] on a stack-allocated fields[bedSize+seq1Seq2Fields]; for a bigBed3 (e.g. GIAB problematicRegions) that's one past the end, producing garbled binary text in the warning dialog. More importantly, for bedSize==3 there is no name filter before the remap, so every interval in the window was remapped and any single failure aborted the whole page. Match the hgTracks behavior (bigBedTrack.c: continue on NULL) so unmappable items are silently dropped and the clicked item still renders. refs #36335
• src/hg/hgc/gencodeClick.c
  • lines changed 64, context: html, text, full: html, text
    8c8823d9a87b6046094577a808dda4ed4172b416 Thu Apr 23 11:09:48 2026 -0700
    Make quickLifted GENCODE tracks usable: click details, position links, coloring. refs #36059 - Re-vet wgEncodeGencode* in trackHub.c:isVetted() so the quickLift hub no longer emits `avoidHandler on` for GENCODE children. Without this, hgc bypasses findNameBasedHandler and doGencodeGene is never reached, so the details page falls through to the generic showGenePos output. - In gencodeClick.c doGencodeGene/helpers, use quickLiftDb for the MySQL connection (the attrs/tag/pubMed/refSeq/uniProt tables live in the source assembly), use trackHubSkipHubName(tdb->track) for the genePred table name and the Basic/Comp/PseudoGene/PolyA prefix dispatch checks, and teach isGrcHuman/isGrcH37Native to consult the source db — otherwise the page errAborted with "BUG: gencodeClick on wrong database: hub_NNNNN_hs1". - Lift the Position values (transcript + gene bounds, 2-way pseudo, PolyA) through the quickLift chain before printing, so the details page shows destination-assembly coords and the Position link lands at a window that actually contains the gene. - htcDnaNearGene (hgc.c): when quickLifted, lift seqName/winStart/winEnd back to source coords before hgSeqItemsInRange. The prior code pointed the query at the source-assembly table but still passed the destination window, so the "Genomic Sequence from assembly" flow returned "No results returned from query." No longer reachable from the GENCODE details page (doGencodeGene writes its own Sequences table) but still hit by other quickLifted genePred tracks. - simpleTracks.c genePredItemClassColor: the hTableExists() guard was checking `database` (the destination hub db like hub_NNNNN_hs1) even though the MySQL conn was already routed to liftDb; the lookup was skipped and every item fell back to tg->ixColor, rendering all black. Check `db` instead so the gClass_* palette (coding / nonCoding / pseudo / problem) is applied. Verified end-to-end on hgwdev-braney: Gerardo's SHH test case (ENST00000297261.7) and Basic/Comp/PseudoGene/PolyA subtracks; no regression on the non-quickLifted hg38 click.
• src/hg/hgc/geneReviewsClick.c
  • lines changed 6, context: html, text, full: html, text
    7120a354ec4870b3bc2112c384bdb0af837ed44e Thu Apr 23 14:12:36 2026 -0700
    hgc: make quickLifted NCBI RefSeq / UCSC RefSeq click details work. refs #36125 - trackHub.c isVetted(): accept refGene, ncbiRefSeq* subtracks, and ncbiOrtho so the generated quickLift hub.txt doesn't emit 'avoidHandler on' for them. Without this, hgc skips findNameBasedHandler and the detail click falls through to genericClickHandler, showing none of the rich RefSeq fields. - hgc.c findNameBasedHandler: when the tdb has 'quickLifted on', strip the hub_NNN_ prefix from the dispatch table before comparisons so refGene / ncbiRefSeq* match their native handlers. - doNcbiRefSeq / doRefGene: route hAllocConn to quickLiftDb (source), use trackHubSkipHubName for track/table name comparisons, and pass srcDb into replaceInUrl, hTableExists, AceView / MGIid / jaxOrtholog / hg-prefix checks -- otherwise these paths errAborted with "Unknown database hub_NNN_<db>" on a quickLifted click. - printRefSeqInfo / prRefGeneInfo / gbCdnaGetVersion: use sqlGetDatabase(conn) rather than the global `database` for host-db checks. - Predicted Protein / Predicted mRNA links for quickLifted tracks now point at htcTranslatedPredMRna / htcGeneMrna so the sequences come from the destination genome at the lifted exon coordinates, rather than the NCBI-authored refPep / seqNcbiRefSeq extFiles on the source. Native behavior is unchanged. - showGenePos: fetch via quickLiftSql + calcLiftOverGenePreds when the track is quickLifted so the Position line is in destination coordinates. The swapped chainHash comes from the track's quickLiftUrl bigChain, matching the pattern getGenePredForPositionSql already uses. - Suppress the mRNA/Genomic Alignments block and its trailing <hr> for quickLifted refGene / ncbiRefSeq* clicks. The PSLs come back in source coords and the htcCdnaAli links don't line up with the destination window. - getAlignmentsTName: use sqlGetDatabase(conn) rather than global `database` so split-table resolution looks up the right db. - printGeneCards: take a db argument; callers pass srcDb so the GeneCards link renders on quickLifted pages (the "startsWith hg" check was matching hub_NNN_hs1 as false). - geneReviewsClick.c prGRShortRefGene: take a struct sqlConnection * rather than opening its own on `database` (hub_NNN_hs1 -> Unknown database abort). Callers in prRefGeneInfo and doOmimGene2 pass their existing source-db conn, so the Related GeneReviews line now shows on both native and quickLifted refGene pages. Verified end-to-end on hgwdev-braney with hg38 -> hs1 quickLift of the refSeqComposite: ncbiRefSeqCurated and refGene clicks on SHH now render the full doNcbiRefSeq / doRefGene details (RefSeq / Status / Description / Synonyms / OMIM / Protein / HGNC / Entrez Gene / GeneCards / AceView / Summary / Position / Gene Symbol); Predicted mRNA and Predicted Protein links return destination-derived sequences; Genomic Sequence reaches the Get-DNA-in-window page; Ctrl/Cmd+drag zoom no longer ends up with an HTML error page inside the zoom dialog. Non-quickLifted hg38 refSeq details are unchanged (alignments still shown, GeneReviews still present). The duplicate-subtracks symptom from the ticket's step (i) is not addressed here -- it's an architectural consequence of the shared `refSeqComposite` cart key applying to both the destination's native composite and the quickLift hub's composite, and needs cart-scoping work in quickLift v2. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgc/hgc.c
  • lines changed 11, context: html, text, full: html, text
    8c8823d9a87b6046094577a808dda4ed4172b416 Thu Apr 23 11:09:48 2026 -0700
    Make quickLifted GENCODE tracks usable: click details, position links, coloring. refs #36059 - Re-vet wgEncodeGencode* in trackHub.c:isVetted() so the quickLift hub no longer emits `avoidHandler on` for GENCODE children. Without this, hgc bypasses findNameBasedHandler and doGencodeGene is never reached, so the details page falls through to the generic showGenePos output. - In gencodeClick.c doGencodeGene/helpers, use quickLiftDb for the MySQL connection (the attrs/tag/pubMed/refSeq/uniProt tables live in the source assembly), use trackHubSkipHubName(tdb->track) for the genePred table name and the Basic/Comp/PseudoGene/PolyA prefix dispatch checks, and teach isGrcHuman/isGrcH37Native to consult the source db — otherwise the page errAborted with "BUG: gencodeClick on wrong database: hub_NNNNN_hs1". - Lift the Position values (transcript + gene bounds, 2-way pseudo, PolyA) through the quickLift chain before printing, so the details page shows destination-assembly coords and the Position link lands at a window that actually contains the gene. - htcDnaNearGene (hgc.c): when quickLifted, lift seqName/winStart/winEnd back to source coords before hgSeqItemsInRange. The prior code pointed the query at the source-assembly table but still passed the destination window, so the "Genomic Sequence from assembly" flow returned "No results returned from query." No longer reachable from the GENCODE details page (doGencodeGene writes its own Sequences table) but still hit by other quickLifted genePred tracks. - simpleTracks.c genePredItemClassColor: the hTableExists() guard was checking `database` (the destination hub db like hub_NNNNN_hs1) even though the MySQL conn was already routed to liftDb; the lookup was skipped and every item fell back to tg->ixColor, rendering all black. Check `db` instead so the gClass_* palette (coding / nonCoding / pseudo / problem) is applied. Verified end-to-end on hgwdev-braney: Gerardo's SHH test case (ENST00000297261.7) and Basic/Comp/PseudoGene/PolyA subtracks; no regression on the non-quickLifted hg38 click.
  • lines changed 126, context: html, text, full: html, text
    7120a354ec4870b3bc2112c384bdb0af837ed44e Thu Apr 23 14:12:36 2026 -0700
    hgc: make quickLifted NCBI RefSeq / UCSC RefSeq click details work. refs #36125 - trackHub.c isVetted(): accept refGene, ncbiRefSeq* subtracks, and ncbiOrtho so the generated quickLift hub.txt doesn't emit 'avoidHandler on' for them. Without this, hgc skips findNameBasedHandler and the detail click falls through to genericClickHandler, showing none of the rich RefSeq fields. - hgc.c findNameBasedHandler: when the tdb has 'quickLifted on', strip the hub_NNN_ prefix from the dispatch table before comparisons so refGene / ncbiRefSeq* match their native handlers. - doNcbiRefSeq / doRefGene: route hAllocConn to quickLiftDb (source), use trackHubSkipHubName for track/table name comparisons, and pass srcDb into replaceInUrl, hTableExists, AceView / MGIid / jaxOrtholog / hg-prefix checks -- otherwise these paths errAborted with "Unknown database hub_NNN_<db>" on a quickLifted click. - printRefSeqInfo / prRefGeneInfo / gbCdnaGetVersion: use sqlGetDatabase(conn) rather than the global `database` for host-db checks. - Predicted Protein / Predicted mRNA links for quickLifted tracks now point at htcTranslatedPredMRna / htcGeneMrna so the sequences come from the destination genome at the lifted exon coordinates, rather than the NCBI-authored refPep / seqNcbiRefSeq extFiles on the source. Native behavior is unchanged. - showGenePos: fetch via quickLiftSql + calcLiftOverGenePreds when the track is quickLifted so the Position line is in destination coordinates. The swapped chainHash comes from the track's quickLiftUrl bigChain, matching the pattern getGenePredForPositionSql already uses. - Suppress the mRNA/Genomic Alignments block and its trailing <hr> for quickLifted refGene / ncbiRefSeq* clicks. The PSLs come back in source coords and the htcCdnaAli links don't line up with the destination window. - getAlignmentsTName: use sqlGetDatabase(conn) rather than global `database` so split-table resolution looks up the right db. - printGeneCards: take a db argument; callers pass srcDb so the GeneCards link renders on quickLifted pages (the "startsWith hg" check was matching hub_NNN_hs1 as false). - geneReviewsClick.c prGRShortRefGene: take a struct sqlConnection * rather than opening its own on `database` (hub_NNN_hs1 -> Unknown database abort). Callers in prRefGeneInfo and doOmimGene2 pass their existing source-db conn, so the Related GeneReviews line now shows on both native and quickLifted refGene pages. Verified end-to-end on hgwdev-braney with hg38 -> hs1 quickLift of the refSeqComposite: ncbiRefSeqCurated and refGene clicks on SHH now render the full doNcbiRefSeq / doRefGene details (RefSeq / Status / Description / Synonyms / OMIM / Protein / HGNC / Entrez Gene / GeneCards / AceView / Summary / Position / Gene Symbol); Predicted mRNA and Predicted Protein links return destination-derived sequences; Genomic Sequence reaches the Get-DNA-in-window page; Ctrl/Cmd+drag zoom no longer ends up with an HTML error page inside the zoom dialog. Non-quickLifted hg38 refSeq details are unchanged (alignments still shown, GeneReviews still present). The duplicate-subtracks symptom from the ticket's step (i) is not addressed here -- it's an architectural consequence of the shared `refSeqComposite` cart key applying to both the destination's native composite and the quickLift hub's composite, and needs cart-scoping work in quickLift v2. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgc/hgc.h
  • lines changed 1, context: html, text, full: html, text
    7120a354ec4870b3bc2112c384bdb0af837ed44e Thu Apr 23 14:12:36 2026 -0700
    hgc: make quickLifted NCBI RefSeq / UCSC RefSeq click details work. refs #36125 - trackHub.c isVetted(): accept refGene, ncbiRefSeq* subtracks, and ncbiOrtho so the generated quickLift hub.txt doesn't emit 'avoidHandler on' for them. Without this, hgc skips findNameBasedHandler and the detail click falls through to genericClickHandler, showing none of the rich RefSeq fields. - hgc.c findNameBasedHandler: when the tdb has 'quickLifted on', strip the hub_NNN_ prefix from the dispatch table before comparisons so refGene / ncbiRefSeq* match their native handlers. - doNcbiRefSeq / doRefGene: route hAllocConn to quickLiftDb (source), use trackHubSkipHubName for track/table name comparisons, and pass srcDb into replaceInUrl, hTableExists, AceView / MGIid / jaxOrtholog / hg-prefix checks -- otherwise these paths errAborted with "Unknown database hub_NNN_<db>" on a quickLifted click. - printRefSeqInfo / prRefGeneInfo / gbCdnaGetVersion: use sqlGetDatabase(conn) rather than the global `database` for host-db checks. - Predicted Protein / Predicted mRNA links for quickLifted tracks now point at htcTranslatedPredMRna / htcGeneMrna so the sequences come from the destination genome at the lifted exon coordinates, rather than the NCBI-authored refPep / seqNcbiRefSeq extFiles on the source. Native behavior is unchanged. - showGenePos: fetch via quickLiftSql + calcLiftOverGenePreds when the track is quickLifted so the Position line is in destination coordinates. The swapped chainHash comes from the track's quickLiftUrl bigChain, matching the pattern getGenePredForPositionSql already uses. - Suppress the mRNA/Genomic Alignments block and its trailing <hr> for quickLifted refGene / ncbiRefSeq* clicks. The PSLs come back in source coords and the htcCdnaAli links don't line up with the destination window. - getAlignmentsTName: use sqlGetDatabase(conn) rather than global `database` so split-table resolution looks up the right db. - printGeneCards: take a db argument; callers pass srcDb so the GeneCards link renders on quickLifted pages (the "startsWith hg" check was matching hub_NNN_hs1 as false). - geneReviewsClick.c prGRShortRefGene: take a struct sqlConnection * rather than opening its own on `database` (hub_NNN_hs1 -> Unknown database abort). Callers in prRefGeneInfo and doOmimGene2 pass their existing source-db conn, so the Related GeneReviews line now shows on both native and quickLifted refGene pages. Verified end-to-end on hgwdev-braney with hg38 -> hs1 quickLift of the refSeqComposite: ncbiRefSeqCurated and refGene clicks on SHH now render the full doNcbiRefSeq / doRefGene details (RefSeq / Status / Description / Synonyms / OMIM / Protein / HGNC / Entrez Gene / GeneCards / AceView / Summary / Position / Gene Symbol); Predicted mRNA and Predicted Protein links return destination-derived sequences; Genomic Sequence reaches the Get-DNA-in-window page; Ctrl/Cmd+drag zoom no longer ends up with an HTML error page inside the zoom dialog. Non-quickLifted hg38 refSeq details are unchanged (alignments still shown, GeneReviews still present). The duplicate-subtracks symptom from the ticket's step (i) is not addressed here -- it's an architectural consequence of the shared `refSeqComposite` cart key applying to both the destination's native composite and the quickLift hub's composite, and needs cart-scoping work in quickLift v2. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/bigBed.html
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    65091fe6f6487c23d650a144e947fc1c582d3f40 Tue Apr 21 02:16:16 2026 -0700
    abelSv: move under lrSv supertrack as short-read comparison subtrack Move the Abel et al. 2020 CCDG 17,795-genome SV callset from a top-level hg38 track to a subtrack of the lrSv supertrack (parallel to onekg3202Sr) and relabel shortLabel/longLabel to flag Illumina short-read provenance. The same bigBed is now visible on hg38 in the long-read SV browsing context. Also: - Clarify abelSv.html variant counts: 738,624 upstream unique SVs across both callsets, 737,998 after B37->hg38 liftOver (626 unmapped). B38=458,106, B37lift=279,892. - lrSv.html: fix triple-slash https:/// in the Ebert et al. Science reference URL. - bigBed.html: add closing </li> on the extra-fields pipe-separator bullet and tighten a comma in the same sentence. refs #36258, refs #37376
• src/hg/htdocs/goldenPath/help/bigMaf.html
  • lines changed 4, context: html, text, full: html, text
    cc610239716fe32f9c774d98a71f75e8c6b5fba3 Tue Apr 21 17:23:50 2026 -0700
    mafToBigMafSummary: new utility that emits bed3+4 input ready for bedToBigBed -as=mafSummary.as, replacing the hgLoadMafSummary -test / cut -f2- / sort hack documented in bigMaf.html. Companion to mafToBigMaf. The summary scoring/merging logic is intentionally duplicated from hgLoadMafSummary.c (see header comment) — that code is stable and refactoring would force retesting all the makedocs that call hgLoadMafSummary. Also fixes a bug in the duplicated copy of mafSplitSrcGetChrom: the original errAborts on plain 'hg38.chrY' style master src because of an inverted differentString check; rewritten with cleaner correct logic. Updates bigMaf.html and trackDb/trackDbLibrary.shtml to reference the new tool. refs #37404
• src/hg/htdocs/goldenPath/help/facetedComposite.html
  • lines changed 250, context: html, text, full: html, text
    4a6170904fe3901af94b7cf0494e9e991e40115e Wed Apr 22 03:39:05 2026 -0700
    First pass at a faceted composite help doc, refs #36320
• src/hg/htdocs/goldenPath/help/trackDb/changes.html
  • lines changed 7, context: html, text, full: html, text
    689349fca5a4865a1891db8cd39d392657b2b09b Wed Apr 22 02:54:09 2026 -0700
    Replacing the subtrackUrl setting for faceted composites with subtrackUrls, which supports outlinks in multiple fields. refs #36320
  • lines changed 1, context: html, text, full: html, text
    a470786ea3c54bfcfac6192a0aaacdb23c02a819 Thu Apr 23 08:20:45 2026 -0700
    Fixing small typo in the trackDb changes doc, refs #36320
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.css
  • lines changed 12, context: html, text, full: html, text
    75a1bac8b8addd47d90c5061d9167c581677be5b Thu Apr 23 08:41:25 2026 -0700
    Fix for trackDb docs anchors landing under the javascript search box. Now they're pushed down a bit below it (more on narrow displays). No ticket
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 3, context: html, text, full: html, text
    689349fca5a4865a1891db8cd39d392657b2b09b Wed Apr 22 02:54:09 2026 -0700
    Replacing the subtrackUrl setting for faceted composites with subtrackUrls, which supports outlinks in multiple fields. refs #36320
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 3, context: html, text, full: html, text
    689349fca5a4865a1891db8cd39d392657b2b09b Wed Apr 22 02:54:09 2026 -0700
    Replacing the subtrackUrl setting for faceted composites with subtrackUrls, which supports outlinks in multiple fields. refs #36320
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 2, context: html, text, full: html, text
    cc610239716fe32f9c774d98a71f75e8c6b5fba3 Tue Apr 21 17:23:50 2026 -0700
    mafToBigMafSummary: new utility that emits bed3+4 input ready for bedToBigBed -as=mafSummary.as, replacing the hgLoadMafSummary -test / cut -f2- / sort hack documented in bigMaf.html. Companion to mafToBigMaf. The summary scoring/merging logic is intentionally duplicated from hgLoadMafSummary.c (see header comment) — that code is stable and refactoring would force retesting all the makedocs that call hgLoadMafSummary. Also fixes a bug in the duplicated copy of mafSplitSrcGetChrom: the original errAborts on plain 'hg38.chrY' style master src because of an inverted differentString check; rewritten with cleaner correct logic. Updates bigMaf.html and trackDb/trackDbLibrary.shtml to reference the new tool. refs #37404
  • lines changed 7, context: html, text, full: html, text
    689349fca5a4865a1891db8cd39d392657b2b09b Wed Apr 22 02:54:09 2026 -0700
    Replacing the subtrackUrl setting for faceted composites with subtrackUrls, which supports outlinks in multiple fields. refs #36320
  • lines changed 1, context: html, text, full: html, text
    ac8d49f37257e983488864f0bb6712a9260e10c1 Fri Apr 24 14:05:10 2026 -0700
    Fix incorrect skipFields syntax in trackDbLibrary.shtml to match the comma-separated form used in the example and parsed by hgc.c. refs #36203
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 35, context: html, text, full: html, text
    3972ba54c468ace338d4a5578de1d20bf6c1f9ec Mon Apr 20 15:39:26 2026 -0700
    Adding Rule 4 (long-exon rule, Lindeboom 2016) to NMD Escape tracks and releasing on Apr. 22, 2026. refs #33737 Script: added a fourth rule to genePredNmdEsc. Coding exons longer than 400 bp (excluding the last coding exon, which is already covered by the 50 bp rule) are flagged as NMD-escape regions. Rebuilt the Gencode and NCBI RefSeq bigBed files. trackDb: - nmd.ra: appended "/400nt" to the nmdEsc longLabels, set nmdEscGencode default visibility to dense so the track is visible in cart-reset views, changed all four NMDetective subtracks from "visibility full" to "visibility hide", updated pennantIcon to the Apr. 22, 2026 release date and anchor. - nmd.html: mention long internal exons in the overview description, update the rule count from three to four. - nmdEscTranscripts.html: add the long-exon rule to the rule list and color legend (gold, #FFD700), expand the Background section with mechanisms for the intronless, start-proximal, and long-exon rules, correct the 50 bp rule description to include the entire last coding exon, fix Lindeboom 2016 author initials (RG -> RGH). News: - newsarch.html: add the 2026-04-22 NMD Escape news entry covering all four rules, with acknowledgements to Guido Neidhardt and Andreas Lahner for suggesting the track and the Decipher Genome Browser team for inspiring the visualization. - indexNews.html: add the front-page news link. makedoc: - nmd.txt: dated note for the Rule 4 rebuild.
  • lines changed 2, context: html, text, full: html, text
    d23d0116ff17b126a498c8d02bdef578d0ab1b53 Wed Apr 22 12:51:20 2026 -0700
    Update NMD Escape newsarch entry to match shipped Rule 2 definition. refs #33737 Rule 2 is no longer the 'intronless transcript rule' after the round 4 gate refinement (single coding exon AND no 3'UTR intron). Updated the newsarch entry to match.
  • lines changed 16, context: html, text, full: html, text
    395a8efc6994c18a3b0bdfcee82217ff9d78b739 Wed Apr 22 12:54:59 2026 -0700
    Expand NMD Escape newsarch rules into sub-bullets. refs #33737 Break the four-rule summary into individual sub-bullets under the ruleset line so each rule is visible at a glance.
• src/hg/htdocs/inc/hgMyData.html
  • lines changed 4, context: html, text, full: html, text
    4f03efa12fa7a52cad6b78f24d295ff5d80405c0 Thu Apr 23 12:14:00 2026 -0700
    Try to make it more obvious that clicking the 'view' button next to a track file in hubspace connects the whole hub. Add a banner above the table indicating this and with a link that connects the entire hub, refs Max/Baihe email
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    3972ba54c468ace338d4a5578de1d20bf6c1f9ec Mon Apr 20 15:39:26 2026 -0700
    Adding Rule 4 (long-exon rule, Lindeboom 2016) to NMD Escape tracks and releasing on Apr. 22, 2026. refs #33737 Script: added a fourth rule to genePredNmdEsc. Coding exons longer than 400 bp (excluding the last coding exon, which is already covered by the 50 bp rule) are flagged as NMD-escape regions. Rebuilt the Gencode and NCBI RefSeq bigBed files. trackDb: - nmd.ra: appended "/400nt" to the nmdEsc longLabels, set nmdEscGencode default visibility to dense so the track is visible in cart-reset views, changed all four NMDetective subtracks from "visibility full" to "visibility hide", updated pennantIcon to the Apr. 22, 2026 release date and anchor. - nmd.html: mention long internal exons in the overview description, update the rule count from three to four. - nmdEscTranscripts.html: add the long-exon rule to the rule list and color legend (gold, #FFD700), expand the Background section with mechanisms for the intronless, start-proximal, and long-exon rules, correct the 50 bp rule description to include the entire last coding exon, fix Lindeboom 2016 author initials (RG -> RGH). News: - newsarch.html: add the 2026-04-22 NMD Escape news entry covering all four rules, with acknowledgements to Guido Neidhardt and Andreas Lahner for suggesting the track and the Decipher Genome Browser team for inspiring the visualization. - indexNews.html: add the front-page news link. makedoc: - nmd.txt: dated note for the Rule 4 rebuild.
• src/hg/htdocs/style/hgMyData.css
  • lines changed 8, context: html, text, full: html, text
    d40ace87860e49440a8ffcd09a4a68a682ad07ec Thu Apr 23 12:57:12 2026 -0700
    add nowrap rules to more settings in the hubSpace data table to prevent row heights from growing when a filename is too long for the current window size and forces an adjustment by Data Tables. adjust columns when the window size grows dynamically. this should ensure the view in buttons are always the same size regardless of screen width or table content, refs Max/Baihe email
• src/hg/htdocs/style/makefile
  • lines changed 1, context: html, text, full: html, text
    7d049679cd9efc4dacc25fc0f181e85d7221d48b Tue Apr 21 12:44:36 2026 -0700
    adding liftRequest.js refs #31811
• src/hg/hubApi/liftOver.c
  • lines changed 1, context: html, text, full: html, text
    908c2b249f2cea98192862b2ce49af1a43e48838 Tue Apr 21 12:37:24 2026 -0700
    updated ottoRequest table schema for more general requests refs #31811
  • lines changed 6, context: html, text, full: html, text
    83f8234095a0b5e6edb8aaaeabb8e78443830ea3 Thu Apr 23 13:48:43 2026 -0700
    turn off the email notification from here, let the otto cron job do the email refs #31811
  • lines changed 1, context: html, text, full: html, text
    b3a76833aa84a341e86d0bacef2ff1f6b9b44851 Thu Apr 23 14:30:24 2026 -0700
    rename workflowId column to buildDir and expand its size refs #31811
  • lines changed 1, context: html, text, full: html, text
    1cbaa9ddcb7a13929a2217db78d6b36ff738fe15 Fri Apr 24 10:52:34 2026 -0700
    doneStatus can simply be status refs #31811
• src/hg/inc/hubSpace.h
  • lines changed 2, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/inc/ottoRequest.h
  • lines changed 5, context: html, text, full: html, text
    435e92d0ad49164d1b5b156e3fb5ef5ff7b19041 Tue Apr 21 12:29:50 2026 -0700
    make the ottoRequest table a bit more generic so it can handle both liftOver and assembly requests refs #31811
  • lines changed 1, context: html, text, full: html, text
    fcfb91470c294d3b991dbd0d24cba67de9ed65cb Tue Apr 21 14:20:57 2026 -0700
    create ottoRequest cron watch script refs #31811
  • lines changed 2, context: html, text, full: html, text
    b3a76833aa84a341e86d0bacef2ff1f6b9b44851 Thu Apr 23 14:30:24 2026 -0700
    rename workflowId column to buildDir and expand its size refs #31811
  • lines changed 1, context: html, text, full: html, text
    1cbaa9ddcb7a13929a2217db78d6b36ff738fe15 Fri Apr 24 10:52:34 2026 -0700
    doneStatus can simply be status refs #31811
• src/hg/inc/quickLift.h
  • lines changed 7, context: html, text, full: html, text
    81d00f3eec6ea6978c9a71ed6a48c84a0bd0c987 Wed Apr 22 14:51:08 2026 -0700
    hgFind: remap bigBed search hits from source to destination coords when the track is quickLifted. Previously a search for e.g. "BRCA2" on a quickLifted hub (hg38 tracks displayed on HG02257.pat) returned hits at hg38 chr13 coordinates; clicking the result errored with "Sorry, couldn't locate chr13:... in <dest>". Adds quickLiftLiftPos() in hg/lib/quickLift.c, which reads the source->dest liftOverChainFile and calls liftOverRemapRange. Called from bigBedIntervalListToHgPositions in hg/lib/bigBedFind.c whenever tdb has quickLiftUrl/quickLiftDb; hits that don't map through the chain are dropped. refs #36340
• src/hg/inc/trackHub.h
  • lines changed 5, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/inc/userdata.h
  • lines changed 31, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    ae1db8bd101ae572e4382748dc4b19b176449fa0 Thu Apr 23 09:22:05 2026 -0700
    Fix hubSpace quota calculation to use quotax(1024x1024x1024) rather than quotax10^9, refs #37425
• src/hg/js/facetedComposite.js
  • lines changed 33, context: html, text, full: html, text
    689349fca5a4865a1891db8cd39d392657b2b09b Wed Apr 22 02:54:09 2026 -0700
    Replacing the subtrackUrl setting for faceted composites with subtrackUrls, which supports outlinks in multiple fields. refs #36320
  • lines changed 25, context: html, text, full: html, text
    72de5a10dd13d893dd4111ac8acfdc29579760e8 Sat Apr 25 10:18:50 2026 -0700
    Fixing a conflict in faceted composites between the use of primaryKey values as data elements (for subtrack names) and the features around linking out (id|label stuff). refs #36320
• src/hg/js/hgMyData.js
  • lines changed 455, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 36, context: html, text, full: html, text
    0db69910b2561b37d888bdff69895117eea55175 Thu Apr 23 12:00:09 2026 -0700
    Make file names in hubSpace links to view/download the files. Add a copy icon next to each file that copies the url for easy linking to hub.txts, refs Max/Baihe email
  • lines changed 34, context: html, text, full: html, text
    4f03efa12fa7a52cad6b78f24d295ff5d80405c0 Thu Apr 23 12:14:00 2026 -0700
    Try to make it more obvious that clicking the 'view' button next to a track file in hubspace connects the whole hub. Add a banner above the table indicating this and with a link that connects the entire hub, refs Max/Baihe email
  • lines changed 24, context: html, text, full: html, text
    d40ace87860e49440a8ffcd09a4a68a682ad07ec Thu Apr 23 12:57:12 2026 -0700
    add nowrap rules to more settings in the hubSpace data table to prevent row heights from growing when a filename is too long for the current window size and forces an adjustment by Data Tables. adjust columns when the window size grows dynamically. this should ensure the view in buttons are always the same size regardless of screen width or table content, refs Max/Baihe email
• src/hg/js/hgTracks.js
  • lines changed 13, context: html, text, full: html, text
    d5580b384522b44b2d374446d33304a1adf2e13a Mon Apr 20 14:05:06 2026 -0700
    hgTracks: wrap setInHistory calls in try/catch, refs #37367
• src/hg/js/hui.js
  • lines changed 33, context: html, text, full: html, text
    8e279300b1726f355767b467bc699685e90d487b Tue Apr 21 06:27:16 2026 -0700
    composite hgTrackUi: fix btn_minus_all to hide parent, remember last vis, refs #37182 Two fixes around composite visibility on hgTrackUi: 1) The global [-] button (btn_minus_all) unchecked all subtracks but left the composite visibility dropdown unchanged. The earlier fix in 814472876ea covered only the matrix-corner [-] (_matSetMatrixCheckBoxes); the global button goes through matSubCBsCheck, which is now updated to the same pattern. 2) [-] / [+] and individual subCB clicks now remember the prior visibility via a data-last-viz attribute on the dropdown. Hiding stashes the current value; re-showing restores it (falling back to pack/dense if nothing saved) instead of always jumping to pack. Factored into two helpers in hui.js: hideCompositeSaveVis() and an extended exposeAll(). subCfg.onUserCbChange (individual subCB/matCB path) delegates to the same helpers so behavior is uniform. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/js/liftRequest.js
  • lines changed 26, context: html, text, full: html, text
    113937fa86799fcf930f93aade0355a698088982 Tue Apr 21 12:45:53 2026 -0700
    fixups to avoid jshint errors refs #31811
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    3e3270b639bae3a1dee7a4a69ffda4a6298c81cf Tue Apr 21 12:44:10 2026 -0700
    adding liftRequest.js refs #31811
• src/hg/js/subCfg.js
  • lines changed 16, context: html, text, full: html, text
    8e279300b1726f355767b467bc699685e90d487b Tue Apr 21 06:27:16 2026 -0700
    composite hgTrackUi: fix btn_minus_all to hide parent, remember last vis, refs #37182 Two fixes around composite visibility on hgTrackUi: 1) The global [-] button (btn_minus_all) unchecked all subtracks but left the composite visibility dropdown unchanged. The earlier fix in 814472876ea covered only the matrix-corner [-] (_matSetMatrixCheckBoxes); the global button goes through matSubCBsCheck, which is now updated to the same pattern. 2) [-] / [+] and individual subCB clicks now remember the prior visibility via a data-last-viz attribute on the dropdown. Hiding stashes the current value; re-showing restores it (falling back to pack/dense if nothing saved) instead of always jumping to pack. Factored into two helpers in hui.js: hideCompositeSaveVis() and an extended exposeAll(). subCfg.onUserCbChange (individual subCB/matCB path) delegates to the same helpers so behavior is uniform. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/js/utils.js
  • lines changed 1, context: html, text, full: html, text
    9776e92bfd35a04bcb3d1bcfc165213f249ed89e Tue Apr 21 12:03:30 2026 -0700
    mdbSearch javascript was constructing faulty URLs for hgApi, breaking then ENCODE track search (and probably file search too), refs #37421
• src/hg/lib/bigBedFind.c
  • lines changed 27, context: html, text, full: html, text
    81d00f3eec6ea6978c9a71ed6a48c84a0bd0c987 Wed Apr 22 14:51:08 2026 -0700
    hgFind: remap bigBed search hits from source to destination coords when the track is quickLifted. Previously a search for e.g. "BRCA2" on a quickLifted hub (hg38 tracks displayed on HG02257.pat) returned hits at hg38 chr13 coordinates; clicking the result errored with "Sorry, couldn't locate chr13:... in <dest>". Adds quickLiftLiftPos() in hg/lib/quickLift.c, which reads the source->dest liftOverChainFile and calls liftOverRemapRange. Called from bigBedIntervalListToHgPositions in hg/lib/bigBedFind.c whenever tdb has quickLiftUrl/quickLiftDb; hits that don't map through the chain are dropped. refs #36340
• src/hg/lib/hubConnect.c
  • lines changed 31, context: html, text, full: html, text
    6d37e3250000dee12e193601c4cdbae21e4d099b Mon Apr 20 14:59:37 2026 -0700
    make assumesHub session portability work for assembly hubs: when the current db is hub_<id>_<genome> and the hub's id differs from the local hubStatus id, remap the db cart variable and any db-keyed cart vars (e.g. position.<db>) along with the hub_<id>_* track settings that were already being renamed. refs #34986
• src/hg/lib/hubSpace.as
  • lines changed 1, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/lib/hubSpace.c
  • lines changed 33, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/lib/hubSpace.sql
  • lines changed 1, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/lib/hubSpaceQuotas.c
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    ae1db8bd101ae572e4382748dc4b19b176449fa0 Thu Apr 23 09:22:05 2026 -0700
    Fix hubSpace quota calculation to use quotax(1024x1024x1024) rather than quotax10^9, refs #37425
• src/hg/lib/hui.c
  • lines changed 39, context: html, text, full: html, text
    5aed2d465f12c3b82dbb6ae78b3bf5529fd0a2ba Mon Apr 20 17:13:12 2026 -0700
    hgc/hgTrackUi: populate quickLift source track description when the source assembly is a hub or GenArk. getTrackHtml() had an empty TODO branch for trackHubDatabase(db) || isGenArk(db); wire it up to open the source hub (via the connected hub or genarkUrl), load its trackDb list, find the track by bare name, and call trackHubAddDescription to fill tdb->html. refs #37389
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    66ea6cb4eaf2036e464be55b295765ed5105a0fb Wed Apr 22 09:42:25 2026 -0700
    hgTrackUi/hui: render filter UI on supertrack configuration pages Supertracks (group of tracks with superTrack on, no data of their own) previously had no way to expose a shared filter: their trackDb stanza can declare filter.* / filterByRange.* / filterValues.*, but those settings were never drawn on the supertrack's hgTrackUi page. So users had to open each subtrack's own configuration page and set the same filter there, and the "lrSv.filter.svLen" cart namespace went unused. This change wires that up: - hgTrackUi.c (superTrackUi): after listing the subtracks, if the supertrack tdb declares any filter.* settings call scoreCfgUi() to render the standard filter UI. Cart variables land under the supertrack's own name (e.g. "lrSv.filter.svLen.min"), and subtracks already inherit them through cartOptionalStringClosestToHome() walking tdb->parent. Subtrack-level values continue to override. - hui.c: - buildFilterBy() / filterByValues(): tolerate a NULL autoSql object, so supertracks (which have no data table) don't errAbort when they declare filterValues.* of virtual aggregated fields. Missing-field errAbort still fires in the normal subtrack case. - scoreCfgUi() / cfgByCfgType(): when called with title == NULL (the supertrack filter path), suppress the default "<p>" separator and the "<BR>" between the title bar and the filter block; the caller renders its own section heading. - asForTdb(): handle conn == NULL by returning NULL rather than crashing, since supertrack filter rendering has no associated sqlConnection. refs #37426
• src/hg/lib/joiner.c
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    abc896118b1b7aaf66ff3ade939f34edf49ac97a Thu Apr 23 13:56:57 2026 -0700
    switch gencode all,joiner to use macros instead of growing every release #37436
• src/hg/lib/ottoRequest.as
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    435e92d0ad49164d1b5b156e3fb5ef5ff7b19041 Tue Apr 21 12:29:50 2026 -0700
    make the ottoRequest table a bit more generic so it can handle both liftOver and assembly requests refs #31811
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    fcfb91470c294d3b991dbd0d24cba67de9ed65cb Tue Apr 21 14:20:57 2026 -0700
    create ottoRequest cron watch script refs #31811
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    b3a76833aa84a341e86d0bacef2ff1f6b9b44851 Thu Apr 23 14:30:24 2026 -0700
    rename workflowId column to buildDir and expand its size refs #31811
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    1cbaa9ddcb7a13929a2217db78d6b36ff738fe15 Fri Apr 24 10:52:34 2026 -0700
    doneStatus can simply be status refs #31811
• src/hg/lib/ottoRequest.c
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    435e92d0ad49164d1b5b156e3fb5ef5ff7b19041 Tue Apr 21 12:29:50 2026 -0700
    make the ottoRequest table a bit more generic so it can handle both liftOver and assembly requests refs #31811
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    b3a76833aa84a341e86d0bacef2ff1f6b9b44851 Thu Apr 23 14:30:24 2026 -0700
    rename workflowId column to buildDir and expand its size refs #31811
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    1cbaa9ddcb7a13929a2217db78d6b36ff738fe15 Fri Apr 24 10:52:34 2026 -0700
    doneStatus can simply be status refs #31811
• src/hg/lib/ottoRequest.sql
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    435e92d0ad49164d1b5b156e3fb5ef5ff7b19041 Tue Apr 21 12:29:50 2026 -0700
    make the ottoRequest table a bit more generic so it can handle both liftOver and assembly requests refs #31811
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    fcfb91470c294d3b991dbd0d24cba67de9ed65cb Tue Apr 21 14:20:57 2026 -0700
    create ottoRequest cron watch script refs #31811
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    b3a76833aa84a341e86d0bacef2ff1f6b9b44851 Thu Apr 23 14:30:24 2026 -0700
    rename workflowId column to buildDir and expand its size refs #31811
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    1cbaa9ddcb7a13929a2217db78d6b36ff738fe15 Fri Apr 24 10:52:34 2026 -0700
    doneStatus can simply be status refs #31811
• src/hg/lib/quickLift.c
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    81d00f3eec6ea6978c9a71ed6a48c84a0bd0c987 Wed Apr 22 14:51:08 2026 -0700
    hgFind: remap bigBed search hits from source to destination coords when the track is quickLifted. Previously a search for e.g. "BRCA2" on a quickLifted hub (hg38 tracks displayed on HG02257.pat) returned hits at hg38 chr13 coordinates; clicking the result errored with "Sorry, couldn't locate chr13:... in <dest>". Adds quickLiftLiftPos() in hg/lib/quickLift.c, which reads the source->dest liftOverChainFile and calls liftOverRemapRange. Called from bigBedIntervalListToHgPositions in hg/lib/bigBedFind.c whenever tdb has quickLiftUrl/quickLiftDb; hits that don't map through the chain are dropped. refs #36340
• src/hg/lib/trackHub.c
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    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    8c8823d9a87b6046094577a808dda4ed4172b416 Thu Apr 23 11:09:48 2026 -0700
    Make quickLifted GENCODE tracks usable: click details, position links, coloring. refs #36059 - Re-vet wgEncodeGencode* in trackHub.c:isVetted() so the quickLift hub no longer emits `avoidHandler on` for GENCODE children. Without this, hgc bypasses findNameBasedHandler and doGencodeGene is never reached, so the details page falls through to the generic showGenePos output. - In gencodeClick.c doGencodeGene/helpers, use quickLiftDb for the MySQL connection (the attrs/tag/pubMed/refSeq/uniProt tables live in the source assembly), use trackHubSkipHubName(tdb->track) for the genePred table name and the Basic/Comp/PseudoGene/PolyA prefix dispatch checks, and teach isGrcHuman/isGrcH37Native to consult the source db — otherwise the page errAborted with "BUG: gencodeClick on wrong database: hub_NNNNN_hs1". - Lift the Position values (transcript + gene bounds, 2-way pseudo, PolyA) through the quickLift chain before printing, so the details page shows destination-assembly coords and the Position link lands at a window that actually contains the gene. - htcDnaNearGene (hgc.c): when quickLifted, lift seqName/winStart/winEnd back to source coords before hgSeqItemsInRange. The prior code pointed the query at the source-assembly table but still passed the destination window, so the "Genomic Sequence from assembly" flow returned "No results returned from query." No longer reachable from the GENCODE details page (doGencodeGene writes its own Sequences table) but still hit by other quickLifted genePred tracks. - simpleTracks.c genePredItemClassColor: the hTableExists() guard was checking `database` (the destination hub db like hub_NNNNN_hs1) even though the MySQL conn was already routed to liftDb; the lookup was skipped and every item fell back to tg->ixColor, rendering all black. Check `db` instead so the gClass_* palette (coding / nonCoding / pseudo / problem) is applied. Verified end-to-end on hgwdev-braney: Gerardo's SHH test case (ENST00000297261.7) and Basic/Comp/PseudoGene/PolyA subtracks; no regression on the non-quickLifted hg38 click.
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    7120a354ec4870b3bc2112c384bdb0af837ed44e Thu Apr 23 14:12:36 2026 -0700
    hgc: make quickLifted NCBI RefSeq / UCSC RefSeq click details work. refs #36125 - trackHub.c isVetted(): accept refGene, ncbiRefSeq* subtracks, and ncbiOrtho so the generated quickLift hub.txt doesn't emit 'avoidHandler on' for them. Without this, hgc skips findNameBasedHandler and the detail click falls through to genericClickHandler, showing none of the rich RefSeq fields. - hgc.c findNameBasedHandler: when the tdb has 'quickLifted on', strip the hub_NNN_ prefix from the dispatch table before comparisons so refGene / ncbiRefSeq* match their native handlers. - doNcbiRefSeq / doRefGene: route hAllocConn to quickLiftDb (source), use trackHubSkipHubName for track/table name comparisons, and pass srcDb into replaceInUrl, hTableExists, AceView / MGIid / jaxOrtholog / hg-prefix checks -- otherwise these paths errAborted with "Unknown database hub_NNN_<db>" on a quickLifted click. - printRefSeqInfo / prRefGeneInfo / gbCdnaGetVersion: use sqlGetDatabase(conn) rather than the global `database` for host-db checks. - Predicted Protein / Predicted mRNA links for quickLifted tracks now point at htcTranslatedPredMRna / htcGeneMrna so the sequences come from the destination genome at the lifted exon coordinates, rather than the NCBI-authored refPep / seqNcbiRefSeq extFiles on the source. Native behavior is unchanged. - showGenePos: fetch via quickLiftSql + calcLiftOverGenePreds when the track is quickLifted so the Position line is in destination coordinates. The swapped chainHash comes from the track's quickLiftUrl bigChain, matching the pattern getGenePredForPositionSql already uses. - Suppress the mRNA/Genomic Alignments block and its trailing <hr> for quickLifted refGene / ncbiRefSeq* clicks. The PSLs come back in source coords and the htcCdnaAli links don't line up with the destination window. - getAlignmentsTName: use sqlGetDatabase(conn) rather than global `database` so split-table resolution looks up the right db. - printGeneCards: take a db argument; callers pass srcDb so the GeneCards link renders on quickLifted pages (the "startsWith hg" check was matching hub_NNN_hs1 as false). - geneReviewsClick.c prGRShortRefGene: take a struct sqlConnection * rather than opening its own on `database` (hub_NNN_hs1 -> Unknown database abort). Callers in prRefGeneInfo and doOmimGene2 pass their existing source-db conn, so the Related GeneReviews line now shows on both native and quickLifted refGene pages. Verified end-to-end on hgwdev-braney with hg38 -> hs1 quickLift of the refSeqComposite: ncbiRefSeqCurated and refGene clicks on SHH now render the full doNcbiRefSeq / doRefGene details (RefSeq / Status / Description / Synonyms / OMIM / Protein / HGNC / Entrez Gene / GeneCards / AceView / Summary / Position / Gene Symbol); Predicted mRNA and Predicted Protein links return destination-derived sequences; Genomic Sequence reaches the Get-DNA-in-window page; Ctrl/Cmd+drag zoom no longer ends up with an HTML error page inside the zoom dialog. Non-quickLifted hg38 refSeq details are unchanged (alignments still shown, GeneReviews still present). The duplicate-subtracks symptom from the ticket's step (i) is not addressed here -- it's an architectural consequence of the shared `refSeqComposite` cart key applying to both the destination's native composite and the quickLift hub's composite, and needs cart-scoping work in quickLift v2. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/lib/userdata.c
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    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/logCrawl/parseQuickLiftLogs/parseQuickLiftLogs
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    bd2a9f1bb1cd2b0f8881a4ab4e5385455e8e69aa Thu Apr 23 11:26:06 2026 -0700
    add parseQuickLiftLogs to kent/src
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
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    7d1bd72b73f54dbacbb39445fbb6a1a3b0227433 Tue Apr 21 13:55:18 2026 -0700
    Adding liftOver runs for liftOver files a user requested, refs #37380
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
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    597461b5be887ae783de796a596034cc2d946448 Mon Apr 20 16:09:41 2026 -0700
    adding assemblies per user requests
• src/hg/makeDb/doc/danRer11/choriCloneEnds.txt
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    d93c426ef1ad5fbb32b754408599eaf380a199e5 Tue Apr 21 13:34:58 2026 -0700
    choriCloneEnds: reorganize danRer11 CHORI BAC clone end placements as a superTrack, refs #35059 - Rename ncbiCloneEndsCH1073 to choriCloneEnds throughout (trackDb, HTML, makeDoc, scripts dir, /hive and /gbdb layout). User-visible label is now "CHORI Clones" since all three libraries (CH1073, CH73, CH211) are CHORI/BACPAC BAC libraries; data source (NCBI Clone DB) is cited in Methods. - Wrap the existing CH1073 track in a choriCloneEnds superTrack and add two new subtracks built from the parallel unique_concordant GFFs at ftp.ncbi.nih.gov/repository/clone/reports/Danio_rerio/ : CH73 (99,141 placements, 23 oversize) CH211 (70,231 placements, 46 oversize) CH1073 is rebuilt with the same pipeline (210,777 placements). - Build all three bigBeds with -extraIndex=name and register searchTable / searchType bigBed stanzas with searchIndex name on each subtrack, so clone names (CH1073-100A1, CH73-1A1, CH211-1A1, ...) resolve from the Genome Browser position box. - Single shared HTML description page; Methods now links to the NCBI FTP source and to the UCSC makeDoc and scripts dir on GitHub. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/danRer11/ncbiCloneEndsCH1073.txt
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    8faeb3cba60c7cb842bc17c17a57c9b53ef1b478 Tue Apr 21 02:51:32 2026 -0700
    ncbiCloneEndsCH1073: add NCBI CH1073 BAC library clone end placements track on danRer11, refs #35059 210,777 unique-concordant clone-insert placements from NCBI's CH1073 (RZPD-1073 / DanioKey) library clone report. Separate from the existing bacEndPairsLift (danRer4 -> danRer11 UCSC-BLAT lift), which is left in place. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    d93c426ef1ad5fbb32b754408599eaf380a199e5 Tue Apr 21 13:34:58 2026 -0700
    choriCloneEnds: reorganize danRer11 CHORI BAC clone end placements as a superTrack, refs #35059 - Rename ncbiCloneEndsCH1073 to choriCloneEnds throughout (trackDb, HTML, makeDoc, scripts dir, /hive and /gbdb layout). User-visible label is now "CHORI Clones" since all three libraries (CH1073, CH73, CH211) are CHORI/BACPAC BAC libraries; data source (NCBI Clone DB) is cited in Methods. - Wrap the existing CH1073 track in a choriCloneEnds superTrack and add two new subtracks built from the parallel unique_concordant GFFs at ftp.ncbi.nih.gov/repository/clone/reports/Danio_rerio/ : CH73 (99,141 placements, 23 oversize) CH211 (70,231 placements, 46 oversize) CH1073 is rebuilt with the same pipeline (210,777 placements). - Build all three bigBeds with -extraIndex=name and register searchTable / searchType bigBed stanzas with searchIndex name on each subtrack, so clone names (CH1073-100A1, CH73-1A1, CH211-1A1, ...) resolve from the Genome Browser position box. - Single shared HTML description page; Methods now links to the NCBI FTP source and to the UCSC makeDoc and scripts dir on GitHub. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
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    597461b5be887ae783de796a596034cc2d946448 Mon Apr 20 16:09:41 2026 -0700
    adding assemblies per user requests
• src/hg/makeDb/doc/hg19.gencode.txt
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/doc/hg38/abelSv.txt
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    f058c8fe4601b223ff47468eb3525c05ccd03850 Wed Apr 22 09:17:17 2026 -0700
    srSv: new short-read SV supertrack, split out of lrSv Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr, tommoJpCnv) out of the Long-read SV supertrack into a new sibling supertrack srSv (Short-read SVs), so the lrSv collection contains only long-read callsets. Filter fields (svType, svLen, insLen, AC) are mirrored at the srSv supertrack level to keep the UX parallel to lrSv. - trackDb: new human/srSv.ra with the three subtrack stanzas and updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas removed from human/lrSv.ra. human/trackDb.ra now includes srSv.ra. Also a new human/srSv.html overview page; the SR rows and SR-specific paragraphs removed from human/lrSv.html. - Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/ {lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to scripts/srSv/ with git mv (history preserved) and renamed to drop the "lrSv" prefix. Internal path references in abelSvBuild.sh and abelSvVcfToBed.py updated. - makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and extended with the onekg3202Sr and tommoJpCnv sections moved from lrSv.txt. lrSv.txt leaves a pointer. - Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr, lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*. /gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and /gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/. refs #36258
• src/hg/makeDb/doc/hg38/gencode.txt
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/doc/hg38/gnomadMpc.txt
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    f30798ae5d11e88e0ab7eb2bcab634e253fd0675 Thu Apr 23 10:36:40 2026 -0700
    Add gnomAD MPC v4.1.1 track to hg38. New composite track under the gnomAD container showing per-variant MPC (Missense deleteriousness Prediction by Constraint) scores from gnomAD v4.1.1. Four bigWigs provide per-base scores (one per ALT nucleotide); a companion bigBed carries the ~250K multi-transcript variants with a per-transcript breakdown. Included via 'alpha' for QA review. refs #37434 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/hg38/lrSv.txt
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    5e4ca58df1b5bfe554fe5cc3309a39736ca256ee Tue Apr 21 08:08:52 2026 -0700
    cpc1Sv: restrict to the 58 CPC samples, drop HPRC-specific SVs Rewrite lrSvCpc1VcfToBed.py to identify the 58 CPC sample columns by name prefix (HIFI032* or RY*), recompute AC/AN/NS from those GT columns only, and skip any snarl that no CPC sample carries. The HPRC portion is already represented elsewhere in lrSv, so this keeps the track population-consistent with its label. Rebuild results: 46,092 snarl sites on hs1 (down from 97,205 when combined with HPRC), 36,030 lifted to hg38 (down from 81,261; 10,062 unmapped). Updates cpc1Sv.html, lrSv.ra labels, and the makeDoc. refs #36258
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    8a5a466f5e13a020954014cdefc81400072db516 Tue Apr 21 08:29:55 2026 -0700
    lrSv: add hprc2 hs1 subtrack using T2T-CHM13 wave VCF, refs #36258 The HPRC release-2 pangenome publishes a wave-decomposed VCF against both GRCh38 and T2T-CHM13. We already had the GRCh38 version as the hprc2Sv subtrack on hg38; this adds the parallel T2T-CHM13 build under /gbdb/hs1/lrSv/hprc2.bb. The existing trackDb stanza (bigDataUrl /gbdb/$D/lrSv/hprc2.bb) picks it up on hs1 without changes. 1,451,269 SV rows kept (937,425 INS, 360,960 DEL, 147,898 COMPLEX, 4,986 INV) using the existing lrSvHprc2VcfToBed.py converter. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    06a482a2120d4d85c7c34fb5038213e07f595554 Tue Apr 21 15:00:21 2026 -0700
    lrSv: add tommoJpCnv short-read CNV comparator (multiWig) ToMMo 48KJPN-CNV Frequency Panel: copy-number variation frequencies from short-read whole-genome sequencing of 48,874 Japanese individuals (jMorp 20230828 release, GATK CNV germline workflow at 1 kb resolution). Published as a companion short-read comparator to the long-read tommoJpSv track. Rendered as a multiWig container with two bigWig subtracks (transparent overlay): tommoJpCnvLoss.bw counts samples at CN<2 per bin (red) and tommoJpCnvGain.bw counts samples at CN>2 per bin (green). Values are absolute carrier counts out of 48,874. 2,006,905 bins with at least one CNV carrier; bins that are wholly CN=2 are omitted. Files: - trackDb/human/lrSv.ra: new tommoJpCnv multiWig container - trackDb/human/tommoJpCnv.html: new doc page - trackDb/human/lrSv.html: summary-table row + per-track blurb - scripts/lrSv/lrSvTommoJpCnvVcfToBedGraph.py: VCF -> two bedGraphs - doc/hg38/lrSv.txt: wget, converter invocation, bigWig build steps refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    1732661494ece5e645a9522f15a0f5922b035d1a Wed Apr 22 08:57:11 2026 -0700
    colorsDbSv: rebuild from pbsv+Jasmine source VCFs with richer AS Rebuild the CoLoRSdb SV bigBeds for hg38 and hs1 from the upstream pbsv+Jasmine VCFs that the CoLoRSdb project distributes directly. The previous bigBed stored AF as a string (breaking the numeric filter) and lacked insLen (causing a "filter on field insLen not in AS file" error under the supertrack-level filter). The new build: - stores AF as a float - adds a derived insLen column (alt-ref length delta for INS, 0 otherwise) so the shared lrSv insLen filter applies - keeps every INFO field from the source (SVTYPE, SVLEN, END, AC, AN, NS, AC_Hom, AC_Het, AC_Hemi, AF, HWE, ExcHet, nhomalt) plus REF/ALT - uses the canonical svName(TYPE, featLen, AC) label via lrSvCommon Record counts match the source VCFs: 426,239 on hg38 (59 MB) and 839,714 on hs1 (87 MB). /gbdb symlinks unchanged. The trackDb colorsDbSv stanza is updated to reference the new AS field names (acHom/acHet/acHemi, AF, AN) and to add the insLen filter. Also fixes a nearby `version 1.1` -> `dataVersion 1.1` typo in lrSv1kgOnt that was failing the tagTypes check. refs #36258
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    f058c8fe4601b223ff47468eb3525c05ccd03850 Wed Apr 22 09:17:17 2026 -0700
    srSv: new short-read SV supertrack, split out of lrSv Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr, tommoJpCnv) out of the Long-read SV supertrack into a new sibling supertrack srSv (Short-read SVs), so the lrSv collection contains only long-read callsets. Filter fields (svType, svLen, insLen, AC) are mirrored at the srSv supertrack level to keep the UX parallel to lrSv. - trackDb: new human/srSv.ra with the three subtrack stanzas and updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas removed from human/lrSv.ra. human/trackDb.ra now includes srSv.ra. Also a new human/srSv.html overview page; the SR rows and SR-specific paragraphs removed from human/lrSv.html. - Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/ {lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to scripts/srSv/ with git mv (history preserved) and renamed to drop the "lrSv" prefix. Internal path references in abelSvBuild.sh and abelSvVcfToBed.py updated. - makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and extended with the onekg3202Sr and tommoJpCnv sections moved from lrSv.txt. lrSv.txt leaves a pointer. - Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr, lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*. /gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and /gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/. refs #36258
• src/hg/makeDb/doc/hg38/mpra.txt
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    888e7470c14eeecdca310ed36bb45c3c00ae8052 Tue Apr 21 15:14:04 2026 -0700
    QA fixes for MPRA superTrack. refs #37359 Fix broken mpraVarDb bigDataUrl — pointed at /gbdb/hg38/mpra/mpravardb.bb but the file is at /gbdb/hg38/mpra/mpravardb/mpravardb.bb, causing hgTrackDb -strict to silently drop the subtrack. Rebuild mpravardb.bb after two fixes in mpravardbToBed.py: sanitize UTF-8 in user-visible string fields (curly quotes, primes, NBSP mojibake) that the browser does not transcode, eliminating ~246k non-ASCII occurrences across 42% of rows; and change safe_float / pval_to_score to write NaN and return score 0 for NA / out-of-range p-values instead of 0.0 and score 1000 (previously inflated untested variants to the top of score-sorted views). trackDb stanza cleanup: shorten mpraVarDb longLabel, drop superfluous type bed 4 from superTrack, make bigBed 9+13 explicit, remove redundant mouseOverField, align parent mpra on, add filterValues for cell_line/assay/cellLine and filterByRange sliders for percentile_rank / fdr / log2FC, add labelFields and maxWindowToDraw. Description pages: add cross-species disclosure (mouse reporter cells used to assay human sequences), update mpraVarDb header to post-liftOver count 239,028 with Studies-table footnote, fix mpraVarDb.html download-server paths, soften imprecise "51 MPRA experiments" claim in mpra.html and mprabase.html. relatedTracks.ra: reciprocal mpra <-> wgEncodeReg4 and mpra <-> cCREs. Expand mpra.txt makedoc with upstream provenance and QA-rebuild log.
• src/hg/makeDb/doc/hg38/nmd.txt
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    3972ba54c468ace338d4a5578de1d20bf6c1f9ec Mon Apr 20 15:39:26 2026 -0700
    Adding Rule 4 (long-exon rule, Lindeboom 2016) to NMD Escape tracks and releasing on Apr. 22, 2026. refs #33737 Script: added a fourth rule to genePredNmdEsc. Coding exons longer than 400 bp (excluding the last coding exon, which is already covered by the 50 bp rule) are flagged as NMD-escape regions. Rebuilt the Gencode and NCBI RefSeq bigBed files. trackDb: - nmd.ra: appended "/400nt" to the nmdEsc longLabels, set nmdEscGencode default visibility to dense so the track is visible in cart-reset views, changed all four NMDetective subtracks from "visibility full" to "visibility hide", updated pennantIcon to the Apr. 22, 2026 release date and anchor. - nmd.html: mention long internal exons in the overview description, update the rule count from three to four. - nmdEscTranscripts.html: add the long-exon rule to the rule list and color legend (gold, #FFD700), expand the Background section with mechanisms for the intronless, start-proximal, and long-exon rules, correct the 50 bp rule description to include the entire last coding exon, fix Lindeboom 2016 author initials (RG -> RGH). News: - newsarch.html: add the 2026-04-22 NMD Escape news entry covering all four rules, with acknowledgements to Guido Neidhardt and Andreas Lahner for suggesting the track and the Decipher Genome Browser team for inspiring the visualization. - indexNews.html: add the front-page news link. makedoc: - nmd.txt: dated note for the Rule 4 rebuild.
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    4bd316f5f1ca47328bd3f9a181214b788055f0bc Tue Apr 21 13:29:26 2026 -0700
    NMD Escape QA round 3: switch RefSeq to curated, fix Rule 2 misclassification. refs #33737 Switched the NMD Escape RefSeq subtrack input from hg38.ncbiRefSeq.txt.gz (all) to hg38.ncbiRefSeqCurated.txt.gz (NM_/NR_ only, no XM_/XR_ predicted models) per Max's feedback. longLabel updated to "NCBI RefSeq Curated transcripts". Fixed Rule 2 in genePredNmdEsc to test rec["exonCount"]==1 instead of len(cdsExons)==1. The old test misclassified multi-exon transcripts with a single CDS exon (UTR introns) as "intronless" and silently suppressed their Rule 1/3/4 assignments via the if/else short-circuit. 3,253 RefSeq curated and ~2,000 Gencode transcripts reassigned from Rule 2 to Rules 1/3. Rebuilt both tracks. Added Rule 1 caveat to nmdEscTranscripts.html for transcripts with a penultimate coding exon shorter than 50 bp. Added reciprocal relatedTracks.ra entries for nmd <-> mane and nmd <-> ncbiRefSeq. QA cleanups: non-ASCII prime char replaced with &#8242;, mailing list links given target="_blank" across all three HTML pages, dead commented nmdGencode block removed from nmd.ra, AutoSQL field comments updated to cover Rule 4 color and the gene-symbol-to-transcript-ID fallback. Makedoc updated with the full Gencode + RefSeq pipeline and /gbdb symlinks.
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    34d2eee845f5f45e571d1e153c632683b8a93f75 Tue Apr 21 16:17:53 2026 -0700
    Refine NMD Escape Rule 2 gate to "single coding exon and no 3'UTR intron". refs #33737 Previously Rule 2 required exonCount==1 (truly intronless). This overcorrected for single-CDS-exon transcripts whose only introns are in the 5'UTR: biologically these have no EJC downstream of the stop codon (5'UTR EJCs are cleared by the scanning 40S or sit upstream of the terminating ribosome) and are NMD-immune, but the code pushed them to Rules 1/3 under a less accurate "last coding exon" label. New gate: len(cdsExons) == 1 AND no exon-exon junction strictly downstream of the stop codon (strand-aware). Transcripts with a single coding exon but a 3'UTR intron correctly stay in Rules 1/3 because that intron deposits an EJC that can trigger NMD. 3,113 RefSeq Curated and 10,790 Gencode V49 transcripts move into Rule 2. 140 RefSeq and 1,135 Gencode single-CDS-exon transcripts with 3'UTR introns correctly remain in Rules 1/3. Description page and makedoc updated.
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    0151d00a4a1d73a78c35f6158c6c936ff338faeb Fri Apr 24 10:37:34 2026 -0700
    NMD Escape: MANE subtrack, Rule 1 bug fix, transcript filter. refs #33737 - Add nmdEscMane subtrack (MANE Select Plus Clinical 1.5), built from /gbdb/hg38/mane/mane.bb. Reuses nmdEscTranscripts.html. - Fix Rule 1: measure 50 bp upstream of the transcript's last splice junction (including 3'UTR introns) rather than stripping 3'UTR from the exon list first. The old logic painted the entire last CDS exon as NMD-escape whenever the transcript had only one CDS exon, even when a 3'UTR intron sat far past the stop codon (e.g. NBDY: 207 bp of CDS over-painted for a junction 2.6 kb past the stop). - Add --rule1-mode {cds,mrna} (default cds): cds counts only CDS bp on the walk-back (paints up to 50 bp of CDS matching the rule label literally); mrna counts mRNA bp and clips to CDS (tracks the 55 bp rule literature). Documented in makeDoc. - Rule 4: when a 3'UTR intron exists, the last CDS-containing exon has a downstream EJC and is now eligible for the long-exon rule. - Mouseover lists contributing transcript accessions when 1-3 items collapse into a region; falls back to a count above that. - Add filterText/filterType/filterLabel on all three escape subtracks so a user can narrow the display to one transcript. - genePredNmdEsc: --gene-sym-field (default 17 for Gencode; pass 18 for MANE, whose HGNC symbol lives in bigGenePred geneName2). - Add findShortTxLongUtrIntron.py helper for finding MANE transcripts with long UTR introns (used to pick NMD edge-case test cases). Post-fix collapsed-region counts (--rule1-mode=cds): MANE 1.5: 67,752 Gencode V49: 233,375 RefSeq Curated: 112,356
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    3a62ea7e9a8cb3503586a0a78570331308c9bc58 Mon Apr 27 02:23:00 2026 -0700
    NMD Escape MANE: expose NM_ accession via labelFields. refs #33737 Per QA, the MANE subtrack now shows the NCBI RefSeq accession by default instead of the HGNC gene symbol, with the ENST and gene symbol still selectable via labelFields. - genePredNmdEsc: new --ncbi-id-field N option (default -1 = unused). When set, the named bigGenePred column is captured per-transcript and written into a new ncbiIds output column. For MANE pass 21. - genePredNmdEsc: new --no-collapse option. By default, regions with identical (chrom, start, end, rule) from multiple transcripts collapse into one row with comma-separated lists. With --no-collapse the script emits one row per (transcript, region). Used for MANE so each label-field column holds a single value: the 74 MANE Plus Clinical genes (e.g. LMNA) get two rows per region instead of one row with a two-element list. - nmdEscCollapsed.as: add lstring ncbiIds column. Schema is now bed9+3. - nmd.ra (nmdEscMane only): labelFields ncbiIds,name,transcripts; defaultLabelFields ncbiIds; labelSeparator " / ". Gencode and RefSeq subtracks unchanged - they default to the gene symbol (name column) and have an empty ncbiIds column. - doc/hg38/nmd.txt: bump all three bedToBigBed invocations to bed9+3 and document the --ncbi-id-field 21 + --no-collapse invocation for MANE. Counts: MANE 68,028 (--no-collapse); Gencode 233,375; RefSeq 112,356.
• src/hg/makeDb/doc/hg38/promoterAi.txt
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    f9a89b0e1ce3c937b4fbb879736c1619c35c271f Tue Apr 21 12:11:02 2026 -0700
    QA fixes for PromoterAI track. refs #37278 Description page: replaced the wrong reference (Gao et al. 2023, the PrimateAI-3D paper) with the actual PromoterAI citation (Jaganathan et al. Science 2025, PMID 40440429), corrected the score-direction wording (negative = under-expression, positive = over-expression, not "tolerated vs disruptive"), fixed the Data Access source link (Illumina BaseSpace, not the GitHub repo), and corrected the mouseover blurb to match mouseOverFunction noAverage behavior. Converter and AS: the overlap bigBed now carries the real per-transcript strand from the source TSV (was hardcoded '+'), with a new strands column in the AS, and the name field concatenates unique gene symbols so bidirectional-promoter items read as "HES4,ISG15" etc. BED score is now |PromoterAI|*1000 so scoreFilter is meaningful. Rewrote the converter to stream (sorted input), which drops peak memory from ~40 GB to a few MB. trackDb: added filterLabel/filterLimits on scoreDiff (the filter was unusable without labels), scoreFilter + scoreLabel, alwaysZero and autoScale off on the bigWig subtracks, color 200,0,0 / altColor 0,0,200 so signed bigWig bars draw red (over-expression) above zero and blue (under-expression) below, matching the overlap track itemRgb. Added maxWindowToDraw and maxItems on the overlap subtrack. Makedoc updated to describe the streaming pipeline, the new strands column, and the rebuild workflow.
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    6c567fd9a03e87610681a43d2183ebb43547d1ad Fri Apr 24 17:58:57 2026 -0700
    PromoterAI: review followups. refs #37278 Move /gbdb/hg38/promoterAi/ to /gbdb/hg38/_promoterAi/ to match the underscore-prefix exclusion rule for hgdownload sync (same pattern as PrimateAI-3D under refs #37274). bigDataUrls and the makedoc updated. Bump bigWig maxHeightPixels from 128:20:8 to 128:40:8 -- the peer-track default of 20 is too cramped for a signed -1..+1 score. Description page: drop the wrong primateai3d.basespace.illumina.com link in Data Access; PromoterAI is not on BaseSpace, it's distributed via the license agreement on the GitHub page (a download link is emailed after submission). Reword Data Access and Methods accordingly. Description page: add Illumina's recommended interpretation thresholds (|score| >= 0.1, >= 0.2, >= 0.5) from the PromoterAI GitHub README, with a note that higher cutoffs select smaller, higher-confidence sets.
• src/hg/makeDb/doc/hg38/srSv.txt
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    f058c8fe4601b223ff47468eb3525c05ccd03850 Wed Apr 22 09:17:17 2026 -0700
    srSv: new short-read SV supertrack, split out of lrSv Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr, tommoJpCnv) out of the Long-read SV supertrack into a new sibling supertrack srSv (Short-read SVs), so the lrSv collection contains only long-read callsets. Filter fields (svType, svLen, insLen, AC) are mirrored at the srSv supertrack level to keep the UX parallel to lrSv. - trackDb: new human/srSv.ra with the three subtrack stanzas and updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas removed from human/lrSv.ra. human/trackDb.ra now includes srSv.ra. Also a new human/srSv.html overview page; the SR rows and SR-specific paragraphs removed from human/lrSv.html. - Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/ {lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to scripts/srSv/ with git mv (history preserved) and renamed to drop the "lrSv" prefix. Internal path references in abelSvBuild.sh and abelSvVcfToBed.py updated. - makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and extended with the onekg3202Sr and tommoJpCnv sections moved from lrSv.txt. lrSv.txt leaves a pointer. - Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr, lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*. /gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and /gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/. refs #36258
• src/hg/makeDb/doc/hg38/varFreqs.txt
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    366afa4a74c46ec6fb2b667a2902a873feec40cf Mon Apr 20 23:00:05 2026 -0700
    varFreqsAll: rebuild combined bigBed to include GA4K and CoLoRSdb Regenerate the All Databases Combined track with the two long-read PacBio subtracks (GA4K 552 samples and CoLoRSdb v1.2.0 1,027 samples) that were added to varFreqs since the March build. Source count rises from 21 to 23 databases; final bigBed is 37.7 GB with 1.17B records and 113 fields. Updates varFreqs.ra filterValues.sources and per- database AF/AC filters for the two new sources, and databases.tsv + varFreqs.txt (build notes). refs #36642
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    695f40f9d6139a4df393522c067f1702aff8d3bd Wed Apr 22 03:13:39 2026 -0700
    varFreqs: add SVatalog 101 short-read SNV frequencies subtrack SNV/indel allele frequencies from the 101-sample GWAS SVatalog cohort (Chirmade et al. 2026, Heredity, PMID 41203876), called from 10X Genomics linked short-read WGS with GATK HaplotypeCaller v4.0.0.0 and phased with SHAPEIT v4.2.0. Sibling of the lrSv chirmade101Sv structural-variant track, which is built from the same 101 samples. 8,814,835 autosomal + chrX sites. Source release ships only AF; AC and AN are synthesized in the emitted VCF as AC=round(AF*202) and AN=202 (2*101 diploid), with the gnomAD v3.1 non-Finnish European AF and dbSNP rsID passed through as GNOMAD_NFE_AF and RSID info fields. VCF is bgzipped + tabix-indexed (172 MB + 1.6 MB .tbi). Files: - scripts/varFreqs/svatalogFreqToVcf.py (new): per-chrom allele-freq TSV -> single VCF with hg38 ##contig header - trackDb/human/varFreqs.ra: new svatalogSnv vcfTabix subtrack - trackDb/human/svatalogSnv.html (new): doc page - trackDb/human/varFreqs.html: new row in Available Datasets table - doc/hg38/varFreqs.txt: wget-free build block (input files were downloaded manually from Zenodo 13367574) Note: the All Databases Combined varFreqs bigBed has NOT been rebuilt to include this new source yet; a subsequent merge pass will add it. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/hs1/lrSv.txt
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    9a11061ca6b40fe16bdfd09b1af53192f6c7c85b Tue Apr 21 08:13:02 2026 -0700
    lrSv: add HTML doc pages and conversion scripts for recent subtracks, + hs1 HGSVC3 Subtrack stanzas for these SV callsets landed in earlier commits but the conversion scripts and per-track HTML description pages were never added; trackDb therefore had no doc to serve. This commit catches up. Docs (new): - colorsDbSv.html CoLoRSdb 1,427-sample long-read SVs - gustafsonSv.html 1KG ONT 100 (Gustafson 2024, PMID 39358015) - hgsvc2Sv.html HGSVC2 (Ebert 2021, PMID 33632895) - hprc2Sv.html HPRC release-2 pangenome SVs (no PMID yet; see humanpangenome.org/hprc-data-release-2/) - onekg3202Sr.html 1KG 3202 Illumina SHORT-READ GATK-SV (Byrska-Bishop 2022, PMID 36055201) Scripts (new): - lrSvGustafson.as / lrSvGustafsonVcfToBed.py - lrSvHgsvc2.as / lrSvHgsvc2TsvToBed.py (merges insdel + inv tables) - lrSvHprc2.as / lrSvHprc2VcfToBed.py (streams wave-decomposed VCF, explodes multi-allelic rows, filters to SV-sized or INV) - lrSv1kg3202Sr.as / lrSv1kg3202SrVcfToBed.py HGSVC3 also on hs1: - hgsvc3Sv.html: note that the hs1 build is native (not lifted): HGSVC3 aligned all assemblies to both GRCh38 and T2T-CHM13 and released separate annotation tables per reference. Added the T2T-CHM13 source URL to the Methods section and the hs1 hgsvc3.bb download link to Data Access. - doc/hs1/lrSv.txt (new): hs1-specific wget + build steps; refers back to doc/hg38/lrSv.txt for the full process. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    8a5a466f5e13a020954014cdefc81400072db516 Tue Apr 21 08:29:55 2026 -0700
    lrSv: add hprc2 hs1 subtrack using T2T-CHM13 wave VCF, refs #36258 The HPRC release-2 pangenome publishes a wave-decomposed VCF against both GRCh38 and T2T-CHM13. We already had the GRCh38 version as the hprc2Sv subtrack on hg38; this adds the parallel T2T-CHM13 build under /gbdb/hs1/lrSv/hprc2.bb. The existing trackDb stanza (bigDataUrl /gbdb/$D/lrSv/hprc2.bb) picks it up on hs1 without changes. 1,451,269 SV rows kept (937,425 INS, 360,960 DEL, 147,898 COMPLEX, 4,986 INV) using the existing lrSvHprc2VcfToBed.py converter. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    597461b5be887ae783de796a596034cc2d946448 Mon Apr 20 16:09:41 2026 -0700
    adding assemblies per user requests
• src/hg/makeDb/doc/mm39/gencode.txt
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
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    1a9024a64f170308fb0d1adcb548399f960e46c2 Mon Apr 20 23:51:10 2026 -0700
    NCBI changed the name of GCA_030272585.1
• src/hg/makeDb/doc/vgp577way/577.acc.sciName.comName.clade.tsv
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    e8b16ae601a09359f4b4fa543d365f3d02bd6e6d Wed Apr 22 13:25:09 2026 -0700
    listing of assemblies with names and clade groupings for this 577-way alignment refs #34370
• src/hg/makeDb/doc/vgp577way/linkSizes.sh
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    633cc56e1b1043b0ab6e1fd0e9b90154e2c03c0c Mon Apr 20 13:00:51 2026 -0700
    document procedure for import of VGP 577-way maf result refs #34370
• src/hg/makeDb/doc/vgp577way/mafCoverage.pl
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    633cc56e1b1043b0ab6e1fd0e9b90154e2c03c0c Mon Apr 20 13:00:51 2026 -0700
    document procedure for import of VGP 577-way maf result refs #34370
• src/hg/makeDb/doc/vgp577way/mkIRowsJL.sh
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    633cc56e1b1043b0ab6e1fd0e9b90154e2c03c0c Mon Apr 20 13:00:51 2026 -0700
    document procedure for import of VGP 577-way maf result refs #34370
• src/hg/makeDb/doc/vgp577way/mkNbeds.sh
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    633cc56e1b1043b0ab6e1fd0e9b90154e2c03c0c Mon Apr 20 13:00:51 2026 -0700
    document procedure for import of VGP 577-way maf result refs #34370
• src/hg/makeDb/doc/vgp577way/queryCounts.sh
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    633cc56e1b1043b0ab6e1fd0e9b90154e2c03c0c Mon Apr 20 13:00:51 2026 -0700
    document procedure for import of VGP 577-way maf result refs #34370
• src/hg/makeDb/doc/vgp577way/sumBlocks.py
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    633cc56e1b1043b0ab6e1fd0e9b90154e2c03c0c Mon Apr 20 13:00:51 2026 -0700
    document procedure for import of VGP 577-way maf result refs #34370
• src/hg/makeDb/doc/vgp577way/vgp577way.txt
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    633cc56e1b1043b0ab6e1fd0e9b90154e2c03c0c Mon Apr 20 13:00:51 2026 -0700
    document procedure for import of VGP 577-way maf result refs #34370
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    a83601f74d58302315fa0e3c151ff29df6637afb Wed Apr 22 14:39:15 2026 -0700
    more general procedure refs #34370
• src/hg/makeDb/outside/gencode/bin/buildGencodeToUcscLift
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/outside/gencode/bin/gencodeBackMapMetadataIds
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/outside/gencode/bin/gencodeBuildRelease
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/outside/gencode/bin/gencodeExonSupportToTable
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbs
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/outside/gencode/bin/gencodeGxfToAttrs
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/outside/gencode/bin/gencodeGxfToGenePred
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/outside/gencode/bin/gencodeJoinerCheck
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/outside/gencode/bin/gencodeMakeAttrs
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/outside/gencode/bin/gencodeMakeTracks
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/outside/gencode/bin/gencodePolyaGxfToGenePred
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/outside/gencode/lib/gencode/gencodeTags.py
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/schema/all.joiner
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    abc896118b1b7aaf66ff3ade939f34edf49ac97a Thu Apr 23 13:56:57 2026 -0700
    switch gencode all,joiner to use macros instead of growing every release #37436
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/scripts/choriCloneEnds/cloneEnds.as
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    d93c426ef1ad5fbb32b754408599eaf380a199e5 Tue Apr 21 13:34:58 2026 -0700
    choriCloneEnds: reorganize danRer11 CHORI BAC clone end placements as a superTrack, refs #35059 - Rename ncbiCloneEndsCH1073 to choriCloneEnds throughout (trackDb, HTML, makeDoc, scripts dir, /hive and /gbdb layout). User-visible label is now "CHORI Clones" since all three libraries (CH1073, CH73, CH211) are CHORI/BACPAC BAC libraries; data source (NCBI Clone DB) is cited in Methods. - Wrap the existing CH1073 track in a choriCloneEnds superTrack and add two new subtracks built from the parallel unique_concordant GFFs at ftp.ncbi.nih.gov/repository/clone/reports/Danio_rerio/ : CH73 (99,141 placements, 23 oversize) CH211 (70,231 placements, 46 oversize) CH1073 is rebuilt with the same pipeline (210,777 placements). - Build all three bigBeds with -extraIndex=name and register searchTable / searchType bigBed stanzas with searchIndex name on each subtrack, so clone names (CH1073-100A1, CH73-1A1, CH211-1A1, ...) resolve from the Genome Browser position box. - Single shared HTML description page; Methods now links to the NCBI FTP source and to the UCSC makeDoc and scripts dir on GitHub. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/choriCloneEnds/makeBed.py
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    d93c426ef1ad5fbb32b754408599eaf380a199e5 Tue Apr 21 13:34:58 2026 -0700
    choriCloneEnds: reorganize danRer11 CHORI BAC clone end placements as a superTrack, refs #35059 - Rename ncbiCloneEndsCH1073 to choriCloneEnds throughout (trackDb, HTML, makeDoc, scripts dir, /hive and /gbdb layout). User-visible label is now "CHORI Clones" since all three libraries (CH1073, CH73, CH211) are CHORI/BACPAC BAC libraries; data source (NCBI Clone DB) is cited in Methods. - Wrap the existing CH1073 track in a choriCloneEnds superTrack and add two new subtracks built from the parallel unique_concordant GFFs at ftp.ncbi.nih.gov/repository/clone/reports/Danio_rerio/ : CH73 (99,141 placements, 23 oversize) CH211 (70,231 placements, 46 oversize) CH1073 is rebuilt with the same pipeline (210,777 placements). - Build all three bigBeds with -extraIndex=name and register searchTable / searchType bigBed stanzas with searchIndex name on each subtrack, so clone names (CH1073-100A1, CH73-1A1, CH211-1A1, ...) resolve from the Genome Browser position box. - Single shared HTML description page; Methods now links to the NCBI FTP source and to the UCSC makeDoc and scripts dir on GitHub. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/choriCloneEnds/refSeqNames.py
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    d93c426ef1ad5fbb32b754408599eaf380a199e5 Tue Apr 21 13:34:58 2026 -0700
    choriCloneEnds: reorganize danRer11 CHORI BAC clone end placements as a superTrack, refs #35059 - Rename ncbiCloneEndsCH1073 to choriCloneEnds throughout (trackDb, HTML, makeDoc, scripts dir, /hive and /gbdb layout). User-visible label is now "CHORI Clones" since all three libraries (CH1073, CH73, CH211) are CHORI/BACPAC BAC libraries; data source (NCBI Clone DB) is cited in Methods. - Wrap the existing CH1073 track in a choriCloneEnds superTrack and add two new subtracks built from the parallel unique_concordant GFFs at ftp.ncbi.nih.gov/repository/clone/reports/Danio_rerio/ : CH73 (99,141 placements, 23 oversize) CH211 (70,231 placements, 46 oversize) CH1073 is rebuilt with the same pipeline (210,777 placements). - Build all three bigBeds with -extraIndex=name and register searchTable / searchType bigBed stanzas with searchIndex name on each subtrack, so clone names (CH1073-100A1, CH73-1A1, CH211-1A1, ...) resolve from the Genome Browser position box. - Single shared HTML description page; Methods now links to the NCBI FTP source and to the UCSC makeDoc and scripts dir on GitHub. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/gnomadMpc/gnomadMpc.as
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    f30798ae5d11e88e0ab7eb2bcab634e253fd0675 Thu Apr 23 10:36:40 2026 -0700
    Add gnomAD MPC v4.1.1 track to hg38. New composite track under the gnomAD container showing per-variant MPC (Missense deleteriousness Prediction by Constraint) scores from gnomAD v4.1.1. Four bigWigs provide per-base scores (one per ALT nucleotide); a companion bigBed carries the ~250K multi-transcript variants with a per-transcript breakdown. Included via 'alpha' for QA review. refs #37434 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/gnomadMpc/gnomadMpcToBed.py
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    f30798ae5d11e88e0ab7eb2bcab634e253fd0675 Thu Apr 23 10:36:40 2026 -0700
    Add gnomAD MPC v4.1.1 track to hg38. New composite track under the gnomAD container showing per-variant MPC (Missense deleteriousness Prediction by Constraint) scores from gnomAD v4.1.1. Four bigWigs provide per-base scores (one per ALT nucleotide); a companion bigBed carries the ~250K multi-transcript variants with a per-transcript breakdown. Included via 'alpha' for QA review. refs #37434 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/gnomadMpc/gnomadMpcToWig.py
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    f30798ae5d11e88e0ab7eb2bcab634e253fd0675 Thu Apr 23 10:36:40 2026 -0700
    Add gnomAD MPC v4.1.1 track to hg38. New composite track under the gnomAD container showing per-variant MPC (Missense deleteriousness Prediction by Constraint) scores from gnomAD v4.1.1. Four bigWigs provide per-base scores (one per ALT nucleotide); a companion bigBed carries the ~250K multi-transcript variants with a per-transcript breakdown. Included via 'alpha' for QA review. refs #37434 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/lrSv/lrSv.as
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSv1kg3202Sr.as
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    9a11061ca6b40fe16bdfd09b1af53192f6c7c85b Tue Apr 21 08:13:02 2026 -0700
    lrSv: add HTML doc pages and conversion scripts for recent subtracks, + hs1 HGSVC3 Subtrack stanzas for these SV callsets landed in earlier commits but the conversion scripts and per-track HTML description pages were never added; trackDb therefore had no doc to serve. This commit catches up. Docs (new): - colorsDbSv.html CoLoRSdb 1,427-sample long-read SVs - gustafsonSv.html 1KG ONT 100 (Gustafson 2024, PMID 39358015) - hgsvc2Sv.html HGSVC2 (Ebert 2021, PMID 33632895) - hprc2Sv.html HPRC release-2 pangenome SVs (no PMID yet; see humanpangenome.org/hprc-data-release-2/) - onekg3202Sr.html 1KG 3202 Illumina SHORT-READ GATK-SV (Byrska-Bishop 2022, PMID 36055201) Scripts (new): - lrSvGustafson.as / lrSvGustafsonVcfToBed.py - lrSvHgsvc2.as / lrSvHgsvc2TsvToBed.py (merges insdel + inv tables) - lrSvHprc2.as / lrSvHprc2VcfToBed.py (streams wave-decomposed VCF, explodes multi-allelic rows, filters to SV-sized or INV) - lrSv1kg3202Sr.as / lrSv1kg3202SrVcfToBed.py HGSVC3 also on hs1: - hgsvc3Sv.html: note that the hs1 build is native (not lifted): HGSVC3 aligned all assemblies to both GRCh38 and T2T-CHM13 and released separate annotation tables per reference. Added the T2T-CHM13 source URL to the Methods section and the hs1 hgsvc3.bb download link to Data Access. - doc/hs1/lrSv.txt (new): hs1-specific wget + build steps; refers back to doc/hg38/lrSv.txt for the full process. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/lrSv/lrSv1kg3202SrVcfToBed.py
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    9a11061ca6b40fe16bdfd09b1af53192f6c7c85b Tue Apr 21 08:13:02 2026 -0700
    lrSv: add HTML doc pages and conversion scripts for recent subtracks, + hs1 HGSVC3 Subtrack stanzas for these SV callsets landed in earlier commits but the conversion scripts and per-track HTML description pages were never added; trackDb therefore had no doc to serve. This commit catches up. Docs (new): - colorsDbSv.html CoLoRSdb 1,427-sample long-read SVs - gustafsonSv.html 1KG ONT 100 (Gustafson 2024, PMID 39358015) - hgsvc2Sv.html HGSVC2 (Ebert 2021, PMID 33632895) - hprc2Sv.html HPRC release-2 pangenome SVs (no PMID yet; see humanpangenome.org/hprc-data-release-2/) - onekg3202Sr.html 1KG 3202 Illumina SHORT-READ GATK-SV (Byrska-Bishop 2022, PMID 36055201) Scripts (new): - lrSvGustafson.as / lrSvGustafsonVcfToBed.py - lrSvHgsvc2.as / lrSvHgsvc2TsvToBed.py (merges insdel + inv tables) - lrSvHprc2.as / lrSvHprc2VcfToBed.py (streams wave-decomposed VCF, explodes multi-allelic rows, filters to SV-sized or INV) - lrSv1kg3202Sr.as / lrSv1kg3202SrVcfToBed.py HGSVC3 also on hs1: - hgsvc3Sv.html: note that the hs1 build is native (not lifted): HGSVC3 aligned all assemblies to both GRCh38 and T2T-CHM13 and released separate annotation tables per reference. Added the T2T-CHM13 source URL to the Methods section and the hs1 hgsvc3.bb download link to Data Access. - doc/hs1/lrSv.txt (new): hs1-specific wget + build steps; refers back to doc/hg38/lrSv.txt for the full process. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/lrSv/lrSv1kgOnt.as
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSv1kgOntVcfToBed.py
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvAou1k.as
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvAou1kCsvToBed.py
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvApr.as
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvAprVcfToBed.py
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvChirmade101.as
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvChirmade101TsvToBed.py
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvColorsDbSv.as
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    1732661494ece5e645a9522f15a0f5922b035d1a Wed Apr 22 08:57:11 2026 -0700
    colorsDbSv: rebuild from pbsv+Jasmine source VCFs with richer AS Rebuild the CoLoRSdb SV bigBeds for hg38 and hs1 from the upstream pbsv+Jasmine VCFs that the CoLoRSdb project distributes directly. The previous bigBed stored AF as a string (breaking the numeric filter) and lacked insLen (causing a "filter on field insLen not in AS file" error under the supertrack-level filter). The new build: - stores AF as a float - adds a derived insLen column (alt-ref length delta for INS, 0 otherwise) so the shared lrSv insLen filter applies - keeps every INFO field from the source (SVTYPE, SVLEN, END, AC, AN, NS, AC_Hom, AC_Het, AC_Hemi, AF, HWE, ExcHet, nhomalt) plus REF/ALT - uses the canonical svName(TYPE, featLen, AC) label via lrSvCommon Record counts match the source VCFs: 426,239 on hg38 (59 MB) and 839,714 on hs1 (87 MB). /gbdb symlinks unchanged. The trackDb colorsDbSv stanza is updated to reference the new AS field names (acHom/acHet/acHemi, AF, AN) and to add the insLen filter. Also fixes a nearby `version 1.1` -> `dataVersion 1.1` typo in lrSv1kgOnt that was failing the tagTypes check. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvColorsDbSvBuild.sh
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    1732661494ece5e645a9522f15a0f5922b035d1a Wed Apr 22 08:57:11 2026 -0700
    colorsDbSv: rebuild from pbsv+Jasmine source VCFs with richer AS Rebuild the CoLoRSdb SV bigBeds for hg38 and hs1 from the upstream pbsv+Jasmine VCFs that the CoLoRSdb project distributes directly. The previous bigBed stored AF as a string (breaking the numeric filter) and lacked insLen (causing a "filter on field insLen not in AS file" error under the supertrack-level filter). The new build: - stores AF as a float - adds a derived insLen column (alt-ref length delta for INS, 0 otherwise) so the shared lrSv insLen filter applies - keeps every INFO field from the source (SVTYPE, SVLEN, END, AC, AN, NS, AC_Hom, AC_Het, AC_Hemi, AF, HWE, ExcHet, nhomalt) plus REF/ALT - uses the canonical svName(TYPE, featLen, AC) label via lrSvCommon Record counts match the source VCFs: 426,239 on hg38 (59 MB) and 839,714 on hs1 (87 MB). /gbdb symlinks unchanged. The trackDb colorsDbSv stanza is updated to reference the new AS field names (acHom/acHet/acHemi, AF, AN) and to add the insLen filter. Also fixes a nearby `version 1.1` -> `dataVersion 1.1` typo in lrSv1kgOnt that was failing the tagTypes check. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvColorsDbSvVcfToBed.py
  • lines changed 174, context: html, text, full: html, text
    1732661494ece5e645a9522f15a0f5922b035d1a Wed Apr 22 08:57:11 2026 -0700
    colorsDbSv: rebuild from pbsv+Jasmine source VCFs with richer AS Rebuild the CoLoRSdb SV bigBeds for hg38 and hs1 from the upstream pbsv+Jasmine VCFs that the CoLoRSdb project distributes directly. The previous bigBed stored AF as a string (breaking the numeric filter) and lacked insLen (causing a "filter on field insLen not in AS file" error under the supertrack-level filter). The new build: - stores AF as a float - adds a derived insLen column (alt-ref length delta for INS, 0 otherwise) so the shared lrSv insLen filter applies - keeps every INFO field from the source (SVTYPE, SVLEN, END, AC, AN, NS, AC_Hom, AC_Het, AC_Hemi, AF, HWE, ExcHet, nhomalt) plus REF/ALT - uses the canonical svName(TYPE, featLen, AC) label via lrSvCommon Record counts match the source VCFs: 426,239 on hg38 (59 MB) and 839,714 on hs1 (87 MB). /gbdb symlinks unchanged. The trackDb colorsDbSv stanza is updated to reference the new AS field names (acHom/acHet/acHemi, AF, AN) and to add the insLen filter. Also fixes a nearby `version 1.1` -> `dataVersion 1.1` typo in lrSv1kgOnt that was failing the tagTypes check. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvCommon.py
  • lines changed 138, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvCpc1.as
  • lines changed 5, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvCpc1VcfToBed.py
  • lines changed 95, context: html, text, full: html, text
    5e4ca58df1b5bfe554fe5cc3309a39736ca256ee Tue Apr 21 08:08:52 2026 -0700
    cpc1Sv: restrict to the 58 CPC samples, drop HPRC-specific SVs Rewrite lrSvCpc1VcfToBed.py to identify the 58 CPC sample columns by name prefix (HIFI032* or RY*), recompute AC/AN/NS from those GT columns only, and skip any snarl that no CPC sample carries. The HPRC portion is already represented elsewhere in lrSv, so this keeps the track population-consistent with its label. Rebuild results: 46,092 snarl sites on hs1 (down from 97,205 when combined with HPRC), 36,030 lifted to hg38 (down from 81,261; 10,062 unmapped). Updates cpc1Sv.html, lrSv.ra labels, and the makeDoc. refs #36258
  • lines changed 23, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvDecode.as
  • lines changed 3, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvDecodeVcfToBed.py
  • lines changed 23, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvGa4kSv.as
  • lines changed 3, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvGa4kSvVcfToBed.py
  • lines changed 24, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvGustafson.as
  • lines changed 19, context: html, text, full: html, text
    9a11061ca6b40fe16bdfd09b1af53192f6c7c85b Tue Apr 21 08:13:02 2026 -0700
    lrSv: add HTML doc pages and conversion scripts for recent subtracks, + hs1 HGSVC3 Subtrack stanzas for these SV callsets landed in earlier commits but the conversion scripts and per-track HTML description pages were never added; trackDb therefore had no doc to serve. This commit catches up. Docs (new): - colorsDbSv.html CoLoRSdb 1,427-sample long-read SVs - gustafsonSv.html 1KG ONT 100 (Gustafson 2024, PMID 39358015) - hgsvc2Sv.html HGSVC2 (Ebert 2021, PMID 33632895) - hprc2Sv.html HPRC release-2 pangenome SVs (no PMID yet; see humanpangenome.org/hprc-data-release-2/) - onekg3202Sr.html 1KG 3202 Illumina SHORT-READ GATK-SV (Byrska-Bishop 2022, PMID 36055201) Scripts (new): - lrSvGustafson.as / lrSvGustafsonVcfToBed.py - lrSvHgsvc2.as / lrSvHgsvc2TsvToBed.py (merges insdel + inv tables) - lrSvHprc2.as / lrSvHprc2VcfToBed.py (streams wave-decomposed VCF, explodes multi-allelic rows, filters to SV-sized or INV) - lrSv1kg3202Sr.as / lrSv1kg3202SrVcfToBed.py HGSVC3 also on hs1: - hgsvc3Sv.html: note that the hs1 build is native (not lifted): HGSVC3 aligned all assemblies to both GRCh38 and T2T-CHM13 and released separate annotation tables per reference. Added the T2T-CHM13 source URL to the Methods section and the hs1 hgsvc3.bb download link to Data Access. - doc/hs1/lrSv.txt (new): hs1-specific wget + build steps; refers back to doc/hg38/lrSv.txt for the full process. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 3, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvGustafsonVcfToBed.py
  • lines changed 114, context: html, text, full: html, text
    9a11061ca6b40fe16bdfd09b1af53192f6c7c85b Tue Apr 21 08:13:02 2026 -0700
    lrSv: add HTML doc pages and conversion scripts for recent subtracks, + hs1 HGSVC3 Subtrack stanzas for these SV callsets landed in earlier commits but the conversion scripts and per-track HTML description pages were never added; trackDb therefore had no doc to serve. This commit catches up. Docs (new): - colorsDbSv.html CoLoRSdb 1,427-sample long-read SVs - gustafsonSv.html 1KG ONT 100 (Gustafson 2024, PMID 39358015) - hgsvc2Sv.html HGSVC2 (Ebert 2021, PMID 33632895) - hprc2Sv.html HPRC release-2 pangenome SVs (no PMID yet; see humanpangenome.org/hprc-data-release-2/) - onekg3202Sr.html 1KG 3202 Illumina SHORT-READ GATK-SV (Byrska-Bishop 2022, PMID 36055201) Scripts (new): - lrSvGustafson.as / lrSvGustafsonVcfToBed.py - lrSvHgsvc2.as / lrSvHgsvc2TsvToBed.py (merges insdel + inv tables) - lrSvHprc2.as / lrSvHprc2VcfToBed.py (streams wave-decomposed VCF, explodes multi-allelic rows, filters to SV-sized or INV) - lrSv1kg3202Sr.as / lrSv1kg3202SrVcfToBed.py HGSVC3 also on hs1: - hgsvc3Sv.html: note that the hs1 build is native (not lifted): HGSVC3 aligned all assemblies to both GRCh38 and T2T-CHM13 and released separate annotation tables per reference. Added the T2T-CHM13 source URL to the Methods section and the hs1 hgsvc3.bb download link to Data Access. - doc/hs1/lrSv.txt (new): hs1-specific wget + build steps; refers back to doc/hg38/lrSv.txt for the full process. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 27, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvHgsvc2.as
  • lines changed 40, context: html, text, full: html, text
    9a11061ca6b40fe16bdfd09b1af53192f6c7c85b Tue Apr 21 08:13:02 2026 -0700
    lrSv: add HTML doc pages and conversion scripts for recent subtracks, + hs1 HGSVC3 Subtrack stanzas for these SV callsets landed in earlier commits but the conversion scripts and per-track HTML description pages were never added; trackDb therefore had no doc to serve. This commit catches up. Docs (new): - colorsDbSv.html CoLoRSdb 1,427-sample long-read SVs - gustafsonSv.html 1KG ONT 100 (Gustafson 2024, PMID 39358015) - hgsvc2Sv.html HGSVC2 (Ebert 2021, PMID 33632895) - hprc2Sv.html HPRC release-2 pangenome SVs (no PMID yet; see humanpangenome.org/hprc-data-release-2/) - onekg3202Sr.html 1KG 3202 Illumina SHORT-READ GATK-SV (Byrska-Bishop 2022, PMID 36055201) Scripts (new): - lrSvGustafson.as / lrSvGustafsonVcfToBed.py - lrSvHgsvc2.as / lrSvHgsvc2TsvToBed.py (merges insdel + inv tables) - lrSvHprc2.as / lrSvHprc2VcfToBed.py (streams wave-decomposed VCF, explodes multi-allelic rows, filters to SV-sized or INV) - lrSv1kg3202Sr.as / lrSv1kg3202SrVcfToBed.py HGSVC3 also on hs1: - hgsvc3Sv.html: note that the hs1 build is native (not lifted): HGSVC3 aligned all assemblies to both GRCh38 and T2T-CHM13 and released separate annotation tables per reference. Added the T2T-CHM13 source URL to the Methods section and the hs1 hgsvc3.bb download link to Data Access. - doc/hs1/lrSv.txt (new): hs1-specific wget + build steps; refers back to doc/hg38/lrSv.txt for the full process. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 3, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvHgsvc2TsvToBed.py
  • lines changed 163, context: html, text, full: html, text
    9a11061ca6b40fe16bdfd09b1af53192f6c7c85b Tue Apr 21 08:13:02 2026 -0700
    lrSv: add HTML doc pages and conversion scripts for recent subtracks, + hs1 HGSVC3 Subtrack stanzas for these SV callsets landed in earlier commits but the conversion scripts and per-track HTML description pages were never added; trackDb therefore had no doc to serve. This commit catches up. Docs (new): - colorsDbSv.html CoLoRSdb 1,427-sample long-read SVs - gustafsonSv.html 1KG ONT 100 (Gustafson 2024, PMID 39358015) - hgsvc2Sv.html HGSVC2 (Ebert 2021, PMID 33632895) - hprc2Sv.html HPRC release-2 pangenome SVs (no PMID yet; see humanpangenome.org/hprc-data-release-2/) - onekg3202Sr.html 1KG 3202 Illumina SHORT-READ GATK-SV (Byrska-Bishop 2022, PMID 36055201) Scripts (new): - lrSvGustafson.as / lrSvGustafsonVcfToBed.py - lrSvHgsvc2.as / lrSvHgsvc2TsvToBed.py (merges insdel + inv tables) - lrSvHprc2.as / lrSvHprc2VcfToBed.py (streams wave-decomposed VCF, explodes multi-allelic rows, filters to SV-sized or INV) - lrSv1kg3202Sr.as / lrSv1kg3202SrVcfToBed.py HGSVC3 also on hs1: - hgsvc3Sv.html: note that the hs1 build is native (not lifted): HGSVC3 aligned all assemblies to both GRCh38 and T2T-CHM13 and released separate annotation tables per reference. Added the T2T-CHM13 source URL to the Methods section and the hs1 hgsvc3.bb download link to Data Access. - doc/hs1/lrSv.txt (new): hs1-specific wget + build steps; refers back to doc/hg38/lrSv.txt for the full process. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 18, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvHgsvc3.as
  • lines changed 3, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvHgsvc3TsvToBed.py
  • lines changed 22, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvHprc2.as
  • lines changed 20, context: html, text, full: html, text
    9a11061ca6b40fe16bdfd09b1af53192f6c7c85b Tue Apr 21 08:13:02 2026 -0700
    lrSv: add HTML doc pages and conversion scripts for recent subtracks, + hs1 HGSVC3 Subtrack stanzas for these SV callsets landed in earlier commits but the conversion scripts and per-track HTML description pages were never added; trackDb therefore had no doc to serve. This commit catches up. Docs (new): - colorsDbSv.html CoLoRSdb 1,427-sample long-read SVs - gustafsonSv.html 1KG ONT 100 (Gustafson 2024, PMID 39358015) - hgsvc2Sv.html HGSVC2 (Ebert 2021, PMID 33632895) - hprc2Sv.html HPRC release-2 pangenome SVs (no PMID yet; see humanpangenome.org/hprc-data-release-2/) - onekg3202Sr.html 1KG 3202 Illumina SHORT-READ GATK-SV (Byrska-Bishop 2022, PMID 36055201) Scripts (new): - lrSvGustafson.as / lrSvGustafsonVcfToBed.py - lrSvHgsvc2.as / lrSvHgsvc2TsvToBed.py (merges insdel + inv tables) - lrSvHprc2.as / lrSvHprc2VcfToBed.py (streams wave-decomposed VCF, explodes multi-allelic rows, filters to SV-sized or INV) - lrSv1kg3202Sr.as / lrSv1kg3202SrVcfToBed.py HGSVC3 also on hs1: - hgsvc3Sv.html: note that the hs1 build is native (not lifted): HGSVC3 aligned all assemblies to both GRCh38 and T2T-CHM13 and released separate annotation tables per reference. Added the T2T-CHM13 source URL to the Methods section and the hs1 hgsvc3.bb download link to Data Access. - doc/hs1/lrSv.txt (new): hs1-specific wget + build steps; refers back to doc/hg38/lrSv.txt for the full process. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 4, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvHprc2VcfToBed.py
  • lines changed 180, context: html, text, full: html, text
    9a11061ca6b40fe16bdfd09b1af53192f6c7c85b Tue Apr 21 08:13:02 2026 -0700
    lrSv: add HTML doc pages and conversion scripts for recent subtracks, + hs1 HGSVC3 Subtrack stanzas for these SV callsets landed in earlier commits but the conversion scripts and per-track HTML description pages were never added; trackDb therefore had no doc to serve. This commit catches up. Docs (new): - colorsDbSv.html CoLoRSdb 1,427-sample long-read SVs - gustafsonSv.html 1KG ONT 100 (Gustafson 2024, PMID 39358015) - hgsvc2Sv.html HGSVC2 (Ebert 2021, PMID 33632895) - hprc2Sv.html HPRC release-2 pangenome SVs (no PMID yet; see humanpangenome.org/hprc-data-release-2/) - onekg3202Sr.html 1KG 3202 Illumina SHORT-READ GATK-SV (Byrska-Bishop 2022, PMID 36055201) Scripts (new): - lrSvGustafson.as / lrSvGustafsonVcfToBed.py - lrSvHgsvc2.as / lrSvHgsvc2TsvToBed.py (merges insdel + inv tables) - lrSvHprc2.as / lrSvHprc2VcfToBed.py (streams wave-decomposed VCF, explodes multi-allelic rows, filters to SV-sized or INV) - lrSv1kg3202Sr.as / lrSv1kg3202SrVcfToBed.py HGSVC3 also on hs1: - hgsvc3Sv.html: note that the hs1 build is native (not lifted): HGSVC3 aligned all assemblies to both GRCh38 and T2T-CHM13 and released separate annotation tables per reference. Added the T2T-CHM13 source URL to the Methods section and the hs1 hgsvc3.bb download link to Data Access. - doc/hs1/lrSv.txt (new): hs1-specific wget + build steps; refers back to doc/hg38/lrSv.txt for the full process. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvKwanho.as
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvKwanhoTsvToBed.py
  • lines changed 42, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvTommoJp.as
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvTommoJpCnvVcfToBedGraph.py
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    06a482a2120d4d85c7c34fb5038213e07f595554 Tue Apr 21 15:00:21 2026 -0700
    lrSv: add tommoJpCnv short-read CNV comparator (multiWig) ToMMo 48KJPN-CNV Frequency Panel: copy-number variation frequencies from short-read whole-genome sequencing of 48,874 Japanese individuals (jMorp 20230828 release, GATK CNV germline workflow at 1 kb resolution). Published as a companion short-read comparator to the long-read tommoJpSv track. Rendered as a multiWig container with two bigWig subtracks (transparent overlay): tommoJpCnvLoss.bw counts samples at CN<2 per bin (red) and tommoJpCnvGain.bw counts samples at CN>2 per bin (green). Values are absolute carrier counts out of 48,874. 2,006,905 bins with at least one CNV carrier; bins that are wholly CN=2 are omitted. Files: - trackDb/human/lrSv.ra: new tommoJpCnv multiWig container - trackDb/human/tommoJpCnv.html: new doc page - trackDb/human/lrSv.html: summary-table row + per-track blurb - scripts/lrSv/lrSvTommoJpCnvVcfToBedGraph.py: VCF -> two bedGraphs - doc/hg38/lrSv.txt: wget, converter invocation, bigWig build steps refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/lrSv/lrSvTommoJpVcfToBed.py
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvVcfToBed.py
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/mpravardb/mpravardbToBed.py
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    888e7470c14eeecdca310ed36bb45c3c00ae8052 Tue Apr 21 15:14:04 2026 -0700
    QA fixes for MPRA superTrack. refs #37359 Fix broken mpraVarDb bigDataUrl — pointed at /gbdb/hg38/mpra/mpravardb.bb but the file is at /gbdb/hg38/mpra/mpravardb/mpravardb.bb, causing hgTrackDb -strict to silently drop the subtrack. Rebuild mpravardb.bb after two fixes in mpravardbToBed.py: sanitize UTF-8 in user-visible string fields (curly quotes, primes, NBSP mojibake) that the browser does not transcode, eliminating ~246k non-ASCII occurrences across 42% of rows; and change safe_float / pval_to_score to write NaN and return score 0 for NA / out-of-range p-values instead of 0.0 and score 1000 (previously inflated untested variants to the top of score-sorted views). trackDb stanza cleanup: shorten mpraVarDb longLabel, drop superfluous type bed 4 from superTrack, make bigBed 9+13 explicit, remove redundant mouseOverField, align parent mpra on, add filterValues for cell_line/assay/cellLine and filterByRange sliders for percentile_rank / fdr / log2FC, add labelFields and maxWindowToDraw. Description pages: add cross-species disclosure (mouse reporter cells used to assay human sequences), update mpraVarDb header to post-liftOver count 239,028 with Studies-table footnote, fix mpraVarDb.html download-server paths, soften imprecise "51 MPRA experiments" claim in mpra.html and mprabase.html. relatedTracks.ra: reciprocal mpra <-> wgEncodeReg4 and mpra <-> cCREs. Expand mpra.txt makedoc with upstream provenance and QA-rebuild log.
• src/hg/makeDb/scripts/ncbiCloneEndsCH1073/cloneEnds.as
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    8faeb3cba60c7cb842bc17c17a57c9b53ef1b478 Tue Apr 21 02:51:32 2026 -0700
    ncbiCloneEndsCH1073: add NCBI CH1073 BAC library clone end placements track on danRer11, refs #35059 210,777 unique-concordant clone-insert placements from NCBI's CH1073 (RZPD-1073 / DanioKey) library clone report. Separate from the existing bacEndPairsLift (danRer4 -> danRer11 UCSC-BLAT lift), which is left in place. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncbiCloneEndsCH1073/makeBed.py
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    8faeb3cba60c7cb842bc17c17a57c9b53ef1b478 Tue Apr 21 02:51:32 2026 -0700
    ncbiCloneEndsCH1073: add NCBI CH1073 BAC library clone end placements track on danRer11, refs #35059 210,777 unique-concordant clone-insert placements from NCBI's CH1073 (RZPD-1073 / DanioKey) library clone report. Separate from the existing bacEndPairsLift (danRer4 -> danRer11 UCSC-BLAT lift), which is left in place. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncbiCloneEndsCH1073/refSeqNames.py
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    8faeb3cba60c7cb842bc17c17a57c9b53ef1b478 Tue Apr 21 02:51:32 2026 -0700
    ncbiCloneEndsCH1073: add NCBI CH1073 BAC library clone end placements track on danRer11, refs #35059 210,777 unique-concordant clone-insert placements from NCBI's CH1073 (RZPD-1073 / DanioKey) library clone report. Separate from the existing bacEndPairsLift (danRer4 -> danRer11 UCSC-BLAT lift), which is left in place. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/nmd/findShortTxLongUtrIntron.py
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    0151d00a4a1d73a78c35f6158c6c936ff338faeb Fri Apr 24 10:37:34 2026 -0700
    NMD Escape: MANE subtrack, Rule 1 bug fix, transcript filter. refs #33737 - Add nmdEscMane subtrack (MANE Select Plus Clinical 1.5), built from /gbdb/hg38/mane/mane.bb. Reuses nmdEscTranscripts.html. - Fix Rule 1: measure 50 bp upstream of the transcript's last splice junction (including 3'UTR introns) rather than stripping 3'UTR from the exon list first. The old logic painted the entire last CDS exon as NMD-escape whenever the transcript had only one CDS exon, even when a 3'UTR intron sat far past the stop codon (e.g. NBDY: 207 bp of CDS over-painted for a junction 2.6 kb past the stop). - Add --rule1-mode {cds,mrna} (default cds): cds counts only CDS bp on the walk-back (paints up to 50 bp of CDS matching the rule label literally); mrna counts mRNA bp and clips to CDS (tracks the 55 bp rule literature). Documented in makeDoc. - Rule 4: when a 3'UTR intron exists, the last CDS-containing exon has a downstream EJC and is now eligible for the long-exon rule. - Mouseover lists contributing transcript accessions when 1-3 items collapse into a region; falls back to a count above that. - Add filterText/filterType/filterLabel on all three escape subtracks so a user can narrow the display to one transcript. - genePredNmdEsc: --gene-sym-field (default 17 for Gencode; pass 18 for MANE, whose HGNC symbol lives in bigGenePred geneName2). - Add findShortTxLongUtrIntron.py helper for finding MANE transcripts with long UTR introns (used to pick NMD edge-case test cases). Post-fix collapsed-region counts (--rule1-mode=cds): MANE 1.5: 67,752 Gencode V49: 233,375 RefSeq Curated: 112,356
• src/hg/makeDb/scripts/nmd/genePredNmdEsc
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    3972ba54c468ace338d4a5578de1d20bf6c1f9ec Mon Apr 20 15:39:26 2026 -0700
    Adding Rule 4 (long-exon rule, Lindeboom 2016) to NMD Escape tracks and releasing on Apr. 22, 2026. refs #33737 Script: added a fourth rule to genePredNmdEsc. Coding exons longer than 400 bp (excluding the last coding exon, which is already covered by the 50 bp rule) are flagged as NMD-escape regions. Rebuilt the Gencode and NCBI RefSeq bigBed files. trackDb: - nmd.ra: appended "/400nt" to the nmdEsc longLabels, set nmdEscGencode default visibility to dense so the track is visible in cart-reset views, changed all four NMDetective subtracks from "visibility full" to "visibility hide", updated pennantIcon to the Apr. 22, 2026 release date and anchor. - nmd.html: mention long internal exons in the overview description, update the rule count from three to four. - nmdEscTranscripts.html: add the long-exon rule to the rule list and color legend (gold, #FFD700), expand the Background section with mechanisms for the intronless, start-proximal, and long-exon rules, correct the 50 bp rule description to include the entire last coding exon, fix Lindeboom 2016 author initials (RG -> RGH). News: - newsarch.html: add the 2026-04-22 NMD Escape news entry covering all four rules, with acknowledgements to Guido Neidhardt and Andreas Lahner for suggesting the track and the Decipher Genome Browser team for inspiring the visualization. - indexNews.html: add the front-page news link. makedoc: - nmd.txt: dated note for the Rule 4 rebuild.
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    4bd316f5f1ca47328bd3f9a181214b788055f0bc Tue Apr 21 13:29:26 2026 -0700
    NMD Escape QA round 3: switch RefSeq to curated, fix Rule 2 misclassification. refs #33737 Switched the NMD Escape RefSeq subtrack input from hg38.ncbiRefSeq.txt.gz (all) to hg38.ncbiRefSeqCurated.txt.gz (NM_/NR_ only, no XM_/XR_ predicted models) per Max's feedback. longLabel updated to "NCBI RefSeq Curated transcripts". Fixed Rule 2 in genePredNmdEsc to test rec["exonCount"]==1 instead of len(cdsExons)==1. The old test misclassified multi-exon transcripts with a single CDS exon (UTR introns) as "intronless" and silently suppressed their Rule 1/3/4 assignments via the if/else short-circuit. 3,253 RefSeq curated and ~2,000 Gencode transcripts reassigned from Rule 2 to Rules 1/3. Rebuilt both tracks. Added Rule 1 caveat to nmdEscTranscripts.html for transcripts with a penultimate coding exon shorter than 50 bp. Added reciprocal relatedTracks.ra entries for nmd <-> mane and nmd <-> ncbiRefSeq. QA cleanups: non-ASCII prime char replaced with &#8242;, mailing list links given target="_blank" across all three HTML pages, dead commented nmdGencode block removed from nmd.ra, AutoSQL field comments updated to cover Rule 4 color and the gene-symbol-to-transcript-ID fallback. Makedoc updated with the full Gencode + RefSeq pipeline and /gbdb symlinks.
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    34d2eee845f5f45e571d1e153c632683b8a93f75 Tue Apr 21 16:17:53 2026 -0700
    Refine NMD Escape Rule 2 gate to "single coding exon and no 3'UTR intron". refs #33737 Previously Rule 2 required exonCount==1 (truly intronless). This overcorrected for single-CDS-exon transcripts whose only introns are in the 5'UTR: biologically these have no EJC downstream of the stop codon (5'UTR EJCs are cleared by the scanning 40S or sit upstream of the terminating ribosome) and are NMD-immune, but the code pushed them to Rules 1/3 under a less accurate "last coding exon" label. New gate: len(cdsExons) == 1 AND no exon-exon junction strictly downstream of the stop codon (strand-aware). Transcripts with a single coding exon but a 3'UTR intron correctly stay in Rules 1/3 because that intron deposits an EJC that can trigger NMD. 3,113 RefSeq Curated and 10,790 Gencode V49 transcripts move into Rule 2. 140 RefSeq and 1,135 Gencode single-CDS-exon transcripts with 3'UTR introns correctly remain in Rules 1/3. Description page and makedoc updated.
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    fe73446acf43f70e385dadbbb281634adf3cac9e Tue Apr 21 16:44:16 2026 -0700
    NMD Escape QA tweaks: hide Gencode subtrack by default, bold rule numbers in mouseovers. refs #33737 - nmdEscGencode default visibility changed from on/dense to off/hide so only the RefSeq Curated subtrack is on by default. Per Lou's request. - RULE_DESCRIPTIONS mouseover strings wrap the rule number in <b>...</b> so the rule shows bold in the tooltip. Both bigBeds rebuilt.
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    0151d00a4a1d73a78c35f6158c6c936ff338faeb Fri Apr 24 10:37:34 2026 -0700
    NMD Escape: MANE subtrack, Rule 1 bug fix, transcript filter. refs #33737 - Add nmdEscMane subtrack (MANE Select Plus Clinical 1.5), built from /gbdb/hg38/mane/mane.bb. Reuses nmdEscTranscripts.html. - Fix Rule 1: measure 50 bp upstream of the transcript's last splice junction (including 3'UTR introns) rather than stripping 3'UTR from the exon list first. The old logic painted the entire last CDS exon as NMD-escape whenever the transcript had only one CDS exon, even when a 3'UTR intron sat far past the stop codon (e.g. NBDY: 207 bp of CDS over-painted for a junction 2.6 kb past the stop). - Add --rule1-mode {cds,mrna} (default cds): cds counts only CDS bp on the walk-back (paints up to 50 bp of CDS matching the rule label literally); mrna counts mRNA bp and clips to CDS (tracks the 55 bp rule literature). Documented in makeDoc. - Rule 4: when a 3'UTR intron exists, the last CDS-containing exon has a downstream EJC and is now eligible for the long-exon rule. - Mouseover lists contributing transcript accessions when 1-3 items collapse into a region; falls back to a count above that. - Add filterText/filterType/filterLabel on all three escape subtracks so a user can narrow the display to one transcript. - genePredNmdEsc: --gene-sym-field (default 17 for Gencode; pass 18 for MANE, whose HGNC symbol lives in bigGenePred geneName2). - Add findShortTxLongUtrIntron.py helper for finding MANE transcripts with long UTR introns (used to pick NMD edge-case test cases). Post-fix collapsed-region counts (--rule1-mode=cds): MANE 1.5: 67,752 Gencode V49: 233,375 RefSeq Curated: 112,356
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    3a62ea7e9a8cb3503586a0a78570331308c9bc58 Mon Apr 27 02:23:00 2026 -0700
    NMD Escape MANE: expose NM_ accession via labelFields. refs #33737 Per QA, the MANE subtrack now shows the NCBI RefSeq accession by default instead of the HGNC gene symbol, with the ENST and gene symbol still selectable via labelFields. - genePredNmdEsc: new --ncbi-id-field N option (default -1 = unused). When set, the named bigGenePred column is captured per-transcript and written into a new ncbiIds output column. For MANE pass 21. - genePredNmdEsc: new --no-collapse option. By default, regions with identical (chrom, start, end, rule) from multiple transcripts collapse into one row with comma-separated lists. With --no-collapse the script emits one row per (transcript, region). Used for MANE so each label-field column holds a single value: the 74 MANE Plus Clinical genes (e.g. LMNA) get two rows per region instead of one row with a two-element list. - nmdEscCollapsed.as: add lstring ncbiIds column. Schema is now bed9+3. - nmd.ra (nmdEscMane only): labelFields ncbiIds,name,transcripts; defaultLabelFields ncbiIds; labelSeparator " / ". Gencode and RefSeq subtracks unchanged - they default to the gene symbol (name column) and have an empty ncbiIds column. - doc/hg38/nmd.txt: bump all three bedToBigBed invocations to bed9+3 and document the --ncbi-id-field 21 + --no-collapse invocation for MANE. Counts: MANE 68,028 (--no-collapse); Gencode 233,375; RefSeq 112,356.
• src/hg/makeDb/scripts/nmd/nmdEscCollapsed.as
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    4bd316f5f1ca47328bd3f9a181214b788055f0bc Tue Apr 21 13:29:26 2026 -0700
    NMD Escape QA round 3: switch RefSeq to curated, fix Rule 2 misclassification. refs #33737 Switched the NMD Escape RefSeq subtrack input from hg38.ncbiRefSeq.txt.gz (all) to hg38.ncbiRefSeqCurated.txt.gz (NM_/NR_ only, no XM_/XR_ predicted models) per Max's feedback. longLabel updated to "NCBI RefSeq Curated transcripts". Fixed Rule 2 in genePredNmdEsc to test rec["exonCount"]==1 instead of len(cdsExons)==1. The old test misclassified multi-exon transcripts with a single CDS exon (UTR introns) as "intronless" and silently suppressed their Rule 1/3/4 assignments via the if/else short-circuit. 3,253 RefSeq curated and ~2,000 Gencode transcripts reassigned from Rule 2 to Rules 1/3. Rebuilt both tracks. Added Rule 1 caveat to nmdEscTranscripts.html for transcripts with a penultimate coding exon shorter than 50 bp. Added reciprocal relatedTracks.ra entries for nmd <-> mane and nmd <-> ncbiRefSeq. QA cleanups: non-ASCII prime char replaced with &#8242;, mailing list links given target="_blank" across all three HTML pages, dead commented nmdGencode block removed from nmd.ra, AutoSQL field comments updated to cover Rule 4 color and the gene-symbol-to-transcript-ID fallback. Makedoc updated with the full Gencode + RefSeq pipeline and /gbdb symlinks.
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    3a62ea7e9a8cb3503586a0a78570331308c9bc58 Mon Apr 27 02:23:00 2026 -0700
    NMD Escape MANE: expose NM_ accession via labelFields. refs #33737 Per QA, the MANE subtrack now shows the NCBI RefSeq accession by default instead of the HGNC gene symbol, with the ENST and gene symbol still selectable via labelFields. - genePredNmdEsc: new --ncbi-id-field N option (default -1 = unused). When set, the named bigGenePred column is captured per-transcript and written into a new ncbiIds output column. For MANE pass 21. - genePredNmdEsc: new --no-collapse option. By default, regions with identical (chrom, start, end, rule) from multiple transcripts collapse into one row with comma-separated lists. With --no-collapse the script emits one row per (transcript, region). Used for MANE so each label-field column holds a single value: the 74 MANE Plus Clinical genes (e.g. LMNA) get two rows per region instead of one row with a two-element list. - nmdEscCollapsed.as: add lstring ncbiIds column. Schema is now bed9+3. - nmd.ra (nmdEscMane only): labelFields ncbiIds,name,transcripts; defaultLabelFields ncbiIds; labelSeparator " / ". Gencode and RefSeq subtracks unchanged - they default to the gene symbol (name column) and have an empty ncbiIds column. - doc/hg38/nmd.txt: bump all three bedToBigBed invocations to bed9+3 and document the --ncbi-id-field 21 + --no-collapse invocation for MANE. Counts: MANE 68,028 (--no-collapse); Gencode 233,375; RefSeq 112,356.
• src/hg/makeDb/scripts/primateai/primateAi.as
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    de2ccf6d827865f11d3c8edd9ceeb1b6394a7380 Tue Apr 21 18:22:59 2026 -0700
    PrimateAI-3D: label items by nucleotide change, add aaChange field and HTML mouseover. Variant analysts typically work at the nucleotide level, and the current item label (amino acid change) collapses distinguishable variants: ~17% of items share their (chrom, pos, AA-change) tuple with another item because of codon degeneracy (e.g. three C>A, C>G, C>T at the same position can all appear as "M>I"). Labeling by nucleotide change makes every item uniquely distinguishable (0.0% collisions on hg38, 0.1% on hg19 from overlapping transcripts). - primateAi.as: field 4 (name) is now "Nucleotide change (e.g. T>C)"; new field aaChange (placed before ref/alt) holds the amino acid change. - primateAiToBigBed.py: write name = "{ref}>{alt}", new aaChange column, and an HTML mouseover with terse labels (Var/AA/Score/Perc/Pred) and a colored prediction string. - primateAi.ra: add labelFields name,aaChange and defaultLabelFields name so users can toggle the on-feature label between nt change (default) and AA change. - primateAi.html: expand Display Conventions with the label-convention rationale and a legend for each mouseover field. refs #37274
• src/hg/makeDb/scripts/primateai/primateAiToBigBed.py
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    50466766840ded6cb8bd5cb868bdf2ff3f613bc0 Tue Apr 21 11:17:15 2026 -0700
    QA fixes for PrimateAI-3D track. Config (primateAi.ra): - Fix broken Ensembl transcript linkout: urls $S expanded to chromosome name; switch to the Ensembl transcript page with $$ - Add numeric filters on percentile and raw score (label notes the paper's 0.821 clinical threshold) - Add maxWindowToDraw 2000000 Data (primateAiToBigBed.py): - Change hardcoded strand '+' to '.': the source file has no strand column - Accept input/output paths as CLI args (previously hardcoded the hg38 input path) - Handle variable field count: ~2.4M rows in the hg19 source are missing the refseq column Description (primateAi.html): - Fix two broken hgTrackUi&... internal links to the Zoonomia 447-way track - Regenerate the first reference via getTrackReferences (wrong article number and wrong PMC ID in the previous text) - Fix the GitHub URL for the conversion script in Methods - Move the Zoonomia 447-way mention out of Description; rephrase the license note to describe precisely what is disabled relatedTracks.ra: - Add reciprocal cross-links for primateAi <-> alphaMissense (hg38), primateAi <-> revel (hg38 + hg19), and primateAi <-> promoterAi (hg38). Also includes promoterAi <-> alphaMissense cross-links. refs #37274 #37279
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    de2ccf6d827865f11d3c8edd9ceeb1b6394a7380 Tue Apr 21 18:22:59 2026 -0700
    PrimateAI-3D: label items by nucleotide change, add aaChange field and HTML mouseover. Variant analysts typically work at the nucleotide level, and the current item label (amino acid change) collapses distinguishable variants: ~17% of items share their (chrom, pos, AA-change) tuple with another item because of codon degeneracy (e.g. three C>A, C>G, C>T at the same position can all appear as "M>I"). Labeling by nucleotide change makes every item uniquely distinguishable (0.0% collisions on hg38, 0.1% on hg19 from overlapping transcripts). - primateAi.as: field 4 (name) is now "Nucleotide change (e.g. T>C)"; new field aaChange (placed before ref/alt) holds the amino acid change. - primateAiToBigBed.py: write name = "{ref}>{alt}", new aaChange column, and an HTML mouseover with terse labels (Var/AA/Score/Perc/Pred) and a colored prediction string. - primateAi.ra: add labelFields name,aaChange and defaultLabelFields name so users can toggle the on-feature label between nt change (default) and AA change. - primateAi.html: expand Display Conventions with the label-convention rationale and a legend for each mouseover field. refs #37274
• src/hg/makeDb/scripts/promoterAiOverlaps.as
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    f9a89b0e1ce3c937b4fbb879736c1619c35c271f Tue Apr 21 12:11:02 2026 -0700
    QA fixes for PromoterAI track. refs #37278 Description page: replaced the wrong reference (Gao et al. 2023, the PrimateAI-3D paper) with the actual PromoterAI citation (Jaganathan et al. Science 2025, PMID 40440429), corrected the score-direction wording (negative = under-expression, positive = over-expression, not "tolerated vs disruptive"), fixed the Data Access source link (Illumina BaseSpace, not the GitHub repo), and corrected the mouseover blurb to match mouseOverFunction noAverage behavior. Converter and AS: the overlap bigBed now carries the real per-transcript strand from the source TSV (was hardcoded '+'), with a new strands column in the AS, and the name field concatenates unique gene symbols so bidirectional-promoter items read as "HES4,ISG15" etc. BED score is now |PromoterAI|*1000 so scoreFilter is meaningful. Rewrote the converter to stream (sorted input), which drops peak memory from ~40 GB to a few MB. trackDb: added filterLabel/filterLimits on scoreDiff (the filter was unusable without labels), scoreFilter + scoreLabel, alwaysZero and autoScale off on the bigWig subtracks, color 200,0,0 / altColor 0,0,200 so signed bigWig bars draw red (over-expression) above zero and blue (under-expression) below, matching the overlap track itemRgb. Added maxWindowToDraw and maxItems on the overlap subtrack. Makedoc updated to describe the streaming pipeline, the new strands column, and the rebuild workflow.
• src/hg/makeDb/scripts/promoterAiToBigWig.py
  • lines changed 111, context: html, text, full: html, text
    f9a89b0e1ce3c937b4fbb879736c1619c35c271f Tue Apr 21 12:11:02 2026 -0700
    QA fixes for PromoterAI track. refs #37278 Description page: replaced the wrong reference (Gao et al. 2023, the PrimateAI-3D paper) with the actual PromoterAI citation (Jaganathan et al. Science 2025, PMID 40440429), corrected the score-direction wording (negative = under-expression, positive = over-expression, not "tolerated vs disruptive"), fixed the Data Access source link (Illumina BaseSpace, not the GitHub repo), and corrected the mouseover blurb to match mouseOverFunction noAverage behavior. Converter and AS: the overlap bigBed now carries the real per-transcript strand from the source TSV (was hardcoded '+'), with a new strands column in the AS, and the name field concatenates unique gene symbols so bidirectional-promoter items read as "HES4,ISG15" etc. BED score is now |PromoterAI|*1000 so scoreFilter is meaningful. Rewrote the converter to stream (sorted input), which drops peak memory from ~40 GB to a few MB. trackDb: added filterLabel/filterLimits on scoreDiff (the filter was unusable without labels), scoreFilter + scoreLabel, alwaysZero and autoScale off on the bigWig subtracks, color 200,0,0 / altColor 0,0,200 so signed bigWig bars draw red (over-expression) above zero and blue (under-expression) below, matching the overlap track itemRgb. Added maxWindowToDraw and maxItems on the overlap subtrack. Makedoc updated to describe the streaming pipeline, the new strands column, and the rebuild workflow.
• src/hg/makeDb/scripts/srSv/abelSv.as
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    f058c8fe4601b223ff47468eb3525c05ccd03850 Wed Apr 22 09:17:17 2026 -0700
    srSv: new short-read SV supertrack, split out of lrSv Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr, tommoJpCnv) out of the Long-read SV supertrack into a new sibling supertrack srSv (Short-read SVs), so the lrSv collection contains only long-read callsets. Filter fields (svType, svLen, insLen, AC) are mirrored at the srSv supertrack level to keep the UX parallel to lrSv. - trackDb: new human/srSv.ra with the three subtrack stanzas and updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas removed from human/lrSv.ra. human/trackDb.ra now includes srSv.ra. Also a new human/srSv.html overview page; the SR rows and SR-specific paragraphs removed from human/lrSv.html. - Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/ {lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to scripts/srSv/ with git mv (history preserved) and renamed to drop the "lrSv" prefix. Internal path references in abelSvBuild.sh and abelSvVcfToBed.py updated. - makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and extended with the onekg3202Sr and tommoJpCnv sections moved from lrSv.txt. lrSv.txt leaves a pointer. - Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr, lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*. /gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and /gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/. refs #36258
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/srSv/abelSvBuild.sh
  • lines changed 7, context: html, text, full: html, text
    f058c8fe4601b223ff47468eb3525c05ccd03850 Wed Apr 22 09:17:17 2026 -0700
    srSv: new short-read SV supertrack, split out of lrSv Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr, tommoJpCnv) out of the Long-read SV supertrack into a new sibling supertrack srSv (Short-read SVs), so the lrSv collection contains only long-read callsets. Filter fields (svType, svLen, insLen, AC) are mirrored at the srSv supertrack level to keep the UX parallel to lrSv. - trackDb: new human/srSv.ra with the three subtrack stanzas and updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas removed from human/lrSv.ra. human/trackDb.ra now includes srSv.ra. Also a new human/srSv.html overview page; the SR rows and SR-specific paragraphs removed from human/lrSv.html. - Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/ {lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to scripts/srSv/ with git mv (history preserved) and renamed to drop the "lrSv" prefix. Internal path references in abelSvBuild.sh and abelSvVcfToBed.py updated. - makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and extended with the onekg3202Sr and tommoJpCnv sections moved from lrSv.txt. lrSv.txt leaves a pointer. - Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr, lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*. /gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and /gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/. refs #36258
• src/hg/makeDb/scripts/srSv/abelSvVcfToBed.py
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    f058c8fe4601b223ff47468eb3525c05ccd03850 Wed Apr 22 09:17:17 2026 -0700
    srSv: new short-read SV supertrack, split out of lrSv Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr, tommoJpCnv) out of the Long-read SV supertrack into a new sibling supertrack srSv (Short-read SVs), so the lrSv collection contains only long-read callsets. Filter fields (svType, svLen, insLen, AC) are mirrored at the srSv supertrack level to keep the UX parallel to lrSv. - trackDb: new human/srSv.ra with the three subtrack stanzas and updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas removed from human/lrSv.ra. human/trackDb.ra now includes srSv.ra. Also a new human/srSv.html overview page; the SR rows and SR-specific paragraphs removed from human/lrSv.html. - Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/ {lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to scripts/srSv/ with git mv (history preserved) and renamed to drop the "lrSv" prefix. Internal path references in abelSvBuild.sh and abelSvVcfToBed.py updated. - makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and extended with the onekg3202Sr and tommoJpCnv sections moved from lrSv.txt. lrSv.txt leaves a pointer. - Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr, lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*. /gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and /gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/. refs #36258
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/srSv/onekg3202Sr.as
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    f058c8fe4601b223ff47468eb3525c05ccd03850 Wed Apr 22 09:17:17 2026 -0700
    srSv: new short-read SV supertrack, split out of lrSv Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr, tommoJpCnv) out of the Long-read SV supertrack into a new sibling supertrack srSv (Short-read SVs), so the lrSv collection contains only long-read callsets. Filter fields (svType, svLen, insLen, AC) are mirrored at the srSv supertrack level to keep the UX parallel to lrSv. - trackDb: new human/srSv.ra with the three subtrack stanzas and updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas removed from human/lrSv.ra. human/trackDb.ra now includes srSv.ra. Also a new human/srSv.html overview page; the SR rows and SR-specific paragraphs removed from human/lrSv.html. - Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/ {lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to scripts/srSv/ with git mv (history preserved) and renamed to drop the "lrSv" prefix. Internal path references in abelSvBuild.sh and abelSvVcfToBed.py updated. - makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and extended with the onekg3202Sr and tommoJpCnv sections moved from lrSv.txt. lrSv.txt leaves a pointer. - Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr, lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*. /gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and /gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/. refs #36258
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/srSv/onekg3202SrVcfToBed.py
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    f058c8fe4601b223ff47468eb3525c05ccd03850 Wed Apr 22 09:17:17 2026 -0700
    srSv: new short-read SV supertrack, split out of lrSv Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr, tommoJpCnv) out of the Long-read SV supertrack into a new sibling supertrack srSv (Short-read SVs), so the lrSv collection contains only long-read callsets. Filter fields (svType, svLen, insLen, AC) are mirrored at the srSv supertrack level to keep the UX parallel to lrSv. - trackDb: new human/srSv.ra with the three subtrack stanzas and updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas removed from human/lrSv.ra. human/trackDb.ra now includes srSv.ra. Also a new human/srSv.html overview page; the SR rows and SR-specific paragraphs removed from human/lrSv.html. - Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/ {lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to scripts/srSv/ with git mv (history preserved) and renamed to drop the "lrSv" prefix. Internal path references in abelSvBuild.sh and abelSvVcfToBed.py updated. - makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and extended with the onekg3202Sr and tommoJpCnv sections moved from lrSv.txt. lrSv.txt leaves a pointer. - Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr, lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*. /gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and /gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/. refs #36258
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/scripts/srSv/tommoJpCnvVcfToBedGraph.py
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    f058c8fe4601b223ff47468eb3525c05ccd03850 Wed Apr 22 09:17:17 2026 -0700
    srSv: new short-read SV supertrack, split out of lrSv Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr, tommoJpCnv) out of the Long-read SV supertrack into a new sibling supertrack srSv (Short-read SVs), so the lrSv collection contains only long-read callsets. Filter fields (svType, svLen, insLen, AC) are mirrored at the srSv supertrack level to keep the UX parallel to lrSv. - trackDb: new human/srSv.ra with the three subtrack stanzas and updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas removed from human/lrSv.ra. human/trackDb.ra now includes srSv.ra. Also a new human/srSv.html overview page; the SR rows and SR-specific paragraphs removed from human/lrSv.html. - Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/ {lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to scripts/srSv/ with git mv (history preserved) and renamed to drop the "lrSv" prefix. Internal path references in abelSvBuild.sh and abelSvVcfToBed.py updated. - makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and extended with the onekg3202Sr and tommoJpCnv sections moved from lrSv.txt. lrSv.txt leaves a pointer. - Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr, lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*. /gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and /gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/. refs #36258
• src/hg/makeDb/scripts/varFreqs/databases.tsv
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    366afa4a74c46ec6fb2b667a2902a873feec40cf Mon Apr 20 23:00:05 2026 -0700
    varFreqsAll: rebuild combined bigBed to include GA4K and CoLoRSdb Regenerate the All Databases Combined track with the two long-read PacBio subtracks (GA4K 552 samples and CoLoRSdb v1.2.0 1,027 samples) that were added to varFreqs since the March build. Source count rises from 21 to 23 databases; final bigBed is 37.7 GB with 1.17B records and 113 fields. Updates varFreqs.ra filterValues.sources and per- database AF/AC filters for the two new sources, and databases.tsv + varFreqs.txt (build notes). refs #36642
• src/hg/makeDb/scripts/varFreqs/svatalogFreqToVcf.py
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    695f40f9d6139a4df393522c067f1702aff8d3bd Wed Apr 22 03:13:39 2026 -0700
    varFreqs: add SVatalog 101 short-read SNV frequencies subtrack SNV/indel allele frequencies from the 101-sample GWAS SVatalog cohort (Chirmade et al. 2026, Heredity, PMID 41203876), called from 10X Genomics linked short-read WGS with GATK HaplotypeCaller v4.0.0.0 and phased with SHAPEIT v4.2.0. Sibling of the lrSv chirmade101Sv structural-variant track, which is built from the same 101 samples. 8,814,835 autosomal + chrX sites. Source release ships only AF; AC and AN are synthesized in the emitted VCF as AC=round(AF*202) and AN=202 (2*101 diploid), with the gnomAD v3.1 non-Finnish European AF and dbSNP rsID passed through as GNOMAD_NFE_AF and RSID info fields. VCF is bgzipped + tabix-indexed (172 MB + 1.6 MB .tbi). Files: - scripts/varFreqs/svatalogFreqToVcf.py (new): per-chrom allele-freq TSV -> single VCF with hg38 ##contig header - trackDb/human/varFreqs.ra: new svatalogSnv vcfTabix subtrack - trackDb/human/svatalogSnv.html (new): doc page - trackDb/human/varFreqs.html: new row in Available Datasets table - doc/hg38/varFreqs.txt: wget-free build block (input files were downloaded manually from Zenodo 13367574) Note: the All Databases Combined varFreqs bigBed has NOT been rebuilt to include this new source yet; a subsequent merge pass will add it. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/abelSv.html
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    65091fe6f6487c23d650a144e947fc1c582d3f40 Tue Apr 21 02:16:16 2026 -0700
    abelSv: move under lrSv supertrack as short-read comparison subtrack Move the Abel et al. 2020 CCDG 17,795-genome SV callset from a top-level hg38 track to a subtrack of the lrSv supertrack (parallel to onekg3202Sr) and relabel shortLabel/longLabel to flag Illumina short-read provenance. The same bigBed is now visible on hg38 in the long-read SV browsing context. Also: - Clarify abelSv.html variant counts: 738,624 upstream unique SVs across both callsets, 737,998 after B37->hg38 liftOver (626 unmapped). B38=458,106, B37lift=279,892. - lrSv.html: fix triple-slash https:/// in the Ebert et al. Science reference URL. - bigBed.html: add closing </li> on the extra-fields pipe-separator bullet and tighten a comma in the same sentence. refs #36258, refs #37376
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/aou1kSv.html
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/aprSv.html
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/chirmade101Sv.html
  • lines changed 32, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/colorsDb.html
  • lines changed 126, context: html, text, full: html, text
    f4d6633d6a724d7b682f9f49ed983e22a5e0975d Mon Apr 20 14:41:07 2026 -0700
    updating a few lrSv subtracks, and moving the colorsDbSnv track under the varFreqs track. refs #36642
• src/hg/makeDb/trackDb/human/colorsDbSv.html
  • lines changed 104, context: html, text, full: html, text
    9a11061ca6b40fe16bdfd09b1af53192f6c7c85b Tue Apr 21 08:13:02 2026 -0700
    lrSv: add HTML doc pages and conversion scripts for recent subtracks, + hs1 HGSVC3 Subtrack stanzas for these SV callsets landed in earlier commits but the conversion scripts and per-track HTML description pages were never added; trackDb therefore had no doc to serve. This commit catches up. Docs (new): - colorsDbSv.html CoLoRSdb 1,427-sample long-read SVs - gustafsonSv.html 1KG ONT 100 (Gustafson 2024, PMID 39358015) - hgsvc2Sv.html HGSVC2 (Ebert 2021, PMID 33632895) - hprc2Sv.html HPRC release-2 pangenome SVs (no PMID yet; see humanpangenome.org/hprc-data-release-2/) - onekg3202Sr.html 1KG 3202 Illumina SHORT-READ GATK-SV (Byrska-Bishop 2022, PMID 36055201) Scripts (new): - lrSvGustafson.as / lrSvGustafsonVcfToBed.py - lrSvHgsvc2.as / lrSvHgsvc2TsvToBed.py (merges insdel + inv tables) - lrSvHprc2.as / lrSvHprc2VcfToBed.py (streams wave-decomposed VCF, explodes multi-allelic rows, filters to SV-sized or INV) - lrSv1kg3202Sr.as / lrSv1kg3202SrVcfToBed.py HGSVC3 also on hs1: - hgsvc3Sv.html: note that the hs1 build is native (not lifted): HGSVC3 aligned all assemblies to both GRCh38 and T2T-CHM13 and released separate annotation tables per reference. Added the T2T-CHM13 source URL to the Methods section and the hs1 hgsvc3.bb download link to Data Access. - doc/hs1/lrSv.txt (new): hs1-specific wget + build steps; refers back to doc/hg38/lrSv.txt for the full process. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 4, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/cpc1Sv.html
  • lines changed 23, context: html, text, full: html, text
    5e4ca58df1b5bfe554fe5cc3309a39736ca256ee Tue Apr 21 08:08:52 2026 -0700
    cpc1Sv: restrict to the 58 CPC samples, drop HPRC-specific SVs Rewrite lrSvCpc1VcfToBed.py to identify the 58 CPC sample columns by name prefix (HIFI032* or RY*), recompute AC/AN/NS from those GT columns only, and skip any snarl that no CPC sample carries. The HPRC portion is already represented elsewhere in lrSv, so this keeps the track population-consistent with its label. Rebuild results: 46,092 snarl sites on hs1 (down from 97,205 when combined with HPRC), 36,030 lifted to hg38 (down from 81,261; 10,062 unmapped). Updates cpc1Sv.html, lrSv.ra labels, and the makeDoc. refs #36258
  • lines changed 36, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/decodeSv.html
  • lines changed 26, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/ga4kSv.html
  • lines changed 29, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/gustafsonSv.html
  • lines changed 96, context: html, text, full: html, text
    9a11061ca6b40fe16bdfd09b1af53192f6c7c85b Tue Apr 21 08:13:02 2026 -0700
    lrSv: add HTML doc pages and conversion scripts for recent subtracks, + hs1 HGSVC3 Subtrack stanzas for these SV callsets landed in earlier commits but the conversion scripts and per-track HTML description pages were never added; trackDb therefore had no doc to serve. This commit catches up. Docs (new): - colorsDbSv.html CoLoRSdb 1,427-sample long-read SVs - gustafsonSv.html 1KG ONT 100 (Gustafson 2024, PMID 39358015) - hgsvc2Sv.html HGSVC2 (Ebert 2021, PMID 33632895) - hprc2Sv.html HPRC release-2 pangenome SVs (no PMID yet; see humanpangenome.org/hprc-data-release-2/) - onekg3202Sr.html 1KG 3202 Illumina SHORT-READ GATK-SV (Byrska-Bishop 2022, PMID 36055201) Scripts (new): - lrSvGustafson.as / lrSvGustafsonVcfToBed.py - lrSvHgsvc2.as / lrSvHgsvc2TsvToBed.py (merges insdel + inv tables) - lrSvHprc2.as / lrSvHprc2VcfToBed.py (streams wave-decomposed VCF, explodes multi-allelic rows, filters to SV-sized or INV) - lrSv1kg3202Sr.as / lrSv1kg3202SrVcfToBed.py HGSVC3 also on hs1: - hgsvc3Sv.html: note that the hs1 build is native (not lifted): HGSVC3 aligned all assemblies to both GRCh38 and T2T-CHM13 and released separate annotation tables per reference. Added the T2T-CHM13 source URL to the Methods section and the hs1 hgsvc3.bb download link to Data Access. - doc/hs1/lrSv.txt (new): hs1-specific wget + build steps; refers back to doc/hg38/lrSv.txt for the full process. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 30, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/han945Sv.html
  • lines changed 10, context: html, text, full: html, text
    f4d6633d6a724d7b682f9f49ed983e22a5e0975d Mon Apr 20 14:41:07 2026 -0700
    updating a few lrSv subtracks, and moving the colorsDbSnv track under the varFreqs track. refs #36642
  • lines changed 1, context: html, text, full: html, text
    b132fa0f0ba226c056f5408a2c02c3d945ccc9c1 Tue Apr 21 08:17:52 2026 -0700
    han945Sv: fix OMIX download link Replace the broken ngdc.cncb.ac.cn/omix/release/OMIX005649 URL in the Data Access section with the correct biosino.org analysis page for this dataset. refs #36258
  • lines changed 26, context: html, text, full: html, text
    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV50lift37.html
  • lines changed 32, context: html, text, full: html, text
    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV50lift37.ra
  • lines changed 210, context: html, text, full: html, text
    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/trackDb/human/hg38/abelSv.ra
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    65091fe6f6487c23d650a144e947fc1c582d3f40 Tue Apr 21 02:16:16 2026 -0700
    abelSv: move under lrSv supertrack as short-read comparison subtrack Move the Abel et al. 2020 CCDG 17,795-genome SV callset from a top-level hg38 track to a subtrack of the lrSv supertrack (parallel to onekg3202Sr) and relabel shortLabel/longLabel to flag Illumina short-read provenance. The same bigBed is now visible on hg38 in the long-read SV browsing context. Also: - Clarify abelSv.html variant counts: 738,624 upstream unique SVs across both callsets, 737,998 after B37->hg38 liftOver (626 unmapped). B38=458,106, B37lift=279,892. - lrSv.html: fix triple-slash https:/// in the Ebert et al. Science reference URL. - bigBed.html: add closing </li> on the extra-fields pipe-separator bullet and tighten a comma in the same sentence. refs #36258, refs #37376
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
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    90668959b76ef7d792bac3cbc4eb509a58c6c317 Thu Apr 23 11:25:38 2026 -0700
    Adding mergeSpannedItems to gnomad CNV and structural variants tracks on hg38, refs Max email
• src/hg/makeDb/trackDb/human/hg38/gnomadMpc.html
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    f30798ae5d11e88e0ab7eb2bcab634e253fd0675 Thu Apr 23 10:36:40 2026 -0700
    Add gnomAD MPC v4.1.1 track to hg38. New composite track under the gnomAD container showing per-variant MPC (Missense deleteriousness Prediction by Constraint) scores from gnomAD v4.1.1. Four bigWigs provide per-base scores (one per ALT nucleotide); a companion bigBed carries the ~250K multi-transcript variants with a per-transcript breakdown. Included via 'alpha' for QA review. refs #37434 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/gnomadMpc.ra
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    f30798ae5d11e88e0ab7eb2bcab634e253fd0675 Thu Apr 23 10:36:40 2026 -0700
    Add gnomAD MPC v4.1.1 track to hg38. New composite track under the gnomAD container showing per-variant MPC (Missense deleteriousness Prediction by Constraint) scores from gnomAD v4.1.1. Four bigWigs provide per-base scores (one per ALT nucleotide); a companion bigBed carries the ~250K multi-transcript variants with a per-transcript breakdown. Included via 'alpha' for QA review. refs #37434 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/mb2.ra
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    689349fca5a4865a1891db8cd39d392657b2b09b Wed Apr 22 02:54:09 2026 -0700
    Replacing the subtrackUrl setting for faceted composites with subtrackUrls, which supports outlinks in multiple fields. refs #36320
• src/hg/makeDb/trackDb/human/hg38/mpra.html
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    888e7470c14eeecdca310ed36bb45c3c00ae8052 Tue Apr 21 15:14:04 2026 -0700
    QA fixes for MPRA superTrack. refs #37359 Fix broken mpraVarDb bigDataUrl — pointed at /gbdb/hg38/mpra/mpravardb.bb but the file is at /gbdb/hg38/mpra/mpravardb/mpravardb.bb, causing hgTrackDb -strict to silently drop the subtrack. Rebuild mpravardb.bb after two fixes in mpravardbToBed.py: sanitize UTF-8 in user-visible string fields (curly quotes, primes, NBSP mojibake) that the browser does not transcode, eliminating ~246k non-ASCII occurrences across 42% of rows; and change safe_float / pval_to_score to write NaN and return score 0 for NA / out-of-range p-values instead of 0.0 and score 1000 (previously inflated untested variants to the top of score-sorted views). trackDb stanza cleanup: shorten mpraVarDb longLabel, drop superfluous type bed 4 from superTrack, make bigBed 9+13 explicit, remove redundant mouseOverField, align parent mpra on, add filterValues for cell_line/assay/cellLine and filterByRange sliders for percentile_rank / fdr / log2FC, add labelFields and maxWindowToDraw. Description pages: add cross-species disclosure (mouse reporter cells used to assay human sequences), update mpraVarDb header to post-liftOver count 239,028 with Studies-table footnote, fix mpraVarDb.html download-server paths, soften imprecise "51 MPRA experiments" claim in mpra.html and mprabase.html. relatedTracks.ra: reciprocal mpra <-> wgEncodeReg4 and mpra <-> cCREs. Expand mpra.txt makedoc with upstream provenance and QA-rebuild log.
• src/hg/makeDb/trackDb/human/hg38/mpra.ra
  • lines changed 27, context: html, text, full: html, text
    888e7470c14eeecdca310ed36bb45c3c00ae8052 Tue Apr 21 15:14:04 2026 -0700
    QA fixes for MPRA superTrack. refs #37359 Fix broken mpraVarDb bigDataUrl — pointed at /gbdb/hg38/mpra/mpravardb.bb but the file is at /gbdb/hg38/mpra/mpravardb/mpravardb.bb, causing hgTrackDb -strict to silently drop the subtrack. Rebuild mpravardb.bb after two fixes in mpravardbToBed.py: sanitize UTF-8 in user-visible string fields (curly quotes, primes, NBSP mojibake) that the browser does not transcode, eliminating ~246k non-ASCII occurrences across 42% of rows; and change safe_float / pval_to_score to write NaN and return score 0 for NA / out-of-range p-values instead of 0.0 and score 1000 (previously inflated untested variants to the top of score-sorted views). trackDb stanza cleanup: shorten mpraVarDb longLabel, drop superfluous type bed 4 from superTrack, make bigBed 9+13 explicit, remove redundant mouseOverField, align parent mpra on, add filterValues for cell_line/assay/cellLine and filterByRange sliders for percentile_rank / fdr / log2FC, add labelFields and maxWindowToDraw. Description pages: add cross-species disclosure (mouse reporter cells used to assay human sequences), update mpraVarDb header to post-liftOver count 239,028 with Studies-table footnote, fix mpraVarDb.html download-server paths, soften imprecise "51 MPRA experiments" claim in mpra.html and mprabase.html. relatedTracks.ra: reciprocal mpra <-> wgEncodeReg4 and mpra <-> cCREs. Expand mpra.txt makedoc with upstream provenance and QA-rebuild log.
• src/hg/makeDb/trackDb/human/hg38/mpraVarDb.html
  • lines changed 14, context: html, text, full: html, text
    888e7470c14eeecdca310ed36bb45c3c00ae8052 Tue Apr 21 15:14:04 2026 -0700
    QA fixes for MPRA superTrack. refs #37359 Fix broken mpraVarDb bigDataUrl — pointed at /gbdb/hg38/mpra/mpravardb.bb but the file is at /gbdb/hg38/mpra/mpravardb/mpravardb.bb, causing hgTrackDb -strict to silently drop the subtrack. Rebuild mpravardb.bb after two fixes in mpravardbToBed.py: sanitize UTF-8 in user-visible string fields (curly quotes, primes, NBSP mojibake) that the browser does not transcode, eliminating ~246k non-ASCII occurrences across 42% of rows; and change safe_float / pval_to_score to write NaN and return score 0 for NA / out-of-range p-values instead of 0.0 and score 1000 (previously inflated untested variants to the top of score-sorted views). trackDb stanza cleanup: shorten mpraVarDb longLabel, drop superfluous type bed 4 from superTrack, make bigBed 9+13 explicit, remove redundant mouseOverField, align parent mpra on, add filterValues for cell_line/assay/cellLine and filterByRange sliders for percentile_rank / fdr / log2FC, add labelFields and maxWindowToDraw. Description pages: add cross-species disclosure (mouse reporter cells used to assay human sequences), update mpraVarDb header to post-liftOver count 239,028 with Studies-table footnote, fix mpraVarDb.html download-server paths, soften imprecise "51 MPRA experiments" claim in mpra.html and mprabase.html. relatedTracks.ra: reciprocal mpra <-> wgEncodeReg4 and mpra <-> cCREs. Expand mpra.txt makedoc with upstream provenance and QA-rebuild log.
• src/hg/makeDb/trackDb/human/hg38/mprabase.html
  • lines changed 9, context: html, text, full: html, text
    888e7470c14eeecdca310ed36bb45c3c00ae8052 Tue Apr 21 15:14:04 2026 -0700
    QA fixes for MPRA superTrack. refs #37359 Fix broken mpraVarDb bigDataUrl — pointed at /gbdb/hg38/mpra/mpravardb.bb but the file is at /gbdb/hg38/mpra/mpravardb/mpravardb.bb, causing hgTrackDb -strict to silently drop the subtrack. Rebuild mpravardb.bb after two fixes in mpravardbToBed.py: sanitize UTF-8 in user-visible string fields (curly quotes, primes, NBSP mojibake) that the browser does not transcode, eliminating ~246k non-ASCII occurrences across 42% of rows; and change safe_float / pval_to_score to write NaN and return score 0 for NA / out-of-range p-values instead of 0.0 and score 1000 (previously inflated untested variants to the top of score-sorted views). trackDb stanza cleanup: shorten mpraVarDb longLabel, drop superfluous type bed 4 from superTrack, make bigBed 9+13 explicit, remove redundant mouseOverField, align parent mpra on, add filterValues for cell_line/assay/cellLine and filterByRange sliders for percentile_rank / fdr / log2FC, add labelFields and maxWindowToDraw. Description pages: add cross-species disclosure (mouse reporter cells used to assay human sequences), update mpraVarDb header to post-liftOver count 239,028 with Studies-table footnote, fix mpraVarDb.html download-server paths, soften imprecise "51 MPRA experiments" claim in mpra.html and mprabase.html. relatedTracks.ra: reciprocal mpra <-> wgEncodeReg4 and mpra <-> cCREs. Expand mpra.txt makedoc with upstream provenance and QA-rebuild log.
• src/hg/makeDb/trackDb/human/hg38/nmd.html
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    3972ba54c468ace338d4a5578de1d20bf6c1f9ec Mon Apr 20 15:39:26 2026 -0700
    Adding Rule 4 (long-exon rule, Lindeboom 2016) to NMD Escape tracks and releasing on Apr. 22, 2026. refs #33737 Script: added a fourth rule to genePredNmdEsc. Coding exons longer than 400 bp (excluding the last coding exon, which is already covered by the 50 bp rule) are flagged as NMD-escape regions. Rebuilt the Gencode and NCBI RefSeq bigBed files. trackDb: - nmd.ra: appended "/400nt" to the nmdEsc longLabels, set nmdEscGencode default visibility to dense so the track is visible in cart-reset views, changed all four NMDetective subtracks from "visibility full" to "visibility hide", updated pennantIcon to the Apr. 22, 2026 release date and anchor. - nmd.html: mention long internal exons in the overview description, update the rule count from three to four. - nmdEscTranscripts.html: add the long-exon rule to the rule list and color legend (gold, #FFD700), expand the Background section with mechanisms for the intronless, start-proximal, and long-exon rules, correct the 50 bp rule description to include the entire last coding exon, fix Lindeboom 2016 author initials (RG -> RGH). News: - newsarch.html: add the 2026-04-22 NMD Escape news entry covering all four rules, with acknowledgements to Guido Neidhardt and Andreas Lahner for suggesting the track and the Decipher Genome Browser team for inspiring the visualization. - indexNews.html: add the front-page news link. makedoc: - nmd.txt: dated note for the Rule 4 rebuild.
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    4bd316f5f1ca47328bd3f9a181214b788055f0bc Tue Apr 21 13:29:26 2026 -0700
    NMD Escape QA round 3: switch RefSeq to curated, fix Rule 2 misclassification. refs #33737 Switched the NMD Escape RefSeq subtrack input from hg38.ncbiRefSeq.txt.gz (all) to hg38.ncbiRefSeqCurated.txt.gz (NM_/NR_ only, no XM_/XR_ predicted models) per Max's feedback. longLabel updated to "NCBI RefSeq Curated transcripts". Fixed Rule 2 in genePredNmdEsc to test rec["exonCount"]==1 instead of len(cdsExons)==1. The old test misclassified multi-exon transcripts with a single CDS exon (UTR introns) as "intronless" and silently suppressed their Rule 1/3/4 assignments via the if/else short-circuit. 3,253 RefSeq curated and ~2,000 Gencode transcripts reassigned from Rule 2 to Rules 1/3. Rebuilt both tracks. Added Rule 1 caveat to nmdEscTranscripts.html for transcripts with a penultimate coding exon shorter than 50 bp. Added reciprocal relatedTracks.ra entries for nmd <-> mane and nmd <-> ncbiRefSeq. QA cleanups: non-ASCII prime char replaced with &#8242;, mailing list links given target="_blank" across all three HTML pages, dead commented nmdGencode block removed from nmd.ra, AutoSQL field comments updated to cover Rule 4 color and the gene-symbol-to-transcript-ID fallback. Makedoc updated with the full Gencode + RefSeq pipeline and /gbdb symlinks.
• src/hg/makeDb/trackDb/human/hg38/nmd.ra
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    3972ba54c468ace338d4a5578de1d20bf6c1f9ec Mon Apr 20 15:39:26 2026 -0700
    Adding Rule 4 (long-exon rule, Lindeboom 2016) to NMD Escape tracks and releasing on Apr. 22, 2026. refs #33737 Script: added a fourth rule to genePredNmdEsc. Coding exons longer than 400 bp (excluding the last coding exon, which is already covered by the 50 bp rule) are flagged as NMD-escape regions. Rebuilt the Gencode and NCBI RefSeq bigBed files. trackDb: - nmd.ra: appended "/400nt" to the nmdEsc longLabels, set nmdEscGencode default visibility to dense so the track is visible in cart-reset views, changed all four NMDetective subtracks from "visibility full" to "visibility hide", updated pennantIcon to the Apr. 22, 2026 release date and anchor. - nmd.html: mention long internal exons in the overview description, update the rule count from three to four. - nmdEscTranscripts.html: add the long-exon rule to the rule list and color legend (gold, #FFD700), expand the Background section with mechanisms for the intronless, start-proximal, and long-exon rules, correct the 50 bp rule description to include the entire last coding exon, fix Lindeboom 2016 author initials (RG -> RGH). News: - newsarch.html: add the 2026-04-22 NMD Escape news entry covering all four rules, with acknowledgements to Guido Neidhardt and Andreas Lahner for suggesting the track and the Decipher Genome Browser team for inspiring the visualization. - indexNews.html: add the front-page news link. makedoc: - nmd.txt: dated note for the Rule 4 rebuild.
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    4bd316f5f1ca47328bd3f9a181214b788055f0bc Tue Apr 21 13:29:26 2026 -0700
    NMD Escape QA round 3: switch RefSeq to curated, fix Rule 2 misclassification. refs #33737 Switched the NMD Escape RefSeq subtrack input from hg38.ncbiRefSeq.txt.gz (all) to hg38.ncbiRefSeqCurated.txt.gz (NM_/NR_ only, no XM_/XR_ predicted models) per Max's feedback. longLabel updated to "NCBI RefSeq Curated transcripts". Fixed Rule 2 in genePredNmdEsc to test rec["exonCount"]==1 instead of len(cdsExons)==1. The old test misclassified multi-exon transcripts with a single CDS exon (UTR introns) as "intronless" and silently suppressed their Rule 1/3/4 assignments via the if/else short-circuit. 3,253 RefSeq curated and ~2,000 Gencode transcripts reassigned from Rule 2 to Rules 1/3. Rebuilt both tracks. Added Rule 1 caveat to nmdEscTranscripts.html for transcripts with a penultimate coding exon shorter than 50 bp. Added reciprocal relatedTracks.ra entries for nmd <-> mane and nmd <-> ncbiRefSeq. QA cleanups: non-ASCII prime char replaced with &#8242;, mailing list links given target="_blank" across all three HTML pages, dead commented nmdGencode block removed from nmd.ra, AutoSQL field comments updated to cover Rule 4 color and the gene-symbol-to-transcript-ID fallback. Makedoc updated with the full Gencode + RefSeq pipeline and /gbdb symlinks.
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    fe73446acf43f70e385dadbbb281634adf3cac9e Tue Apr 21 16:44:16 2026 -0700
    NMD Escape QA tweaks: hide Gencode subtrack by default, bold rule numbers in mouseovers. refs #33737 - nmdEscGencode default visibility changed from on/dense to off/hide so only the RefSeq Curated subtrack is on by default. Per Lou's request. - RULE_DESCRIPTIONS mouseover strings wrap the rule number in <b>...</b> so the rule shows bold in the tooltip. Both bigBeds rebuilt.
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    a86b49667ad82b0f6c3745379f186f4d5753e368 Wed Apr 22 13:52:14 2026 -0700
    Simplify NMD Escape subtrack longLabels. refs #33737 The '50bp/100bp/intronless/400nt' rule-list became inaccurate after the Rule 2 refinement (Rule 2 now covers single coding exon + no 3'UTR intron, not just intronless). Drop the enumerated rules from the longLabel and defer to the track description page for rule detail.
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    0151d00a4a1d73a78c35f6158c6c936ff338faeb Fri Apr 24 10:37:34 2026 -0700
    NMD Escape: MANE subtrack, Rule 1 bug fix, transcript filter. refs #33737 - Add nmdEscMane subtrack (MANE Select Plus Clinical 1.5), built from /gbdb/hg38/mane/mane.bb. Reuses nmdEscTranscripts.html. - Fix Rule 1: measure 50 bp upstream of the transcript's last splice junction (including 3'UTR introns) rather than stripping 3'UTR from the exon list first. The old logic painted the entire last CDS exon as NMD-escape whenever the transcript had only one CDS exon, even when a 3'UTR intron sat far past the stop codon (e.g. NBDY: 207 bp of CDS over-painted for a junction 2.6 kb past the stop). - Add --rule1-mode {cds,mrna} (default cds): cds counts only CDS bp on the walk-back (paints up to 50 bp of CDS matching the rule label literally); mrna counts mRNA bp and clips to CDS (tracks the 55 bp rule literature). Documented in makeDoc. - Rule 4: when a 3'UTR intron exists, the last CDS-containing exon has a downstream EJC and is now eligible for the long-exon rule. - Mouseover lists contributing transcript accessions when 1-3 items collapse into a region; falls back to a count above that. - Add filterText/filterType/filterLabel on all three escape subtracks so a user can narrow the display to one transcript. - genePredNmdEsc: --gene-sym-field (default 17 for Gencode; pass 18 for MANE, whose HGNC symbol lives in bigGenePred geneName2). - Add findShortTxLongUtrIntron.py helper for finding MANE transcripts with long UTR introns (used to pick NMD edge-case test cases). Post-fix collapsed-region counts (--rule1-mode=cds): MANE 1.5: 67,752 Gencode V49: 233,375 RefSeq Curated: 112,356
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    3a62ea7e9a8cb3503586a0a78570331308c9bc58 Mon Apr 27 02:23:00 2026 -0700
    NMD Escape MANE: expose NM_ accession via labelFields. refs #33737 Per QA, the MANE subtrack now shows the NCBI RefSeq accession by default instead of the HGNC gene symbol, with the ENST and gene symbol still selectable via labelFields. - genePredNmdEsc: new --ncbi-id-field N option (default -1 = unused). When set, the named bigGenePred column is captured per-transcript and written into a new ncbiIds output column. For MANE pass 21. - genePredNmdEsc: new --no-collapse option. By default, regions with identical (chrom, start, end, rule) from multiple transcripts collapse into one row with comma-separated lists. With --no-collapse the script emits one row per (transcript, region). Used for MANE so each label-field column holds a single value: the 74 MANE Plus Clinical genes (e.g. LMNA) get two rows per region instead of one row with a two-element list. - nmdEscCollapsed.as: add lstring ncbiIds column. Schema is now bed9+3. - nmd.ra (nmdEscMane only): labelFields ncbiIds,name,transcripts; defaultLabelFields ncbiIds; labelSeparator " / ". Gencode and RefSeq subtracks unchanged - they default to the gene symbol (name column) and have an empty ncbiIds column. - doc/hg38/nmd.txt: bump all three bedToBigBed invocations to bed9+3 and document the --ncbi-id-field 21 + --no-collapse invocation for MANE. Counts: MANE 68,028 (--no-collapse); Gencode 233,375; RefSeq 112,356.
• src/hg/makeDb/trackDb/human/hg38/nmdDetective.html
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    4bd316f5f1ca47328bd3f9a181214b788055f0bc Tue Apr 21 13:29:26 2026 -0700
    NMD Escape QA round 3: switch RefSeq to curated, fix Rule 2 misclassification. refs #33737 Switched the NMD Escape RefSeq subtrack input from hg38.ncbiRefSeq.txt.gz (all) to hg38.ncbiRefSeqCurated.txt.gz (NM_/NR_ only, no XM_/XR_ predicted models) per Max's feedback. longLabel updated to "NCBI RefSeq Curated transcripts". Fixed Rule 2 in genePredNmdEsc to test rec["exonCount"]==1 instead of len(cdsExons)==1. The old test misclassified multi-exon transcripts with a single CDS exon (UTR introns) as "intronless" and silently suppressed their Rule 1/3/4 assignments via the if/else short-circuit. 3,253 RefSeq curated and ~2,000 Gencode transcripts reassigned from Rule 2 to Rules 1/3. Rebuilt both tracks. Added Rule 1 caveat to nmdEscTranscripts.html for transcripts with a penultimate coding exon shorter than 50 bp. Added reciprocal relatedTracks.ra entries for nmd <-> mane and nmd <-> ncbiRefSeq. QA cleanups: non-ASCII prime char replaced with &#8242;, mailing list links given target="_blank" across all three HTML pages, dead commented nmdGencode block removed from nmd.ra, AutoSQL field comments updated to cover Rule 4 color and the gene-symbol-to-transcript-ID fallback. Makedoc updated with the full Gencode + RefSeq pipeline and /gbdb symlinks.
• src/hg/makeDb/trackDb/human/hg38/nmdEscTranscripts.html
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    3972ba54c468ace338d4a5578de1d20bf6c1f9ec Mon Apr 20 15:39:26 2026 -0700
    Adding Rule 4 (long-exon rule, Lindeboom 2016) to NMD Escape tracks and releasing on Apr. 22, 2026. refs #33737 Script: added a fourth rule to genePredNmdEsc. Coding exons longer than 400 bp (excluding the last coding exon, which is already covered by the 50 bp rule) are flagged as NMD-escape regions. Rebuilt the Gencode and NCBI RefSeq bigBed files. trackDb: - nmd.ra: appended "/400nt" to the nmdEsc longLabels, set nmdEscGencode default visibility to dense so the track is visible in cart-reset views, changed all four NMDetective subtracks from "visibility full" to "visibility hide", updated pennantIcon to the Apr. 22, 2026 release date and anchor. - nmd.html: mention long internal exons in the overview description, update the rule count from three to four. - nmdEscTranscripts.html: add the long-exon rule to the rule list and color legend (gold, #FFD700), expand the Background section with mechanisms for the intronless, start-proximal, and long-exon rules, correct the 50 bp rule description to include the entire last coding exon, fix Lindeboom 2016 author initials (RG -> RGH). News: - newsarch.html: add the 2026-04-22 NMD Escape news entry covering all four rules, with acknowledgements to Guido Neidhardt and Andreas Lahner for suggesting the track and the Decipher Genome Browser team for inspiring the visualization. - indexNews.html: add the front-page news link. makedoc: - nmd.txt: dated note for the Rule 4 rebuild.
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    4bd316f5f1ca47328bd3f9a181214b788055f0bc Tue Apr 21 13:29:26 2026 -0700
    NMD Escape QA round 3: switch RefSeq to curated, fix Rule 2 misclassification. refs #33737 Switched the NMD Escape RefSeq subtrack input from hg38.ncbiRefSeq.txt.gz (all) to hg38.ncbiRefSeqCurated.txt.gz (NM_/NR_ only, no XM_/XR_ predicted models) per Max's feedback. longLabel updated to "NCBI RefSeq Curated transcripts". Fixed Rule 2 in genePredNmdEsc to test rec["exonCount"]==1 instead of len(cdsExons)==1. The old test misclassified multi-exon transcripts with a single CDS exon (UTR introns) as "intronless" and silently suppressed their Rule 1/3/4 assignments via the if/else short-circuit. 3,253 RefSeq curated and ~2,000 Gencode transcripts reassigned from Rule 2 to Rules 1/3. Rebuilt both tracks. Added Rule 1 caveat to nmdEscTranscripts.html for transcripts with a penultimate coding exon shorter than 50 bp. Added reciprocal relatedTracks.ra entries for nmd <-> mane and nmd <-> ncbiRefSeq. QA cleanups: non-ASCII prime char replaced with &#8242;, mailing list links given target="_blank" across all three HTML pages, dead commented nmdGencode block removed from nmd.ra, AutoSQL field comments updated to cover Rule 4 color and the gene-symbol-to-transcript-ID fallback. Makedoc updated with the full Gencode + RefSeq pipeline and /gbdb symlinks.
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    34d2eee845f5f45e571d1e153c632683b8a93f75 Tue Apr 21 16:17:53 2026 -0700
    Refine NMD Escape Rule 2 gate to "single coding exon and no 3'UTR intron". refs #33737 Previously Rule 2 required exonCount==1 (truly intronless). This overcorrected for single-CDS-exon transcripts whose only introns are in the 5'UTR: biologically these have no EJC downstream of the stop codon (5'UTR EJCs are cleared by the scanning 40S or sit upstream of the terminating ribosome) and are NMD-immune, but the code pushed them to Rules 1/3 under a less accurate "last coding exon" label. New gate: len(cdsExons) == 1 AND no exon-exon junction strictly downstream of the stop codon (strand-aware). Transcripts with a single coding exon but a 3'UTR intron correctly stay in Rules 1/3 because that intron deposits an EJC that can trigger NMD. 3,113 RefSeq Curated and 10,790 Gencode V49 transcripts move into Rule 2. 140 RefSeq and 1,135 Gencode single-CDS-exon transcripts with 3'UTR introns correctly remain in Rules 1/3. Description page and makedoc updated.
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    0151d00a4a1d73a78c35f6158c6c936ff338faeb Fri Apr 24 10:37:34 2026 -0700
    NMD Escape: MANE subtrack, Rule 1 bug fix, transcript filter. refs #33737 - Add nmdEscMane subtrack (MANE Select Plus Clinical 1.5), built from /gbdb/hg38/mane/mane.bb. Reuses nmdEscTranscripts.html. - Fix Rule 1: measure 50 bp upstream of the transcript's last splice junction (including 3'UTR introns) rather than stripping 3'UTR from the exon list first. The old logic painted the entire last CDS exon as NMD-escape whenever the transcript had only one CDS exon, even when a 3'UTR intron sat far past the stop codon (e.g. NBDY: 207 bp of CDS over-painted for a junction 2.6 kb past the stop). - Add --rule1-mode {cds,mrna} (default cds): cds counts only CDS bp on the walk-back (paints up to 50 bp of CDS matching the rule label literally); mrna counts mRNA bp and clips to CDS (tracks the 55 bp rule literature). Documented in makeDoc. - Rule 4: when a 3'UTR intron exists, the last CDS-containing exon has a downstream EJC and is now eligible for the long-exon rule. - Mouseover lists contributing transcript accessions when 1-3 items collapse into a region; falls back to a count above that. - Add filterText/filterType/filterLabel on all three escape subtracks so a user can narrow the display to one transcript. - genePredNmdEsc: --gene-sym-field (default 17 for Gencode; pass 18 for MANE, whose HGNC symbol lives in bigGenePred geneName2). - Add findShortTxLongUtrIntron.py helper for finding MANE transcripts with long UTR introns (used to pick NMD edge-case test cases). Post-fix collapsed-region counts (--rule1-mode=cds): MANE 1.5: 67,752 Gencode V49: 233,375 RefSeq Curated: 112,356
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    65091fe6f6487c23d650a144e947fc1c582d3f40 Tue Apr 21 02:16:16 2026 -0700
    abelSv: move under lrSv supertrack as short-read comparison subtrack Move the Abel et al. 2020 CCDG 17,795-genome SV callset from a top-level hg38 track to a subtrack of the lrSv supertrack (parallel to onekg3202Sr) and relabel shortLabel/longLabel to flag Illumina short-read provenance. The same bigBed is now visible on hg38 in the long-read SV browsing context. Also: - Clarify abelSv.html variant counts: 738,624 upstream unique SVs across both callsets, 737,998 after B37->hg38 liftOver (626 unmapped). B38=458,106, B37lift=279,892. - lrSv.html: fix triple-slash https:/// in the Ebert et al. Science reference URL. - bigBed.html: add closing </li> on the extra-fields pipe-separator bullet and tighten a comma in the same sentence. refs #36258, refs #37376
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    33e9019ef1b239ca1ab8114818f09ad65f58f2d0 Wed Apr 22 13:10:23 2026 -0700
    Release NMD Escape supertrack to beta + public. refs #33737 Drop the 'alpha' gate on include nmd.ra in hg38 trackDb.ra so the supertrack flows through the trackDb push pipeline to hgwbeta and the RR. /gbdb/hg38/nmd/*.bb files are already on the RR.
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    f30798ae5d11e88e0ab7eb2bcab634e253fd0675 Thu Apr 23 10:36:40 2026 -0700
    Add gnomAD MPC v4.1.1 track to hg38. New composite track under the gnomAD container showing per-variant MPC (Missense deleteriousness Prediction by Constraint) scores from gnomAD v4.1.1. Four bigWigs provide per-base scores (one per ALT nucleotide); a companion bigBed carries the ~250K multi-transcript variants with a per-transcript breakdown. Included via 'alpha' for QA review. refs #37434 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV50.html
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV50.ra
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra
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    689349fca5a4865a1891db8cd39d392657b2b09b Wed Apr 22 02:54:09 2026 -0700
    Replacing the subtrackUrl setting for faceted composites with subtrackUrls, which supports outlinks in multiple fields. refs #36320
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    e97b93d010dad47ba66947bcd40501d99b1545d5 Thu Apr 23 09:06:43 2026 -0700
    Using correct URL for ENCODE 4 experiment links, refs #36320
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.ra
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    689349fca5a4865a1891db8cd39d392657b2b09b Wed Apr 22 02:54:09 2026 -0700
    Replacing the subtrackUrl setting for faceted composites with subtrackUrls, which supports outlinks in multiple fields. refs #36320
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra
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    689349fca5a4865a1891db8cd39d392657b2b09b Wed Apr 22 02:54:09 2026 -0700
    Replacing the subtrackUrl setting for faceted composites with subtrackUrls, which supports outlinks in multiple fields. refs #36320
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    e75f51e55d0464a3e659a16a19514fdb9b33bdd9 Wed Apr 22 09:51:32 2026 -0700
    Also adding Experiment linkout to the EncodeReg4TfChip faceted composite, refs #36320
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    e97b93d010dad47ba66947bcd40501d99b1545d5 Thu Apr 23 09:06:43 2026 -0700
    Using correct URL for ENCODE 4 experiment links, refs #36320
• src/hg/makeDb/trackDb/human/hgsvc2Sv.html
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    9a11061ca6b40fe16bdfd09b1af53192f6c7c85b Tue Apr 21 08:13:02 2026 -0700
    lrSv: add HTML doc pages and conversion scripts for recent subtracks, + hs1 HGSVC3 Subtrack stanzas for these SV callsets landed in earlier commits but the conversion scripts and per-track HTML description pages were never added; trackDb therefore had no doc to serve. This commit catches up. Docs (new): - colorsDbSv.html CoLoRSdb 1,427-sample long-read SVs - gustafsonSv.html 1KG ONT 100 (Gustafson 2024, PMID 39358015) - hgsvc2Sv.html HGSVC2 (Ebert 2021, PMID 33632895) - hprc2Sv.html HPRC release-2 pangenome SVs (no PMID yet; see humanpangenome.org/hprc-data-release-2/) - onekg3202Sr.html 1KG 3202 Illumina SHORT-READ GATK-SV (Byrska-Bishop 2022, PMID 36055201) Scripts (new): - lrSvGustafson.as / lrSvGustafsonVcfToBed.py - lrSvHgsvc2.as / lrSvHgsvc2TsvToBed.py (merges insdel + inv tables) - lrSvHprc2.as / lrSvHprc2VcfToBed.py (streams wave-decomposed VCF, explodes multi-allelic rows, filters to SV-sized or INV) - lrSv1kg3202Sr.as / lrSv1kg3202SrVcfToBed.py HGSVC3 also on hs1: - hgsvc3Sv.html: note that the hs1 build is native (not lifted): HGSVC3 aligned all assemblies to both GRCh38 and T2T-CHM13 and released separate annotation tables per reference. Added the T2T-CHM13 source URL to the Methods section and the hs1 hgsvc3.bb download link to Data Access. - doc/hs1/lrSv.txt (new): hs1-specific wget + build steps; refers back to doc/hg38/lrSv.txt for the full process. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/hgsvc3Sv.html
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    9a11061ca6b40fe16bdfd09b1af53192f6c7c85b Tue Apr 21 08:13:02 2026 -0700
    lrSv: add HTML doc pages and conversion scripts for recent subtracks, + hs1 HGSVC3 Subtrack stanzas for these SV callsets landed in earlier commits but the conversion scripts and per-track HTML description pages were never added; trackDb therefore had no doc to serve. This commit catches up. Docs (new): - colorsDbSv.html CoLoRSdb 1,427-sample long-read SVs - gustafsonSv.html 1KG ONT 100 (Gustafson 2024, PMID 39358015) - hgsvc2Sv.html HGSVC2 (Ebert 2021, PMID 33632895) - hprc2Sv.html HPRC release-2 pangenome SVs (no PMID yet; see humanpangenome.org/hprc-data-release-2/) - onekg3202Sr.html 1KG 3202 Illumina SHORT-READ GATK-SV (Byrska-Bishop 2022, PMID 36055201) Scripts (new): - lrSvGustafson.as / lrSvGustafsonVcfToBed.py - lrSvHgsvc2.as / lrSvHgsvc2TsvToBed.py (merges insdel + inv tables) - lrSvHprc2.as / lrSvHprc2VcfToBed.py (streams wave-decomposed VCF, explodes multi-allelic rows, filters to SV-sized or INV) - lrSv1kg3202Sr.as / lrSv1kg3202SrVcfToBed.py HGSVC3 also on hs1: - hgsvc3Sv.html: note that the hs1 build is native (not lifted): HGSVC3 aligned all assemblies to both GRCh38 and T2T-CHM13 and released separate annotation tables per reference. Added the T2T-CHM13 source URL to the Methods section and the hs1 hgsvc3.bb download link to Data Access. - doc/hs1/lrSv.txt (new): hs1-specific wget + build steps; refers back to doc/hg38/lrSv.txt for the full process. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/hprc2Sv.html
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    9a11061ca6b40fe16bdfd09b1af53192f6c7c85b Tue Apr 21 08:13:02 2026 -0700
    lrSv: add HTML doc pages and conversion scripts for recent subtracks, + hs1 HGSVC3 Subtrack stanzas for these SV callsets landed in earlier commits but the conversion scripts and per-track HTML description pages were never added; trackDb therefore had no doc to serve. This commit catches up. Docs (new): - colorsDbSv.html CoLoRSdb 1,427-sample long-read SVs - gustafsonSv.html 1KG ONT 100 (Gustafson 2024, PMID 39358015) - hgsvc2Sv.html HGSVC2 (Ebert 2021, PMID 33632895) - hprc2Sv.html HPRC release-2 pangenome SVs (no PMID yet; see humanpangenome.org/hprc-data-release-2/) - onekg3202Sr.html 1KG 3202 Illumina SHORT-READ GATK-SV (Byrska-Bishop 2022, PMID 36055201) Scripts (new): - lrSvGustafson.as / lrSvGustafsonVcfToBed.py - lrSvHgsvc2.as / lrSvHgsvc2TsvToBed.py (merges insdel + inv tables) - lrSvHprc2.as / lrSvHprc2VcfToBed.py (streams wave-decomposed VCF, explodes multi-allelic rows, filters to SV-sized or INV) - lrSv1kg3202Sr.as / lrSv1kg3202SrVcfToBed.py HGSVC3 also on hs1: - hgsvc3Sv.html: note that the hs1 build is native (not lifted): HGSVC3 aligned all assemblies to both GRCh38 and T2T-CHM13 and released separate annotation tables per reference. Added the T2T-CHM13 source URL to the Methods section and the hs1 hgsvc3.bb download link to Data Access. - doc/hs1/lrSv.txt (new): hs1-specific wget + build steps; refers back to doc/hg38/lrSv.txt for the full process. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    40c7b6fb506ddde686cd56a976b8a07e46db775b Tue Apr 21 08:19:46 2026 -0700
    hprc2Sv: highlight alignments_v2.0.csv as authoritative file list Reframe the existing link to HPRC's alignments_v2.0.csv in the Methods section so it is clear that this CSV points to both the GRCh38 and CHM13 pangenome VCFs used for the track (not just the list of underlying assemblies). Existing S3 download links preserved. refs #36258
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/kwanhoSv.html
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    989d891c0c0a500e584d55f2f368b52f2abe5f1d Tue Apr 21 06:25:48 2026 -0700
    kwanhoSv: flag as preliminary, ask users to contact authors Mark the Kim et al. 2026 PD brain long-read SV subtrack as preliminary in its shortLabel and longLabel, and add a prominent warning banner at the top of the description page telling users to contact the authors (ASAP / Kim lab) before using the data, since the callset will be updated before publication. refs #36258
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/longReadVariants.ra
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    96e0a50a6dc4cba147be2dfed06775ccabf25378 Fri Apr 24 15:26:48 2026 -0700
    Fixing the bigDataUrl since the track disappeared on the RR, refs #36258
• src/hg/makeDb/trackDb/human/lrSv.html
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    f4d6633d6a724d7b682f9f49ed983e22a5e0975d Mon Apr 20 14:41:07 2026 -0700
    updating a few lrSv subtracks, and moving the colorsDbSnv track under the varFreqs track. refs #36642
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    65091fe6f6487c23d650a144e947fc1c582d3f40 Tue Apr 21 02:16:16 2026 -0700
    abelSv: move under lrSv supertrack as short-read comparison subtrack Move the Abel et al. 2020 CCDG 17,795-genome SV callset from a top-level hg38 track to a subtrack of the lrSv supertrack (parallel to onekg3202Sr) and relabel shortLabel/longLabel to flag Illumina short-read provenance. The same bigBed is now visible on hg38 in the long-read SV browsing context. Also: - Clarify abelSv.html variant counts: 738,624 upstream unique SVs across both callsets, 737,998 after B37->hg38 liftOver (626 unmapped). B38=458,106, B37lift=279,892. - lrSv.html: fix triple-slash https:/// in the Ebert et al. Science reference URL. - bigBed.html: add closing </li> on the extra-fields pipe-separator bullet and tighten a comma in the same sentence. refs #36258, refs #37376
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    06a482a2120d4d85c7c34fb5038213e07f595554 Tue Apr 21 15:00:21 2026 -0700
    lrSv: add tommoJpCnv short-read CNV comparator (multiWig) ToMMo 48KJPN-CNV Frequency Panel: copy-number variation frequencies from short-read whole-genome sequencing of 48,874 Japanese individuals (jMorp 20230828 release, GATK CNV germline workflow at 1 kb resolution). Published as a companion short-read comparator to the long-read tommoJpSv track. Rendered as a multiWig container with two bigWig subtracks (transparent overlay): tommoJpCnvLoss.bw counts samples at CN<2 per bin (red) and tommoJpCnvGain.bw counts samples at CN>2 per bin (green). Values are absolute carrier counts out of 48,874. 2,006,905 bins with at least one CNV carrier; bins that are wholly CN=2 are omitted. Files: - trackDb/human/lrSv.ra: new tommoJpCnv multiWig container - trackDb/human/tommoJpCnv.html: new doc page - trackDb/human/lrSv.html: summary-table row + per-track blurb - scripts/lrSv/lrSvTommoJpCnvVcfToBedGraph.py: VCF -> two bedGraphs - doc/hg38/lrSv.txt: wget, converter invocation, bigWig build steps refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    151410cc48b9b1f8b1cb9bee89b7004eca871c61 Wed Apr 22 09:03:35 2026 -0700
    lrSv: harmonize long-read shortLabels, add aprSv/cpc1Sv/abelSv to overview Normalize the shortLabel text of every long-read subtrack to the pattern "<Cohort> <N> SVs" (no commas in N): CoLoRSdb 1427, AoU 1027, ToMMo 333, GA4K 502, deCODE 3622, HPRC v2 233, Kim PD 100 prelim. Short-read comparators (abelSv, onekg3202Sr, tommoJpCnv) are left alone per user instruction. Also add three rows that were missing from lrSv.html's overview table: aprSv (Arab APR 53), cpc1Sv (CPC 58, HPRC-specific SVs removed) and abelSv (CCDG 17,795 Illumina short-read comparator). Updates the comparator footnote to mention both short-read rows. refs #36258
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    f058c8fe4601b223ff47468eb3525c05ccd03850 Wed Apr 22 09:17:17 2026 -0700
    srSv: new short-read SV supertrack, split out of lrSv Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr, tommoJpCnv) out of the Long-read SV supertrack into a new sibling supertrack srSv (Short-read SVs), so the lrSv collection contains only long-read callsets. Filter fields (svType, svLen, insLen, AC) are mirrored at the srSv supertrack level to keep the UX parallel to lrSv. - trackDb: new human/srSv.ra with the three subtrack stanzas and updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas removed from human/lrSv.ra. human/trackDb.ra now includes srSv.ra. Also a new human/srSv.html overview page; the SR rows and SR-specific paragraphs removed from human/lrSv.html. - Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/ {lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to scripts/srSv/ with git mv (history preserved) and renamed to drop the "lrSv" prefix. Internal path references in abelSvBuild.sh and abelSvVcfToBed.py updated. - makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and extended with the onekg3202Sr and tommoJpCnv sections moved from lrSv.txt. lrSv.txt leaves a pointer. - Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr, lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*. /gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and /gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/. refs #36258
• src/hg/makeDb/trackDb/human/lrSv.ra
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    65091fe6f6487c23d650a144e947fc1c582d3f40 Tue Apr 21 02:16:16 2026 -0700
    abelSv: move under lrSv supertrack as short-read comparison subtrack Move the Abel et al. 2020 CCDG 17,795-genome SV callset from a top-level hg38 track to a subtrack of the lrSv supertrack (parallel to onekg3202Sr) and relabel shortLabel/longLabel to flag Illumina short-read provenance. The same bigBed is now visible on hg38 in the long-read SV browsing context. Also: - Clarify abelSv.html variant counts: 738,624 upstream unique SVs across both callsets, 737,998 after B37->hg38 liftOver (626 unmapped). B38=458,106, B37lift=279,892. - lrSv.html: fix triple-slash https:/// in the Ebert et al. Science reference URL. - bigBed.html: add closing </li> on the extra-fields pipe-separator bullet and tighten a comma in the same sentence. refs #36258, refs #37376
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    989d891c0c0a500e584d55f2f368b52f2abe5f1d Tue Apr 21 06:25:48 2026 -0700
    kwanhoSv: flag as preliminary, ask users to contact authors Mark the Kim et al. 2026 PD brain long-read SV subtrack as preliminary in its shortLabel and longLabel, and add a prominent warning banner at the top of the description page telling users to contact the authors (ASAP / Kim lab) before using the data, since the callset will be updated before publication. refs #36258
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    5e4ca58df1b5bfe554fe5cc3309a39736ca256ee Tue Apr 21 08:08:52 2026 -0700
    cpc1Sv: restrict to the 58 CPC samples, drop HPRC-specific SVs Rewrite lrSvCpc1VcfToBed.py to identify the 58 CPC sample columns by name prefix (HIFI032* or RY*), recompute AC/AN/NS from those GT columns only, and skip any snarl that no CPC sample carries. The HPRC portion is already represented elsewhere in lrSv, so this keeps the track population-consistent with its label. Rebuild results: 46,092 snarl sites on hs1 (down from 97,205 when combined with HPRC), 36,030 lifted to hg38 (down from 81,261; 10,062 unmapped). Updates cpc1Sv.html, lrSv.ra labels, and the makeDoc. refs #36258
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    06a482a2120d4d85c7c34fb5038213e07f595554 Tue Apr 21 15:00:21 2026 -0700
    lrSv: add tommoJpCnv short-read CNV comparator (multiWig) ToMMo 48KJPN-CNV Frequency Panel: copy-number variation frequencies from short-read whole-genome sequencing of 48,874 Japanese individuals (jMorp 20230828 release, GATK CNV germline workflow at 1 kb resolution). Published as a companion short-read comparator to the long-read tommoJpSv track. Rendered as a multiWig container with two bigWig subtracks (transparent overlay): tommoJpCnvLoss.bw counts samples at CN<2 per bin (red) and tommoJpCnvGain.bw counts samples at CN>2 per bin (green). Values are absolute carrier counts out of 48,874. 2,006,905 bins with at least one CNV carrier; bins that are wholly CN=2 are omitted. Files: - trackDb/human/lrSv.ra: new tommoJpCnv multiWig container - trackDb/human/tommoJpCnv.html: new doc page - trackDb/human/lrSv.html: summary-table row + per-track blurb - scripts/lrSv/lrSvTommoJpCnvVcfToBedGraph.py: VCF -> two bedGraphs - doc/hg38/lrSv.txt: wget, converter invocation, bigWig build steps refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    1732661494ece5e645a9522f15a0f5922b035d1a Wed Apr 22 08:57:11 2026 -0700
    colorsDbSv: rebuild from pbsv+Jasmine source VCFs with richer AS Rebuild the CoLoRSdb SV bigBeds for hg38 and hs1 from the upstream pbsv+Jasmine VCFs that the CoLoRSdb project distributes directly. The previous bigBed stored AF as a string (breaking the numeric filter) and lacked insLen (causing a "filter on field insLen not in AS file" error under the supertrack-level filter). The new build: - stores AF as a float - adds a derived insLen column (alt-ref length delta for INS, 0 otherwise) so the shared lrSv insLen filter applies - keeps every INFO field from the source (SVTYPE, SVLEN, END, AC, AN, NS, AC_Hom, AC_Het, AC_Hemi, AF, HWE, ExcHet, nhomalt) plus REF/ALT - uses the canonical svName(TYPE, featLen, AC) label via lrSvCommon Record counts match the source VCFs: 426,239 on hg38 (59 MB) and 839,714 on hs1 (87 MB). /gbdb symlinks unchanged. The trackDb colorsDbSv stanza is updated to reference the new AS field names (acHom/acHet/acHemi, AF, AN) and to add the insLen filter. Also fixes a nearby `version 1.1` -> `dataVersion 1.1` typo in lrSv1kgOnt that was failing the tagTypes check. refs #36258
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    151410cc48b9b1f8b1cb9bee89b7004eca871c61 Wed Apr 22 09:03:35 2026 -0700
    lrSv: harmonize long-read shortLabels, add aprSv/cpc1Sv/abelSv to overview Normalize the shortLabel text of every long-read subtrack to the pattern "<Cohort> <N> SVs" (no commas in N): CoLoRSdb 1427, AoU 1027, ToMMo 333, GA4K 502, deCODE 3622, HPRC v2 233, Kim PD 100 prelim. Short-read comparators (abelSv, onekg3202Sr, tommoJpCnv) are left alone per user instruction. Also add three rows that were missing from lrSv.html's overview table: aprSv (Arab APR 53), cpc1Sv (CPC 58, HPRC-specific SVs removed) and abelSv (CCDG 17,795 Illumina short-read comparator). Updates the comparator footnote to mention both short-read rows. refs #36258
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    f058c8fe4601b223ff47468eb3525c05ccd03850 Wed Apr 22 09:17:17 2026 -0700
    srSv: new short-read SV supertrack, split out of lrSv Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr, tommoJpCnv) out of the Long-read SV supertrack into a new sibling supertrack srSv (Short-read SVs), so the lrSv collection contains only long-read callsets. Filter fields (svType, svLen, insLen, AC) are mirrored at the srSv supertrack level to keep the UX parallel to lrSv. - trackDb: new human/srSv.ra with the three subtrack stanzas and updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas removed from human/lrSv.ra. human/trackDb.ra now includes srSv.ra. Also a new human/srSv.html overview page; the SR rows and SR-specific paragraphs removed from human/lrSv.html. - Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/ {lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to scripts/srSv/ with git mv (history preserved) and renamed to drop the "lrSv" prefix. Internal path references in abelSvBuild.sh and abelSvVcfToBed.py updated. - makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and extended with the onekg3202Sr and tommoJpCnv sections moved from lrSv.txt. lrSv.txt leaves a pointer. - Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr, lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*. /gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and /gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/. refs #36258
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/lrSv1kgOnt.html
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/nmdEscape.ra
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    875dc5de11d5e0eb51e94cb37d5b74da447a6c7b Fri Apr 24 06:17:18 2026 -0700
    removing old nmdEscape track from tdb, no redmine
• src/hg/makeDb/trackDb/human/onekg3202Sr.html
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    9a11061ca6b40fe16bdfd09b1af53192f6c7c85b Tue Apr 21 08:13:02 2026 -0700
    lrSv: add HTML doc pages and conversion scripts for recent subtracks, + hs1 HGSVC3 Subtrack stanzas for these SV callsets landed in earlier commits but the conversion scripts and per-track HTML description pages were never added; trackDb therefore had no doc to serve. This commit catches up. Docs (new): - colorsDbSv.html CoLoRSdb 1,427-sample long-read SVs - gustafsonSv.html 1KG ONT 100 (Gustafson 2024, PMID 39358015) - hgsvc2Sv.html HGSVC2 (Ebert 2021, PMID 33632895) - hprc2Sv.html HPRC release-2 pangenome SVs (no PMID yet; see humanpangenome.org/hprc-data-release-2/) - onekg3202Sr.html 1KG 3202 Illumina SHORT-READ GATK-SV (Byrska-Bishop 2022, PMID 36055201) Scripts (new): - lrSvGustafson.as / lrSvGustafsonVcfToBed.py - lrSvHgsvc2.as / lrSvHgsvc2TsvToBed.py (merges insdel + inv tables) - lrSvHprc2.as / lrSvHprc2VcfToBed.py (streams wave-decomposed VCF, explodes multi-allelic rows, filters to SV-sized or INV) - lrSv1kg3202Sr.as / lrSv1kg3202SrVcfToBed.py HGSVC3 also on hs1: - hgsvc3Sv.html: note that the hs1 build is native (not lifted): HGSVC3 aligned all assemblies to both GRCh38 and T2T-CHM13 and released separate annotation tables per reference. Added the T2T-CHM13 source URL to the Methods section and the hs1 hgsvc3.bb download link to Data Access. - doc/hs1/lrSv.txt (new): hs1-specific wget + build steps; refers back to doc/hg38/lrSv.txt for the full process. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/primateAi.html
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    50466766840ded6cb8bd5cb868bdf2ff3f613bc0 Tue Apr 21 11:17:15 2026 -0700
    QA fixes for PrimateAI-3D track. Config (primateAi.ra): - Fix broken Ensembl transcript linkout: urls $S expanded to chromosome name; switch to the Ensembl transcript page with $$ - Add numeric filters on percentile and raw score (label notes the paper's 0.821 clinical threshold) - Add maxWindowToDraw 2000000 Data (primateAiToBigBed.py): - Change hardcoded strand '+' to '.': the source file has no strand column - Accept input/output paths as CLI args (previously hardcoded the hg38 input path) - Handle variable field count: ~2.4M rows in the hg19 source are missing the refseq column Description (primateAi.html): - Fix two broken hgTrackUi&... internal links to the Zoonomia 447-way track - Regenerate the first reference via getTrackReferences (wrong article number and wrong PMC ID in the previous text) - Fix the GitHub URL for the conversion script in Methods - Move the Zoonomia 447-way mention out of Description; rephrase the license note to describe precisely what is disabled relatedTracks.ra: - Add reciprocal cross-links for primateAi <-> alphaMissense (hg38), primateAi <-> revel (hg38 + hg19), and primateAi <-> promoterAi (hg38). Also includes promoterAi <-> alphaMissense cross-links. refs #37274 #37279
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    de2ccf6d827865f11d3c8edd9ceeb1b6394a7380 Tue Apr 21 18:22:59 2026 -0700
    PrimateAI-3D: label items by nucleotide change, add aaChange field and HTML mouseover. Variant analysts typically work at the nucleotide level, and the current item label (amino acid change) collapses distinguishable variants: ~17% of items share their (chrom, pos, AA-change) tuple with another item because of codon degeneracy (e.g. three C>A, C>G, C>T at the same position can all appear as "M>I"). Labeling by nucleotide change makes every item uniquely distinguishable (0.0% collisions on hg38, 0.1% on hg19 from overlapping transcripts). - primateAi.as: field 4 (name) is now "Nucleotide change (e.g. T>C)"; new field aaChange (placed before ref/alt) holds the amino acid change. - primateAiToBigBed.py: write name = "{ref}>{alt}", new aaChange column, and an HTML mouseover with terse labels (Var/AA/Score/Perc/Pred) and a colored prediction string. - primateAi.ra: add labelFields name,aaChange and defaultLabelFields name so users can toggle the on-feature label between nt change (default) and AA change. - primateAi.html: expand Display Conventions with the label-convention rationale and a legend for each mouseover field. refs #37274
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    30374e3fc3390902c35bb463510567f1b6f7a96e Wed Apr 22 13:44:44 2026 -0700
    PrimateAI-3D: clarify origin of the 0.821 threshold per Max. refs #37274 Description previously juxtaposed the paper's 0.821 clinical threshold with the 75/25 benign/pathogenic split in a way that implied the two were related. Per Max on the ticket: the 0.821 threshold comes from Gao et al. 2023 Fig. 5A (calibrated against de novo missense excess in a clinical cohort, n=7,238 pathogenic calls), and the "prediction" column values are Illumina's own calls — not a simple application of the 0.821 threshold (some variants below it are labeled pathogenic and vice versa).
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    6e61d3349b36cbcc01500c1483cc7bfbc141d9ea Wed Apr 22 13:47:33 2026 -0700
    PrimateAI-3D: tighten 0.821 threshold wording per the paper. refs #37274 Confirmed against Gao 2023 (PMC10713091): the calibration cohort is the Deciphering Developmental Disorders (DDD) neurodevelopmental cohort, not ClinVar. The cutoff was chosen so that the count of pathogenic calls (n=7,238) matched the excess of de novo missense mutations above the trinucleotide background expectation in that cohort.
• src/hg/makeDb/trackDb/human/primateAi.ra
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    50466766840ded6cb8bd5cb868bdf2ff3f613bc0 Tue Apr 21 11:17:15 2026 -0700
    QA fixes for PrimateAI-3D track. Config (primateAi.ra): - Fix broken Ensembl transcript linkout: urls $S expanded to chromosome name; switch to the Ensembl transcript page with $$ - Add numeric filters on percentile and raw score (label notes the paper's 0.821 clinical threshold) - Add maxWindowToDraw 2000000 Data (primateAiToBigBed.py): - Change hardcoded strand '+' to '.': the source file has no strand column - Accept input/output paths as CLI args (previously hardcoded the hg38 input path) - Handle variable field count: ~2.4M rows in the hg19 source are missing the refseq column Description (primateAi.html): - Fix two broken hgTrackUi&... internal links to the Zoonomia 447-way track - Regenerate the first reference via getTrackReferences (wrong article number and wrong PMC ID in the previous text) - Fix the GitHub URL for the conversion script in Methods - Move the Zoonomia 447-way mention out of Description; rephrase the license note to describe precisely what is disabled relatedTracks.ra: - Add reciprocal cross-links for primateAi <-> alphaMissense (hg38), primateAi <-> revel (hg38 + hg19), and primateAi <-> promoterAi (hg38). Also includes promoterAi <-> alphaMissense cross-links. refs #37274 #37279
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    de2ccf6d827865f11d3c8edd9ceeb1b6394a7380 Tue Apr 21 18:22:59 2026 -0700
    PrimateAI-3D: label items by nucleotide change, add aaChange field and HTML mouseover. Variant analysts typically work at the nucleotide level, and the current item label (amino acid change) collapses distinguishable variants: ~17% of items share their (chrom, pos, AA-change) tuple with another item because of codon degeneracy (e.g. three C>A, C>G, C>T at the same position can all appear as "M>I"). Labeling by nucleotide change makes every item uniquely distinguishable (0.0% collisions on hg38, 0.1% on hg19 from overlapping transcripts). - primateAi.as: field 4 (name) is now "Nucleotide change (e.g. T>C)"; new field aaChange (placed before ref/alt) holds the amino acid change. - primateAiToBigBed.py: write name = "{ref}>{alt}", new aaChange column, and an HTML mouseover with terse labels (Var/AA/Score/Perc/Pred) and a colored prediction string. - primateAi.ra: add labelFields name,aaChange and defaultLabelFields name so users can toggle the on-feature label between nt change (default) and AA change. - primateAi.html: expand Display Conventions with the label-convention rationale and a legend for each mouseover field. refs #37274
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    d07e0de4fba2fc825dd1fdaa37a7cf1f66e4721d Fri Apr 24 17:36:42 2026 -0700
    PrimateAI-3D: move /gbdb dir to _primateAi/ to match the underscore-prefix exclusion rule for hgdownload sync. refs #37274
• src/hg/makeDb/trackDb/human/promoterAi.html
  • lines changed 51, context: html, text, full: html, text
    f9a89b0e1ce3c937b4fbb879736c1619c35c271f Tue Apr 21 12:11:02 2026 -0700
    QA fixes for PromoterAI track. refs #37278 Description page: replaced the wrong reference (Gao et al. 2023, the PrimateAI-3D paper) with the actual PromoterAI citation (Jaganathan et al. Science 2025, PMID 40440429), corrected the score-direction wording (negative = under-expression, positive = over-expression, not "tolerated vs disruptive"), fixed the Data Access source link (Illumina BaseSpace, not the GitHub repo), and corrected the mouseover blurb to match mouseOverFunction noAverage behavior. Converter and AS: the overlap bigBed now carries the real per-transcript strand from the source TSV (was hardcoded '+'), with a new strands column in the AS, and the name field concatenates unique gene symbols so bidirectional-promoter items read as "HES4,ISG15" etc. BED score is now |PromoterAI|*1000 so scoreFilter is meaningful. Rewrote the converter to stream (sorted input), which drops peak memory from ~40 GB to a few MB. trackDb: added filterLabel/filterLimits on scoreDiff (the filter was unusable without labels), scoreFilter + scoreLabel, alwaysZero and autoScale off on the bigWig subtracks, color 200,0,0 / altColor 0,0,200 so signed bigWig bars draw red (over-expression) above zero and blue (under-expression) below, matching the overlap track itemRgb. Added maxWindowToDraw and maxItems on the overlap subtrack. Makedoc updated to describe the streaming pipeline, the new strands column, and the rebuild workflow.
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    6c567fd9a03e87610681a43d2183ebb43547d1ad Fri Apr 24 17:58:57 2026 -0700
    PromoterAI: review followups. refs #37278 Move /gbdb/hg38/promoterAi/ to /gbdb/hg38/_promoterAi/ to match the underscore-prefix exclusion rule for hgdownload sync (same pattern as PrimateAI-3D under refs #37274). bigDataUrls and the makedoc updated. Bump bigWig maxHeightPixels from 128:20:8 to 128:40:8 -- the peer-track default of 20 is too cramped for a signed -1..+1 score. Description page: drop the wrong primateai3d.basespace.illumina.com link in Data Access; PromoterAI is not on BaseSpace, it's distributed via the license agreement on the GitHub page (a download link is emailed after submission). Reword Data Access and Methods accordingly. Description page: add Illumina's recommended interpretation thresholds (|score| >= 0.1, >= 0.2, >= 0.5) from the PromoterAI GitHub README, with a note that higher cutoffs select smaller, higher-confidence sets.
• src/hg/makeDb/trackDb/human/promoterAi.ra
  • lines changed 24, context: html, text, full: html, text
    f9a89b0e1ce3c937b4fbb879736c1619c35c271f Tue Apr 21 12:11:02 2026 -0700
    QA fixes for PromoterAI track. refs #37278 Description page: replaced the wrong reference (Gao et al. 2023, the PrimateAI-3D paper) with the actual PromoterAI citation (Jaganathan et al. Science 2025, PMID 40440429), corrected the score-direction wording (negative = under-expression, positive = over-expression, not "tolerated vs disruptive"), fixed the Data Access source link (Illumina BaseSpace, not the GitHub repo), and corrected the mouseover blurb to match mouseOverFunction noAverage behavior. Converter and AS: the overlap bigBed now carries the real per-transcript strand from the source TSV (was hardcoded '+'), with a new strands column in the AS, and the name field concatenates unique gene symbols so bidirectional-promoter items read as "HES4,ISG15" etc. BED score is now |PromoterAI|*1000 so scoreFilter is meaningful. Rewrote the converter to stream (sorted input), which drops peak memory from ~40 GB to a few MB. trackDb: added filterLabel/filterLimits on scoreDiff (the filter was unusable without labels), scoreFilter + scoreLabel, alwaysZero and autoScale off on the bigWig subtracks, color 200,0,0 / altColor 0,0,200 so signed bigWig bars draw red (over-expression) above zero and blue (under-expression) below, matching the overlap track itemRgb. Added maxWindowToDraw and maxItems on the overlap subtrack. Makedoc updated to describe the streaming pipeline, the new strands column, and the rebuild workflow.
  • lines changed 9, context: html, text, full: html, text
    6c567fd9a03e87610681a43d2183ebb43547d1ad Fri Apr 24 17:58:57 2026 -0700
    PromoterAI: review followups. refs #37278 Move /gbdb/hg38/promoterAi/ to /gbdb/hg38/_promoterAi/ to match the underscore-prefix exclusion rule for hgdownload sync (same pattern as PrimateAI-3D under refs #37274). bigDataUrls and the makedoc updated. Bump bigWig maxHeightPixels from 128:20:8 to 128:40:8 -- the peer-track default of 20 is too cramped for a signed -1..+1 score. Description page: drop the wrong primateai3d.basespace.illumina.com link in Data Access; PromoterAI is not on BaseSpace, it's distributed via the license agreement on the GitHub page (a download link is emailed after submission). Reword Data Access and Methods accordingly. Description page: add Illumina's recommended interpretation thresholds (|score| >= 0.1, >= 0.2, >= 0.5) from the PromoterAI GitHub README, with a note that higher cutoffs select smaller, higher-confidence sets.
• src/hg/makeDb/trackDb/human/srSv.html
  • lines changed 105, context: html, text, full: html, text
    f058c8fe4601b223ff47468eb3525c05ccd03850 Wed Apr 22 09:17:17 2026 -0700
    srSv: new short-read SV supertrack, split out of lrSv Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr, tommoJpCnv) out of the Long-read SV supertrack into a new sibling supertrack srSv (Short-read SVs), so the lrSv collection contains only long-read callsets. Filter fields (svType, svLen, insLen, AC) are mirrored at the srSv supertrack level to keep the UX parallel to lrSv. - trackDb: new human/srSv.ra with the three subtrack stanzas and updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas removed from human/lrSv.ra. human/trackDb.ra now includes srSv.ra. Also a new human/srSv.html overview page; the SR rows and SR-specific paragraphs removed from human/lrSv.html. - Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/ {lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to scripts/srSv/ with git mv (history preserved) and renamed to drop the "lrSv" prefix. Internal path references in abelSvBuild.sh and abelSvVcfToBed.py updated. - makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and extended with the onekg3202Sr and tommoJpCnv sections moved from lrSv.txt. lrSv.txt leaves a pointer. - Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr, lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*. /gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and /gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/. refs #36258
• src/hg/makeDb/trackDb/human/srSv.ra
  • lines changed 137, context: html, text, full: html, text
    f058c8fe4601b223ff47468eb3525c05ccd03850 Wed Apr 22 09:17:17 2026 -0700
    srSv: new short-read SV supertrack, split out of lrSv Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr, tommoJpCnv) out of the Long-read SV supertrack into a new sibling supertrack srSv (Short-read SVs), so the lrSv collection contains only long-read callsets. Filter fields (svType, svLen, insLen, AC) are mirrored at the srSv supertrack level to keep the UX parallel to lrSv. - trackDb: new human/srSv.ra with the three subtrack stanzas and updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas removed from human/lrSv.ra. human/trackDb.ra now includes srSv.ra. Also a new human/srSv.html overview page; the SR rows and SR-specific paragraphs removed from human/lrSv.html. - Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/ {lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to scripts/srSv/ with git mv (history preserved) and renamed to drop the "lrSv" prefix. Internal path references in abelSvBuild.sh and abelSvVcfToBed.py updated. - makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and extended with the onekg3202Sr and tommoJpCnv sections moved from lrSv.txt. lrSv.txt leaves a pointer. - Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr, lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*. /gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and /gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/. refs #36258
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/svatalogSnv.html
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    695f40f9d6139a4df393522c067f1702aff8d3bd Wed Apr 22 03:13:39 2026 -0700
    varFreqs: add SVatalog 101 short-read SNV frequencies subtrack SNV/indel allele frequencies from the 101-sample GWAS SVatalog cohort (Chirmade et al. 2026, Heredity, PMID 41203876), called from 10X Genomics linked short-read WGS with GATK HaplotypeCaller v4.0.0.0 and phased with SHAPEIT v4.2.0. Sibling of the lrSv chirmade101Sv structural-variant track, which is built from the same 101 samples. 8,814,835 autosomal + chrX sites. Source release ships only AF; AC and AN are synthesized in the emitted VCF as AC=round(AF*202) and AN=202 (2*101 diploid), with the gnomAD v3.1 non-Finnish European AF and dbSNP rsID passed through as GNOMAD_NFE_AF and RSID info fields. VCF is bgzipped + tabix-indexed (172 MB + 1.6 MB .tbi). Files: - scripts/varFreqs/svatalogFreqToVcf.py (new): per-chrom allele-freq TSV -> single VCF with hg38 ##contig header - trackDb/human/varFreqs.ra: new svatalogSnv vcfTabix subtrack - trackDb/human/svatalogSnv.html (new): doc page - trackDb/human/varFreqs.html: new row in Available Datasets table - doc/hg38/varFreqs.txt: wget-free build block (input files were downloaded manually from Zenodo 13367574) Note: the All Databases Combined varFreqs bigBed has NOT been rebuilt to include this new source yet; a subsequent merge pass will add it. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/tommoJpCnv.html
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    06a482a2120d4d85c7c34fb5038213e07f595554 Tue Apr 21 15:00:21 2026 -0700
    lrSv: add tommoJpCnv short-read CNV comparator (multiWig) ToMMo 48KJPN-CNV Frequency Panel: copy-number variation frequencies from short-read whole-genome sequencing of 48,874 Japanese individuals (jMorp 20230828 release, GATK CNV germline workflow at 1 kb resolution). Published as a companion short-read comparator to the long-read tommoJpSv track. Rendered as a multiWig container with two bigWig subtracks (transparent overlay): tommoJpCnvLoss.bw counts samples at CN<2 per bin (red) and tommoJpCnvGain.bw counts samples at CN>2 per bin (green). Values are absolute carrier counts out of 48,874. 2,006,905 bins with at least one CNV carrier; bins that are wholly CN=2 are omitted. Files: - trackDb/human/lrSv.ra: new tommoJpCnv multiWig container - trackDb/human/tommoJpCnv.html: new doc page - trackDb/human/lrSv.html: summary-table row + per-track blurb - scripts/lrSv/lrSvTommoJpCnvVcfToBedGraph.py: VCF -> two bedGraphs - doc/hg38/lrSv.txt: wget, converter invocation, bigWig build steps refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/tommoJpSv.html
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    aaa2d4e074608d3e07ecf7d7a7e35cfa96b0a06d Tue Apr 21 08:29:35 2026 -0700
    tommoJpSv: fix broken jMorp download link The previous dataset-specific URL (tommo-jsv1-20211208-af) returned an error. Point to the general jMorp downloads page instead, where users can find the current ToMMo SV callset. refs #36258
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    06a482a2120d4d85c7c34fb5038213e07f595554 Tue Apr 21 15:00:21 2026 -0700
    lrSv: add tommoJpCnv short-read CNV comparator (multiWig) ToMMo 48KJPN-CNV Frequency Panel: copy-number variation frequencies from short-read whole-genome sequencing of 48,874 Japanese individuals (jMorp 20230828 release, GATK CNV germline workflow at 1 kb resolution). Published as a companion short-read comparator to the long-read tommoJpSv track. Rendered as a multiWig container with two bigWig subtracks (transparent overlay): tommoJpCnvLoss.bw counts samples at CN<2 per bin (red) and tommoJpCnvGain.bw counts samples at CN>2 per bin (green). Values are absolute carrier counts out of 48,874. 2,006,905 bins with at least one CNV carrier; bins that are wholly CN=2 are omitted. Files: - trackDb/human/lrSv.ra: new tommoJpCnv multiWig container - trackDb/human/tommoJpCnv.html: new doc page - trackDb/human/lrSv.html: summary-table row + per-track blurb - scripts/lrSv/lrSvTommoJpCnvVcfToBedGraph.py: VCF -> two bedGraphs - doc/hg38/lrSv.txt: wget, converter invocation, bigWig build steps refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    bac95a147f49cd331052e597006e04b3deee40fc Wed Apr 22 10:43:20 2026 -0700
    lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258
• src/hg/makeDb/trackDb/human/trackDb.ra
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    f058c8fe4601b223ff47468eb3525c05ccd03850 Wed Apr 22 09:17:17 2026 -0700
    srSv: new short-read SV supertrack, split out of lrSv Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr, tommoJpCnv) out of the Long-read SV supertrack into a new sibling supertrack srSv (Short-read SVs), so the lrSv collection contains only long-read callsets. Filter fields (svType, svLen, insLen, AC) are mirrored at the srSv supertrack level to keep the UX parallel to lrSv. - trackDb: new human/srSv.ra with the three subtrack stanzas and updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas removed from human/lrSv.ra. human/trackDb.ra now includes srSv.ra. Also a new human/srSv.html overview page; the SR rows and SR-specific paragraphs removed from human/lrSv.html. - Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/ {lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to scripts/srSv/ with git mv (history preserved) and renamed to drop the "lrSv" prefix. Internal path references in abelSvBuild.sh and abelSvVcfToBed.py updated. - makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and extended with the onekg3202Sr and tommoJpCnv sections moved from lrSv.txt. lrSv.txt leaves a pointer. - Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr, lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*. /gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and /gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/. refs #36258
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    875dc5de11d5e0eb51e94cb37d5b74da447a6c7b Fri Apr 24 06:17:18 2026 -0700
    removing old nmdEscape track from tdb, no redmine
• src/hg/makeDb/trackDb/human/varFreqs.html
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    695f40f9d6139a4df393522c067f1702aff8d3bd Wed Apr 22 03:13:39 2026 -0700
    varFreqs: add SVatalog 101 short-read SNV frequencies subtrack SNV/indel allele frequencies from the 101-sample GWAS SVatalog cohort (Chirmade et al. 2026, Heredity, PMID 41203876), called from 10X Genomics linked short-read WGS with GATK HaplotypeCaller v4.0.0.0 and phased with SHAPEIT v4.2.0. Sibling of the lrSv chirmade101Sv structural-variant track, which is built from the same 101 samples. 8,814,835 autosomal + chrX sites. Source release ships only AF; AC and AN are synthesized in the emitted VCF as AC=round(AF*202) and AN=202 (2*101 diploid), with the gnomAD v3.1 non-Finnish European AF and dbSNP rsID passed through as GNOMAD_NFE_AF and RSID info fields. VCF is bgzipped + tabix-indexed (172 MB + 1.6 MB .tbi). Files: - scripts/varFreqs/svatalogFreqToVcf.py (new): per-chrom allele-freq TSV -> single VCF with hg38 ##contig header - trackDb/human/varFreqs.ra: new svatalogSnv vcfTabix subtrack - trackDb/human/svatalogSnv.html (new): doc page - trackDb/human/varFreqs.html: new row in Available Datasets table - doc/hg38/varFreqs.txt: wget-free build block (input files were downloaded manually from Zenodo 13367574) Note: the All Databases Combined varFreqs bigBed has NOT been rebuilt to include this new source yet; a subsequent merge pass will add it. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/varFreqs.ra
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    f4d6633d6a724d7b682f9f49ed983e22a5e0975d Mon Apr 20 14:41:07 2026 -0700
    updating a few lrSv subtracks, and moving the colorsDbSnv track under the varFreqs track. refs #36642
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    a1f009b6019876a1bc845c6f0892b7bc942e368e Mon Apr 20 14:43:29 2026 -0700
    Hiding regeneron subtracks of varFreqs track again, no permission to distribute these.
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    366afa4a74c46ec6fb2b667a2902a873feec40cf Mon Apr 20 23:00:05 2026 -0700
    varFreqsAll: rebuild combined bigBed to include GA4K and CoLoRSdb Regenerate the All Databases Combined track with the two long-read PacBio subtracks (GA4K 552 samples and CoLoRSdb v1.2.0 1,027 samples) that were added to varFreqs since the March build. Source count rises from 21 to 23 databases; final bigBed is 37.7 GB with 1.17B records and 113 fields. Updates varFreqs.ra filterValues.sources and per- database AF/AC filters for the two new sources, and databases.tsv + varFreqs.txt (build notes). refs #36642
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    695f40f9d6139a4df393522c067f1702aff8d3bd Wed Apr 22 03:13:39 2026 -0700
    varFreqs: add SVatalog 101 short-read SNV frequencies subtrack SNV/indel allele frequencies from the 101-sample GWAS SVatalog cohort (Chirmade et al. 2026, Heredity, PMID 41203876), called from 10X Genomics linked short-read WGS with GATK HaplotypeCaller v4.0.0.0 and phased with SHAPEIT v4.2.0. Sibling of the lrSv chirmade101Sv structural-variant track, which is built from the same 101 samples. 8,814,835 autosomal + chrX sites. Source release ships only AF; AC and AN are synthesized in the emitted VCF as AC=round(AF*202) and AN=202 (2*101 diploid), with the gnomAD v3.1 non-Finnish European AF and dbSNP rsID passed through as GNOMAD_NFE_AF and RSID info fields. VCF is bgzipped + tabix-indexed (172 MB + 1.6 MB .tbi). Files: - scripts/varFreqs/svatalogFreqToVcf.py (new): per-chrom allele-freq TSV -> single VCF with hg38 ##contig header - trackDb/human/varFreqs.ra: new svatalogSnv vcfTabix subtrack - trackDb/human/svatalogSnv.html (new): doc page - trackDb/human/varFreqs.html: new row in Available Datasets table - doc/hg38/varFreqs.txt: wget-free build block (input files were downloaded manually from Zenodo 13367574) Note: the All Databases Combined varFreqs bigBed has NOT been rebuilt to include this new source yet; a subsequent merge pass will add it. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html
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    52ebb985f6e3658f463e971b7acd4c3959d36f92 Wed Apr 22 17:38:06 2026 -0700
    Enlarged classification diagram (40% to 60%) on the cCRE registry and Core Collection description pages. Updated the shortLabels on all 90 Core Collection subtracks with biosample + age + assay labels. refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/coreCollection.html
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    52ebb985f6e3658f463e971b7acd4c3959d36f92 Wed Apr 22 17:38:06 2026 -0700
    Enlarged classification diagram (40% to 60%) on the cCRE registry and Core Collection description pages. Updated the shortLabels on all 90 Core Collection subtracks with biosample + age + assay labels. refs #37131
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    563389a6e1bce94aafe4ec991c064e3d204670ff Wed Apr 22 18:16:44 2026 -0700
    Added signal track color descriptions (DNase green, H3K4me3 red, H3K27ac yellow, CTCF blue) to the mm10 Core Collection description page, with a note that the signal colors are independent from the cCRE classification colors. refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/developmentTimecourseM21mm10FPKM.html
  • lines changed 66, context: html, text, full: html, text
    26c4835e47a40f162ae82c0ea20e1997f42bc4ad Tue Apr 21 16:35:37 2026 -0700
    Moving shared HTML content in mouseDevTimecourse track description pages into shared include files using Claude. refs #37414
• src/hg/makeDb/trackDb/mouse/mm10/developmentTimecourseM21mm10TPM.html
  • lines changed 66, context: html, text, full: html, text
    26c4835e47a40f162ae82c0ea20e1997f42bc4ad Tue Apr 21 16:35:37 2026 -0700
    Moving shared HTML content in mouseDevTimecourse track description pages into shared include files using Claude. refs #37414
• src/hg/makeDb/trackDb/mouse/mm10/developmentTimecourseM4mm10FPKM.html
  • lines changed 66, context: html, text, full: html, text
    26c4835e47a40f162ae82c0ea20e1997f42bc4ad Tue Apr 21 16:35:37 2026 -0700
    Moving shared HTML content in mouseDevTimecourse track description pages into shared include files using Claude. refs #37414
• src/hg/makeDb/trackDb/mouse/mm10/developmentTimecourseM4mm10TPM.html
  • lines changed 66, context: html, text, full: html, text
    26c4835e47a40f162ae82c0ea20e1997f42bc4ad Tue Apr 21 16:35:37 2026 -0700
    Moving shared HTML content in mouseDevTimecourse track description pages into shared include files using Claude. refs #37414
• src/hg/makeDb/trackDb/mouse/mm10/encode4.ccres.ra
  • lines changed 90, context: html, text, full: html, text
    52ebb985f6e3658f463e971b7acd4c3959d36f92 Wed Apr 22 17:38:06 2026 -0700
    Enlarged classification diagram (40% to 60%) on the cCRE registry and Core Collection description pages. Updated the shortLabels on all 90 Core Collection subtracks with biosample + age + assay labels. refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra
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    8b86391ff90bd5b416b1650c4fdcf8199a7e9b3f Fri Apr 24 09:02:39 2026 -0700
    Fixing faceted subtrackUrls labels for mm10 ENCODE 4, refs #36320
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.ra
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    8b86391ff90bd5b416b1650c4fdcf8199a7e9b3f Fri Apr 24 09:02:39 2026 -0700
    Fixing faceted subtrackUrls labels for mm10 ENCODE 4, refs #36320
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra
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    8b86391ff90bd5b416b1650c4fdcf8199a7e9b3f Fri Apr 24 09:02:39 2026 -0700
    Fixing faceted subtrackUrls labels for mm10 ENCODE 4, refs #36320
• src/hg/makeDb/trackDb/mouse/mm10/mouseDevTimecourse.html
  • lines changed 67, context: html, text, full: html, text
    26c4835e47a40f162ae82c0ea20e1997f42bc4ad Tue Apr 21 16:35:37 2026 -0700
    Moving shared HTML content in mouseDevTimecourse track description pages into shared include files using Claude. refs #37414
• src/hg/makeDb/trackDb/mouse/mm39/developmentTimecourseM21mm39FPKM.html
  • lines changed 66, context: html, text, full: html, text
    26c4835e47a40f162ae82c0ea20e1997f42bc4ad Tue Apr 21 16:35:37 2026 -0700
    Moving shared HTML content in mouseDevTimecourse track description pages into shared include files using Claude. refs #37414
• src/hg/makeDb/trackDb/mouse/mm39/developmentTimecourseM21mm39TPM.html
  • lines changed 66, context: html, text, full: html, text
    26c4835e47a40f162ae82c0ea20e1997f42bc4ad Tue Apr 21 16:35:37 2026 -0700
    Moving shared HTML content in mouseDevTimecourse track description pages into shared include files using Claude. refs #37414
• src/hg/makeDb/trackDb/mouse/mm39/mouseDevTimecourse.html
  • lines changed 67, context: html, text, full: html, text
    26c4835e47a40f162ae82c0ea20e1997f42bc4ad Tue Apr 21 16:35:37 2026 -0700
    Moving shared HTML content in mouseDevTimecourse track description pages into shared include files using Claude. refs #37414
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM39.html
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    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM39.ra
  • lines changed 247, context: html, text, full: html, text
    b6aee4c6471cddebd638fec8dbb988c29a69bc22 Thu Apr 23 21:58:41 2026 -0700
    import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command
• src/hg/makeDb/trackDb/mouseDevTimecourseCreditsAndReferences.shared.html
  • lines changed 34, context: html, text, full: html, text
    26c4835e47a40f162ae82c0ea20e1997f42bc4ad Tue Apr 21 16:35:37 2026 -0700
    Moving shared HTML content in mouseDevTimecourse track description pages into shared include files using Claude. refs #37414
• src/hg/makeDb/trackDb/mouseDevTimecourseDisplay.shared.html
  • lines changed 32, context: html, text, full: html, text
    26c4835e47a40f162ae82c0ea20e1997f42bc4ad Tue Apr 21 16:35:37 2026 -0700
    Moving shared HTML content in mouseDevTimecourse track description pages into shared include files using Claude. refs #37414
• src/hg/makeDb/trackDb/relatedTracks.ra
  • lines changed 15, context: html, text, full: html, text
    50466766840ded6cb8bd5cb868bdf2ff3f613bc0 Tue Apr 21 11:17:15 2026 -0700
    QA fixes for PrimateAI-3D track. Config (primateAi.ra): - Fix broken Ensembl transcript linkout: urls $S expanded to chromosome name; switch to the Ensembl transcript page with $$ - Add numeric filters on percentile and raw score (label notes the paper's 0.821 clinical threshold) - Add maxWindowToDraw 2000000 Data (primateAiToBigBed.py): - Change hardcoded strand '+' to '.': the source file has no strand column - Accept input/output paths as CLI args (previously hardcoded the hg38 input path) - Handle variable field count: ~2.4M rows in the hg19 source are missing the refseq column Description (primateAi.html): - Fix two broken hgTrackUi&... internal links to the Zoonomia 447-way track - Regenerate the first reference via getTrackReferences (wrong article number and wrong PMC ID in the previous text) - Fix the GitHub URL for the conversion script in Methods - Move the Zoonomia 447-way mention out of Description; rephrase the license note to describe precisely what is disabled relatedTracks.ra: - Add reciprocal cross-links for primateAi <-> alphaMissense (hg38), primateAi <-> revel (hg38 + hg19), and primateAi <-> promoterAi (hg38). Also includes promoterAi <-> alphaMissense cross-links. refs #37274 #37279
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    4bd316f5f1ca47328bd3f9a181214b788055f0bc Tue Apr 21 13:29:26 2026 -0700
    NMD Escape QA round 3: switch RefSeq to curated, fix Rule 2 misclassification. refs #33737 Switched the NMD Escape RefSeq subtrack input from hg38.ncbiRefSeq.txt.gz (all) to hg38.ncbiRefSeqCurated.txt.gz (NM_/NR_ only, no XM_/XR_ predicted models) per Max's feedback. longLabel updated to "NCBI RefSeq Curated transcripts". Fixed Rule 2 in genePredNmdEsc to test rec["exonCount"]==1 instead of len(cdsExons)==1. The old test misclassified multi-exon transcripts with a single CDS exon (UTR introns) as "intronless" and silently suppressed their Rule 1/3/4 assignments via the if/else short-circuit. 3,253 RefSeq curated and ~2,000 Gencode transcripts reassigned from Rule 2 to Rules 1/3. Rebuilt both tracks. Added Rule 1 caveat to nmdEscTranscripts.html for transcripts with a penultimate coding exon shorter than 50 bp. Added reciprocal relatedTracks.ra entries for nmd <-> mane and nmd <-> ncbiRefSeq. QA cleanups: non-ASCII prime char replaced with &#8242;, mailing list links given target="_blank" across all three HTML pages, dead commented nmdGencode block removed from nmd.ra, AutoSQL field comments updated to cover Rule 4 color and the gene-symbol-to-transcript-ID fallback. Makedoc updated with the full Gencode + RefSeq pipeline and /gbdb symlinks.
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    888e7470c14eeecdca310ed36bb45c3c00ae8052 Tue Apr 21 15:14:04 2026 -0700
    QA fixes for MPRA superTrack. refs #37359 Fix broken mpraVarDb bigDataUrl — pointed at /gbdb/hg38/mpra/mpravardb.bb but the file is at /gbdb/hg38/mpra/mpravardb/mpravardb.bb, causing hgTrackDb -strict to silently drop the subtrack. Rebuild mpravardb.bb after two fixes in mpravardbToBed.py: sanitize UTF-8 in user-visible string fields (curly quotes, primes, NBSP mojibake) that the browser does not transcode, eliminating ~246k non-ASCII occurrences across 42% of rows; and change safe_float / pval_to_score to write NaN and return score 0 for NA / out-of-range p-values instead of 0.0 and score 1000 (previously inflated untested variants to the top of score-sorted views). trackDb stanza cleanup: shorten mpraVarDb longLabel, drop superfluous type bed 4 from superTrack, make bigBed 9+13 explicit, remove redundant mouseOverField, align parent mpra on, add filterValues for cell_line/assay/cellLine and filterByRange sliders for percentile_rank / fdr / log2FC, add labelFields and maxWindowToDraw. Description pages: add cross-species disclosure (mouse reporter cells used to assay human sequences), update mpraVarDb header to post-liftOver count 239,028 with Studies-table footnote, fix mpraVarDb.html download-server paths, soften imprecise "51 MPRA experiments" claim in mpra.html and mprabase.html. relatedTracks.ra: reciprocal mpra <-> wgEncodeReg4 and mpra <-> cCREs. Expand mpra.txt makedoc with upstream provenance and QA-rebuild log.
• src/hg/makeDb/trackDb/tagTypes.tab
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    689349fca5a4865a1891db8cd39d392657b2b09b Wed Apr 22 02:54:09 2026 -0700
    Replacing the subtrackUrl setting for faceted composites with subtrackUrls, which supports outlinks in multiple fields. refs #36320
• src/hg/makeDb/trackDb/zebrafish/danRer11/choriCloneEnds.html
  • lines changed 142, context: html, text, full: html, text
    d93c426ef1ad5fbb32b754408599eaf380a199e5 Tue Apr 21 13:34:58 2026 -0700
    choriCloneEnds: reorganize danRer11 CHORI BAC clone end placements as a superTrack, refs #35059 - Rename ncbiCloneEndsCH1073 to choriCloneEnds throughout (trackDb, HTML, makeDoc, scripts dir, /hive and /gbdb layout). User-visible label is now "CHORI Clones" since all three libraries (CH1073, CH73, CH211) are CHORI/BACPAC BAC libraries; data source (NCBI Clone DB) is cited in Methods. - Wrap the existing CH1073 track in a choriCloneEnds superTrack and add two new subtracks built from the parallel unique_concordant GFFs at ftp.ncbi.nih.gov/repository/clone/reports/Danio_rerio/ : CH73 (99,141 placements, 23 oversize) CH211 (70,231 placements, 46 oversize) CH1073 is rebuilt with the same pipeline (210,777 placements). - Build all three bigBeds with -extraIndex=name and register searchTable / searchType bigBed stanzas with searchIndex name on each subtrack, so clone names (CH1073-100A1, CH73-1A1, CH211-1A1, ...) resolve from the Genome Browser position box. - Single shared HTML description page; Methods now links to the NCBI FTP source and to the UCSC makeDoc and scripts dir on GitHub. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/zebrafish/danRer11/choriCloneEnds.ra
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    d93c426ef1ad5fbb32b754408599eaf380a199e5 Tue Apr 21 13:34:58 2026 -0700
    choriCloneEnds: reorganize danRer11 CHORI BAC clone end placements as a superTrack, refs #35059 - Rename ncbiCloneEndsCH1073 to choriCloneEnds throughout (trackDb, HTML, makeDoc, scripts dir, /hive and /gbdb layout). User-visible label is now "CHORI Clones" since all three libraries (CH1073, CH73, CH211) are CHORI/BACPAC BAC libraries; data source (NCBI Clone DB) is cited in Methods. - Wrap the existing CH1073 track in a choriCloneEnds superTrack and add two new subtracks built from the parallel unique_concordant GFFs at ftp.ncbi.nih.gov/repository/clone/reports/Danio_rerio/ : CH73 (99,141 placements, 23 oversize) CH211 (70,231 placements, 46 oversize) CH1073 is rebuilt with the same pipeline (210,777 placements). - Build all three bigBeds with -extraIndex=name and register searchTable / searchType bigBed stanzas with searchIndex name on each subtrack, so clone names (CH1073-100A1, CH73-1A1, CH211-1A1, ...) resolve from the Genome Browser position box. - Single shared HTML description page; Methods now links to the NCBI FTP source and to the UCSC makeDoc and scripts dir on GitHub. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/zebrafish/danRer11/ncbiCloneEndsCH1073.html
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    8faeb3cba60c7cb842bc17c17a57c9b53ef1b478 Tue Apr 21 02:51:32 2026 -0700
    ncbiCloneEndsCH1073: add NCBI CH1073 BAC library clone end placements track on danRer11, refs #35059 210,777 unique-concordant clone-insert placements from NCBI's CH1073 (RZPD-1073 / DanioKey) library clone report. Separate from the existing bacEndPairsLift (danRer4 -> danRer11 UCSC-BLAT lift), which is left in place. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 123, context: html, text, full: html, text
    d93c426ef1ad5fbb32b754408599eaf380a199e5 Tue Apr 21 13:34:58 2026 -0700
    choriCloneEnds: reorganize danRer11 CHORI BAC clone end placements as a superTrack, refs #35059 - Rename ncbiCloneEndsCH1073 to choriCloneEnds throughout (trackDb, HTML, makeDoc, scripts dir, /hive and /gbdb layout). User-visible label is now "CHORI Clones" since all three libraries (CH1073, CH73, CH211) are CHORI/BACPAC BAC libraries; data source (NCBI Clone DB) is cited in Methods. - Wrap the existing CH1073 track in a choriCloneEnds superTrack and add two new subtracks built from the parallel unique_concordant GFFs at ftp.ncbi.nih.gov/repository/clone/reports/Danio_rerio/ : CH73 (99,141 placements, 23 oversize) CH211 (70,231 placements, 46 oversize) CH1073 is rebuilt with the same pipeline (210,777 placements). - Build all three bigBeds with -extraIndex=name and register searchTable / searchType bigBed stanzas with searchIndex name on each subtrack, so clone names (CH1073-100A1, CH73-1A1, CH211-1A1, ...) resolve from the Genome Browser position box. - Single shared HTML description page; Methods now links to the NCBI FTP source and to the UCSC makeDoc and scripts dir on GitHub. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/zebrafish/danRer11/ncbiCloneEndsCH1073.ra
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    8faeb3cba60c7cb842bc17c17a57c9b53ef1b478 Tue Apr 21 02:51:32 2026 -0700
    ncbiCloneEndsCH1073: add NCBI CH1073 BAC library clone end placements track on danRer11, refs #35059 210,777 unique-concordant clone-insert placements from NCBI's CH1073 (RZPD-1073 / DanioKey) library clone report. Separate from the existing bacEndPairsLift (danRer4 -> danRer11 UCSC-BLAT lift), which is left in place. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    d93c426ef1ad5fbb32b754408599eaf380a199e5 Tue Apr 21 13:34:58 2026 -0700
    choriCloneEnds: reorganize danRer11 CHORI BAC clone end placements as a superTrack, refs #35059 - Rename ncbiCloneEndsCH1073 to choriCloneEnds throughout (trackDb, HTML, makeDoc, scripts dir, /hive and /gbdb layout). User-visible label is now "CHORI Clones" since all three libraries (CH1073, CH73, CH211) are CHORI/BACPAC BAC libraries; data source (NCBI Clone DB) is cited in Methods. - Wrap the existing CH1073 track in a choriCloneEnds superTrack and add two new subtracks built from the parallel unique_concordant GFFs at ftp.ncbi.nih.gov/repository/clone/reports/Danio_rerio/ : CH73 (99,141 placements, 23 oversize) CH211 (70,231 placements, 46 oversize) CH1073 is rebuilt with the same pipeline (210,777 placements). - Build all three bigBeds with -extraIndex=name and register searchTable / searchType bigBed stanzas with searchIndex name on each subtrack, so clone names (CH1073-100A1, CH73-1A1, CH211-1A1, ...) resolve from the Genome Browser position box. - Single shared HTML description page; Methods now links to the NCBI FTP source and to the UCSC makeDoc and scripts dir on GitHub. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra
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    8faeb3cba60c7cb842bc17c17a57c9b53ef1b478 Tue Apr 21 02:51:32 2026 -0700
    ncbiCloneEndsCH1073: add NCBI CH1073 BAC library clone end placements track on danRer11, refs #35059 210,777 unique-concordant clone-insert placements from NCBI's CH1073 (RZPD-1073 / DanioKey) library clone report. Separate from the existing bacEndPairsLift (danRer4 -> danRer11 UCSC-BLAT lift), which is left in place. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    d93c426ef1ad5fbb32b754408599eaf380a199e5 Tue Apr 21 13:34:58 2026 -0700
    choriCloneEnds: reorganize danRer11 CHORI BAC clone end placements as a superTrack, refs #35059 - Rename ncbiCloneEndsCH1073 to choriCloneEnds throughout (trackDb, HTML, makeDoc, scripts dir, /hive and /gbdb layout). User-visible label is now "CHORI Clones" since all three libraries (CH1073, CH73, CH211) are CHORI/BACPAC BAC libraries; data source (NCBI Clone DB) is cited in Methods. - Wrap the existing CH1073 track in a choriCloneEnds superTrack and add two new subtracks built from the parallel unique_concordant GFFs at ftp.ncbi.nih.gov/repository/clone/reports/Danio_rerio/ : CH73 (99,141 placements, 23 oversize) CH211 (70,231 placements, 46 oversize) CH1073 is rebuilt with the same pipeline (210,777 placements). - Build all three bigBeds with -extraIndex=name and register searchTable / searchType bigBed stanzas with searchIndex name on each subtrack, so clone names (CH1073-100A1, CH73-1A1, CH211-1A1, ...) resolve from the Genome Browser position box. - Single shared HTML description page; Methods now links to the NCBI FTP source and to the UCSC makeDoc and scripts dir on GitHub. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/utils/automation/kegAlign.json.ga
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    46668bb54c3c8a7a57bda515be6881edb2382563 Wed Apr 22 14:55:23 2026 -0700
    correctly connecting scoringMatrix input to kegAlign scores refs #31811
• src/hg/utils/mafToBigMafSummary/mafToBigMafSummary.c
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    cc610239716fe32f9c774d98a71f75e8c6b5fba3 Tue Apr 21 17:23:50 2026 -0700
    mafToBigMafSummary: new utility that emits bed3+4 input ready for bedToBigBed -as=mafSummary.as, replacing the hgLoadMafSummary -test / cut -f2- / sort hack documented in bigMaf.html. Companion to mafToBigMaf. The summary scoring/merging logic is intentionally duplicated from hgLoadMafSummary.c (see header comment) — that code is stable and refactoring would force retesting all the makedocs that call hgLoadMafSummary. Also fixes a bug in the duplicated copy of mafSplitSrcGetChrom: the original errAborts on plain 'hg38.chrY' style master src because of an inverted differentString check; rewritten with cleaner correct logic. Updates bigMaf.html and trackDb/trackDbLibrary.shtml to reference the new tool. refs #37404
• src/hg/utils/mafToBigMafSummary/makefile
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    cc610239716fe32f9c774d98a71f75e8c6b5fba3 Tue Apr 21 17:23:50 2026 -0700
    mafToBigMafSummary: new utility that emits bed3+4 input ready for bedToBigBed -as=mafSummary.as, replacing the hgLoadMafSummary -test / cut -f2- / sort hack documented in bigMaf.html. Companion to mafToBigMaf. The summary scoring/merging logic is intentionally duplicated from hgLoadMafSummary.c (see header comment) — that code is stable and refactoring would force retesting all the makedocs that call hgLoadMafSummary. Also fixes a bug in the duplicated copy of mafSplitSrcGetChrom: the original errAborts on plain 'hg38.chrY' style master src because of an inverted differentString check; rewritten with cleaner correct logic. Updates bigMaf.html and trackDb/trackDbLibrary.shtml to reference the new tool. refs #37404
• src/hg/utils/mafToBigMafSummary/tests/expected/testDot.bed
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    cc610239716fe32f9c774d98a71f75e8c6b5fba3 Tue Apr 21 17:23:50 2026 -0700
    mafToBigMafSummary: new utility that emits bed3+4 input ready for bedToBigBed -as=mafSummary.as, replacing the hgLoadMafSummary -test / cut -f2- / sort hack documented in bigMaf.html. Companion to mafToBigMaf. The summary scoring/merging logic is intentionally duplicated from hgLoadMafSummary.c (see header comment) — that code is stable and refactoring would force retesting all the makedocs that call hgLoadMafSummary. Also fixes a bug in the duplicated copy of mafSplitSrcGetChrom: the original errAborts on plain 'hg38.chrY' style master src because of an inverted differentString check; rewritten with cleaner correct logic. Updates bigMaf.html and trackDb/trackDbLibrary.shtml to reference the new tool. refs #37404
• src/hg/utils/mafToBigMafSummary/tests/expected/testPipe.bed
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    cc610239716fe32f9c774d98a71f75e8c6b5fba3 Tue Apr 21 17:23:50 2026 -0700
    mafToBigMafSummary: new utility that emits bed3+4 input ready for bedToBigBed -as=mafSummary.as, replacing the hgLoadMafSummary -test / cut -f2- / sort hack documented in bigMaf.html. Companion to mafToBigMaf. The summary scoring/merging logic is intentionally duplicated from hgLoadMafSummary.c (see header comment) — that code is stable and refactoring would force retesting all the makedocs that call hgLoadMafSummary. Also fixes a bug in the duplicated copy of mafSplitSrcGetChrom: the original errAborts on plain 'hg38.chrY' style master src because of an inverted differentString check; rewritten with cleaner correct logic. Updates bigMaf.html and trackDb/trackDbLibrary.shtml to reference the new tool. refs #37404
• src/hg/utils/mafToBigMafSummary/tests/input/testDot.maf
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    cc610239716fe32f9c774d98a71f75e8c6b5fba3 Tue Apr 21 17:23:50 2026 -0700
    mafToBigMafSummary: new utility that emits bed3+4 input ready for bedToBigBed -as=mafSummary.as, replacing the hgLoadMafSummary -test / cut -f2- / sort hack documented in bigMaf.html. Companion to mafToBigMaf. The summary scoring/merging logic is intentionally duplicated from hgLoadMafSummary.c (see header comment) — that code is stable and refactoring would force retesting all the makedocs that call hgLoadMafSummary. Also fixes a bug in the duplicated copy of mafSplitSrcGetChrom: the original errAborts on plain 'hg38.chrY' style master src because of an inverted differentString check; rewritten with cleaner correct logic. Updates bigMaf.html and trackDb/trackDbLibrary.shtml to reference the new tool. refs #37404
• src/hg/utils/mafToBigMafSummary/tests/input/testPipe.maf
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    cc610239716fe32f9c774d98a71f75e8c6b5fba3 Tue Apr 21 17:23:50 2026 -0700
    mafToBigMafSummary: new utility that emits bed3+4 input ready for bedToBigBed -as=mafSummary.as, replacing the hgLoadMafSummary -test / cut -f2- / sort hack documented in bigMaf.html. Companion to mafToBigMaf. The summary scoring/merging logic is intentionally duplicated from hgLoadMafSummary.c (see header comment) — that code is stable and refactoring would force retesting all the makedocs that call hgLoadMafSummary. Also fixes a bug in the duplicated copy of mafSplitSrcGetChrom: the original errAborts on plain 'hg38.chrY' style master src because of an inverted differentString check; rewritten with cleaner correct logic. Updates bigMaf.html and trackDb/trackDbLibrary.shtml to reference the new tool. refs #37404
• src/hg/utils/mafToBigMafSummary/tests/makefile
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    cc610239716fe32f9c774d98a71f75e8c6b5fba3 Tue Apr 21 17:23:50 2026 -0700
    mafToBigMafSummary: new utility that emits bed3+4 input ready for bedToBigBed -as=mafSummary.as, replacing the hgLoadMafSummary -test / cut -f2- / sort hack documented in bigMaf.html. Companion to mafToBigMaf. The summary scoring/merging logic is intentionally duplicated from hgLoadMafSummary.c (see header comment) — that code is stable and refactoring would force retesting all the makedocs that call hgLoadMafSummary. Also fixes a bug in the duplicated copy of mafSplitSrcGetChrom: the original errAborts on plain 'hg38.chrY' style master src because of an inverted differentString check; rewritten with cleaner correct logic. Updates bigMaf.html and trackDb/trackDbLibrary.shtml to reference the new tool. refs #37404
• src/hg/utils/makefile
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    cc610239716fe32f9c774d98a71f75e8c6b5fba3 Tue Apr 21 17:23:50 2026 -0700
    mafToBigMafSummary: new utility that emits bed3+4 input ready for bedToBigBed -as=mafSummary.as, replacing the hgLoadMafSummary -test / cut -f2- / sort hack documented in bigMaf.html. Companion to mafToBigMaf. The summary scoring/merging logic is intentionally duplicated from hgLoadMafSummary.c (see header comment) — that code is stable and refactoring would force retesting all the makedocs that call hgLoadMafSummary. Also fixes a bug in the duplicated copy of mafSplitSrcGetChrom: the original errAborts on plain 'hg38.chrY' style master src because of an inverted differentString check; rewritten with cleaner correct logic. Updates bigMaf.html and trackDb/trackDbLibrary.shtml to reference the new tool. refs #37404
• src/hg/utils/otto/genCC/doGenCC.py
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    7bf5a5c3241a66ba15f9763638a04d072f4b9b76 Fri Apr 24 12:22:11 2026 -0700
    Moving the 'if args.force' condition to the begining of the function since the md5sum checks are not needed if we are going to run the update manually. Addressing feedback from code review, refs #37417
• src/hg/utils/otto/otto.crontab
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    1915cefe1c6dd5746ee2c3e8a9ba9cfd4ad4e3b5 Tue Apr 21 14:45:24 2026 -0700
    turning on ottoRequest watch script refs #31811
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    f841658912e8c8441e745b2bfdbb86b7c270d811 Tue Apr 21 14:52:59 2026 -0700
    run ottoRequest.py every minute refs #31811
• src/hg/utils/otto/ottoCompareGitVsHiveFiles.py
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    43cdea8bbdc9cc2a3f84eb908763a86e88872afc Tue Apr 21 15:19:17 2026 -0700
    Updating the otto compare script to also print the timestamp for the file on git and hive. This way we can determine which source needs to be updated, no Redmine.
• src/hg/utils/otto/userRequests/README.txt
  • lines changed 29, context: html, text, full: html, text
    584b69eff038b10c2176d2b9299c356af21288cc Wed Apr 22 16:30:53 2026 -0700
    initial scripts to run the galaxy workflow based off of the ottoRequest table entries refs #31811
  • lines changed 68, context: html, text, full: html, text
    d8ade6071b7e59f93d5b703b3c024b345871dce1 Fri Apr 24 08:55:58 2026 -0700
    becoming complete process refs #31811
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    f5cece60b38bd8c2cfd57acf2abb972d66edb6d9 Fri Apr 24 11:43:36 2026 -0700
    rename doneStatus to just status and correctly set status codes refs #31811
• src/hg/utils/otto/userRequests/dbDb.name.clade.tsv
  • lines changed 239, context: html, text, full: html, text
    584b69eff038b10c2176d2b9299c356af21288cc Wed Apr 22 16:30:53 2026 -0700
    initial scripts to run the galaxy workflow based off of the ottoRequest table entries refs #31811
• src/hg/utils/otto/userRequests/ottoRequest.py
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    fcfb91470c294d3b991dbd0d24cba67de9ed65cb Tue Apr 21 14:20:57 2026 -0700
    create ottoRequest cron watch script refs #31811
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    678618e8499dc5e281ed6a1fe18da71e43fa4b3a Wed Apr 22 14:39:31 2026 -0700
    Commenting out a line in the script to match the version running on hive, no Redmine.
  • lines changed 41, context: html, text, full: html, text
    398e258ed1330421291f943298e7f801f7b05bf8 Thu Apr 23 15:05:02 2026 -0700
    and send notification email to the requesting user refs #31811
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    f5cece60b38bd8c2cfd57acf2abb972d66edb6d9 Fri Apr 24 11:43:36 2026 -0700
    rename doneStatus to just status and correctly set status codes refs #31811
• src/hg/utils/otto/userRequests/ottoRequestAlign.sh
  • lines changed 146, context: html, text, full: html, text
    584b69eff038b10c2176d2b9299c356af21288cc Wed Apr 22 16:30:53 2026 -0700
    initial scripts to run the galaxy workflow based off of the ottoRequest table entries refs #31811
  • lines changed 99, context: html, text, full: html, text
    f0b8830616972bad195079b7ce775c919ff1e25f Thu Apr 23 15:13:50 2026 -0700
    correctly decide which is going to be target and query based on the N50 sizes of the two given assemblies refs #31811
  • lines changed 138, context: html, text, full: html, text
    f5cece60b38bd8c2cfd57acf2abb972d66edb6d9 Fri Apr 24 11:43:36 2026 -0700
    rename doneStatus to just status and correctly set status codes refs #31811
• src/hg/utils/otto/userRequests/ottoRequestWatch.sh
  • lines changed 66, context: html, text, full: html, text
    3bb21ba2c8ac7f60effdb9c311ff27e4016f8e57 Thu Apr 23 15:14:35 2026 -0700
    script to use in hiram cron tab to watch for new requests and get the galaxy workflow running refs #31811
  • lines changed 27, context: html, text, full: html, text
    f5cece60b38bd8c2cfd57acf2abb972d66edb6d9 Fri Apr 24 11:43:36 2026 -0700
    rename doneStatus to just status and correctly set status codes refs #31811
• src/hg/utils/otto/userRequests/workflowMonitor.sh
  • lines changed 258, context: html, text, full: html, text
    584b69eff038b10c2176d2b9299c356af21288cc Wed Apr 22 16:30:53 2026 -0700
    initial scripts to run the galaxy workflow based off of the ottoRequest table entries refs #31811
  • lines changed 36, context: html, text, full: html, text
    6d8144be131a358037daea03610b22315527f26f Thu Apr 23 15:12:32 2026 -0700
    better recognition of errors in the workflow refs #31811
  • lines changed 24, context: html, text, full: html, text
    f5cece60b38bd8c2cfd57acf2abb972d66edb6d9 Fri Apr 24 11:43:36 2026 -0700
    rename doneStatus to just status and correctly set status codes refs #31811
• src/lib/cheapcgi.c
  • lines changed 57, context: html, text, full: html, text
    683eb89abf89e45cb554c489382803442e93bc0b Sun Apr 26 19:22:03 2026 -0700
    Adding restrictions on the size of cart content we accept in one request, refs #37452
• src/utils/qa/hubPublicAutoUpdate
  • lines changed 1, context: html, text, full: html, text
    46ad8ee25abcc7c81cd3005972b9069f2f14b5c5 Thu Apr 23 12:09:16 2026 -0700
    Updating hubPublicMail and hubPublicAutoUpdate crons to correctly detect and contact authors of broken public hubs. hubPublicMail now uses curl instead of python-requests (handles Cloudflare bot-blocks and 4xx/5xx responses that requests silently treats as successful), falls back to hubPublic.email as a secondary source so newly-added broken hubs still accumulate failCount, and strips the mailto: prefix in parseEmail. hubPublicAutoUpdate now escapes double quotes on email values. No RM
• src/utils/qa/hubPublicMail
  • lines changed 56, context: html, text, full: html, text
    46ad8ee25abcc7c81cd3005972b9069f2f14b5c5 Thu Apr 23 12:09:16 2026 -0700
    Updating hubPublicMail and hubPublicAutoUpdate crons to correctly detect and contact authors of broken public hubs. hubPublicMail now uses curl instead of python-requests (handles Cloudflare bot-blocks and 4xx/5xx responses that requests silently treats as successful), falls back to hubPublic.email as a secondary source so newly-added broken hubs still accumulate failCount, and strips the mailto: prefix in parseEmail. hubPublicAutoUpdate now escapes double quotes on email values. No RM
• src/utils/qa/makefile
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    0f457bede2db45e9b4e91de2ee2d54502b91bcc4 Fri Apr 24 13:26:53 2026 -0700
    Adding the updateHubSpaceQuota script to the makedoc, no Redmine
• src/utils/qa/quickLiftBench/README.md
  • lines changed 147, context: html, text, full: html, text
    ff2dc690270f4e155d6345af821bc8a2c197e667 Fri Apr 24 17:58:03 2026 -0700
    quickLiftBench: hgTracks render-time benchmark for quickLift, refs #37445 Drives YAML-configured cases against hgTracks with measureTiming=1, parses per-track loadTime/drawTime out of printTrackTiming() output, writes per- iteration TSV plus a per-(case, position) summary with median/p90 and lifted/native ratios. Supports same-hub source-vs-dest, track-pair across assemblies, and lift-on/off side-by-side hub comparisons. Output backs the benchmark numbers for the quickLift Bioinformatics paper (#36829). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/utils/qa/quickLiftBench/cases.yaml
  • lines changed 106, context: html, text, full: html, text
    ff2dc690270f4e155d6345af821bc8a2c197e667 Fri Apr 24 17:58:03 2026 -0700
    quickLiftBench: hgTracks render-time benchmark for quickLift, refs #37445 Drives YAML-configured cases against hgTracks with measureTiming=1, parses per-track loadTime/drawTime out of printTrackTiming() output, writes per- iteration TSV plus a per-(case, position) summary with median/p90 and lifted/native ratios. Supports same-hub source-vs-dest, track-pair across assemblies, and lift-on/off side-by-side hub comparisons. Output backs the benchmark numbers for the quickLift Bioinformatics paper (#36829). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/utils/qa/quickLiftBench/quickLiftBench.py
  • lines changed 510, context: html, text, full: html, text
    ff2dc690270f4e155d6345af821bc8a2c197e667 Fri Apr 24 17:58:03 2026 -0700
    quickLiftBench: hgTracks render-time benchmark for quickLift, refs #37445 Drives YAML-configured cases against hgTracks with measureTiming=1, parses per-track loadTime/drawTime out of printTrackTiming() output, writes per- iteration TSV plus a per-(case, position) summary with median/p90 and lifted/native ratios. Supports same-hub source-vs-dest, track-pair across assemblies, and lift-on/off side-by-side hub comparisons. Output backs the benchmark numbers for the quickLift Bioinformatics paper (#36829). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/utils/qa/updateHubSpaceQuota.sh
  • lines changed 79, context: html, text, full: html, text
    1e5a175df5ea8bc2d6b20d83f02bb3194e7a8afe Fri Apr 24 13:14:28 2026 -0700
    Adding a simple script to update the Hub Space quota, refs #37425
• src/utils/redmineCli
  • lines changed 22, context: html, text, full: html, text
    07c109ea4fe627879544dddf222650ab8c29eaf8 Tue Apr 21 02:55:53 2026 -0700
    redmineCli: add --file-list-add PATH option to append paths idempotently, refs #35059 Existing --file-list overwrites the custom field. The new --file-list-add reads the current value, appends each path that isn't already listed, and writes the combined value back with CRLF separators (matching Redmine's internal format). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    993da626132958795cab63a9b26d64ce2052f40d Tue Apr 21 16:51:13 2026 -0700
    Make redmineCli prepend_attribution idempotent. refs #37339 Skip adding the '**From Claude:**' header if the body already begins with a From Claude attribution line (any bold/italic asterisk variant, case-insensitive). Fixes the periodic doubled header when Claude models mimic prior journal entries that already carried the prefix.
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    c5057c7b3735ac3688a7703f97ead937b3c7c0a6 Thu Apr 23 14:24:06 2026 -0700
    redmineCli: let 'create' accept tracker and status by name The existing resolve_tracker() / resolve_status() helpers already accepted either a name ("To Do", "QA Ready") or a numeric ID, and the list / update subcommands wired them up. The create subcommand declared --tracker and --status as type=int, which rejected the name forms that the redmine skill documents as working. Drop the type=int, route args.tracker / args.status through the resolvers in cmd_create, and update the help text. Numeric IDs continue to work because the resolvers pass digit strings through. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    73169097327bcbfca570a98a34076c25ac069270 Fri Apr 24 08:08:52 2026 -0700
    redmineCli: fix resolve_status crash when --status defaults to int The default for create's --status is the int STATUS_NEW=1. Without type=int on the argparse option, resolve_status received an int and crashed on name_or_id.isdigit(). Wrap in str() to match resolve_tracker.

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• files changed: 398