All File Changes

v498_preview2 to v498_base (2026-05-04 to 2026-05-11) v498

• src/hg/cgilib/cartJson.c
  • lines changed 5, context: html, text, full: html, text
    782bdb2e04aa2724f33c328bb080bedf52c976e5 Fri May 8 12:03:28 2026 -0700
    Hide QuickLift groups from hgIntegrator track list, refs #37519 QuickLift remaps tracks from another assembly on the fly for display, but the underlying data is in the source assembly's coordinates, so output queries against the destination assembly don't make sense. In hgIntegrator this surfaced two ways for QuickLifted tracks: the "Choose fields" pop-up hung, and Get output errored with "Unrecognized type 'genePred' for hub track". Match the hgTables fix by skipping groups whose label starts with "QuickLift" in cartJsonGetGroupedTrackDb (the only consumer is hgIntegrator's React UI). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgCustom/hgCustom.c
  • lines changed 1, context: html, text, full: html, text
    60527238f7fe8afc89824e93b0d8780f1bcf65ad Wed May 6 14:38:50 2026 -0700
    Rename my variants to my annotations where appropriate, refs #33808
• src/hg/hgHubConnect/hooks/pre-create.c
  • lines changed 21, context: html, text, full: html, text
    30a4424ce1b185ef0e6e95969e0b688d686dfb8d Wed May 6 11:52:40 2026 -0700
    HubSpace assembly hub fixes: fixes 1,5,6,8 and prettify error messages, refs #37411
  • lines changed 5, context: html, text, full: html, text
    46a7db400ddc1280555e0bc32ed09311e19efc65 Thu May 7 10:53:58 2026 -0700
    Reword some hubSpace assembly hub error message. Make the duration of some error message notifications longer, change some text around input about why certain inputs are disabled in certain situations, refs #37411
• src/hg/hgHubConnect/hooks/pre-finish.c
  • lines changed 3, context: html, text, full: html, text
    30a4424ce1b185ef0e6e95969e0b688d686dfb8d Wed May 6 11:52:40 2026 -0700
    HubSpace assembly hub fixes: fixes 1,5,6,8 and prettify error messages, refs #37411
• src/hg/hgHubConnect/trackHubWizard.c
  • lines changed 1, context: html, text, full: html, text
    46a7db400ddc1280555e0bc32ed09311e19efc65 Thu May 7 10:53:58 2026 -0700
    Reword some hubSpace assembly hub error message. Make the duration of some error message notifications longer, change some text around input about why certain inputs are disabled in certain situations, refs #37411
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 3, context: html, text, full: html, text
    e146af22d6cc07a6ccca765e2befafc8d4dd1856 Tue May 5 11:32:07 2026 -0700
    Fixing bugs and typos in 0750648 caught by Claude review. The doRipples checkbox cart var was ignored and a copy-paste typo caused bp2Max to be updated with the new value for bp1Max when merging.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 1, context: html, text, full: html, text
    e146af22d6cc07a6ccca765e2befafc8d4dd1856 Tue May 5 11:32:07 2026 -0700
    Fixing bugs and typos in 0750648 caught by Claude review. The doRipples checkbox cart var was ignored and a copy-paste typo caused bp2Max to be updated with the new value for bp1Max when merging.
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 2, context: html, text, full: html, text
    e146af22d6cc07a6ccca765e2befafc8d4dd1856 Tue May 5 11:32:07 2026 -0700
    Fixing bugs and typos in 0750648 caught by Claude review. The doRipples checkbox cart var was ignored and a copy-paste typo caused bp2Max to be updated with the new value for bp1Max when merging.
• src/hg/hgTables/bedList.c
  • lines changed 5, context: html, text, full: html, text
    b2b58edce8b1d75567737b05e21ba9103073c69d Mon May 4 12:11:37 2026 -0700
    Fix myVariants tracks to load via a hardcoded query rather than hRangeQuery because the tableName is already qualified with the database. Remove dead code after refactor. Fix table browser output for myVariants tracks for various options, refs #33808
• src/hg/hgTables/custom.c
  • lines changed 2, context: html, text, full: html, text
    b2b58edce8b1d75567737b05e21ba9103073c69d Mon May 4 12:11:37 2026 -0700
    Fix myVariants tracks to load via a hardcoded query rather than hRangeQuery because the tableName is already qualified with the database. Remove dead code after refactor. Fix table browser output for myVariants tracks for various options, refs #33808
• src/hg/hgTables/filterFields.c
  • lines changed 3, context: html, text, full: html, text
    b2b58edce8b1d75567737b05e21ba9103073c69d Mon May 4 12:11:37 2026 -0700
    Fix myVariants tracks to load via a hardcoded query rather than hRangeQuery because the tableName is already qualified with the database. Remove dead code after refactor. Fix table browser output for myVariants tracks for various options, refs #33808
  • lines changed 36, context: html, text, full: html, text
    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgTables/hgTables.c
  • lines changed 10, context: html, text, full: html, text
    b2b58edce8b1d75567737b05e21ba9103073c69d Mon May 4 12:11:37 2026 -0700
    Fix myVariants tracks to load via a hardcoded query rather than hRangeQuery because the tableName is already qualified with the database. Remove dead code after refactor. Fix table browser output for myVariants tracks for various options, refs #33808
  • lines changed 2, context: html, text, full: html, text
    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 8, context: html, text, full: html, text
    e58fa7f310af32cf0b4e3c6037be9baf268c1ef8 Fri May 8 08:47:46 2026 -0700
    Avoid SQL connect to hub assembly when looking up table info in hgTables, refs #37519
  • lines changed 15, context: html, text, full: html, text
    0daab9c07e1fb7b75223d61b0faa52e34d94302e Fri May 8 10:31:34 2026 -0700
    Block hgTables output for QuickLift tracks and hide QuickLift groups, refs #37519 QuickLift remaps tracks from another assembly on the fly for display, but the underlying bigBed data is in the source assembly's coordinates, so output queries against the destination assembly's region return no results (or, with a whole-genome query, dump source-assembly data with source coordinates). Detect quickLiftUrl on the selected track and errAbort from doTopSubmit and doSummaryStats with a clear message. Also filter groups whose label starts with "QuickLift" out of the Group dropdown in hgTables, and clear the cart's group var if it was pointing at a QuickLift group. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgTables/hgTables.h
  • lines changed 6, context: html, text, full: html, text
    0daab9c07e1fb7b75223d61b0faa52e34d94302e Fri May 8 10:31:34 2026 -0700
    Block hgTables output for QuickLift tracks and hide QuickLift groups, refs #37519 QuickLift remaps tracks from another assembly on the fly for display, but the underlying bigBed data is in the source assembly's coordinates, so output queries against the destination assembly's region return no results (or, with a whole-genome query, dump source-assembly data with source coordinates). Detect quickLiftUrl on the selected track and errAbort from doTopSubmit and doSummaryStats with a clear message. Also filter groups whose label starts with "QuickLift" out of the Group dropdown in hgTables, and clear the cart's group var if it was pointing at a QuickLift group. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgTables/joining.c
  • lines changed 2, context: html, text, full: html, text
    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgTables/mainPage.c
  • lines changed 7, context: html, text, full: html, text
    e58fa7f310af32cf0b4e3c6037be9baf268c1ef8 Fri May 8 08:47:46 2026 -0700
    Avoid SQL connect to hub assembly when looking up table info in hgTables, refs #37519
  • lines changed 9, context: html, text, full: html, text
    0daab9c07e1fb7b75223d61b0faa52e34d94302e Fri May 8 10:31:34 2026 -0700
    Block hgTables output for QuickLift tracks and hide QuickLift groups, refs #37519 QuickLift remaps tracks from another assembly on the fly for display, but the underlying bigBed data is in the source assembly's coordinates, so output queries against the destination assembly's region return no results (or, with a whole-genome query, dump source-assembly data with source coordinates). Detect quickLiftUrl on the selected track and errAbort from doTopSubmit and doSummaryStats with a clear message. Also filter groups whose label starts with "QuickLift" out of the Group dropdown in hgTables, and clear the cart's group var if it was pointing at a QuickLift group. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgTables/sumStats.c
  • lines changed 1, context: html, text, full: html, text
    0daab9c07e1fb7b75223d61b0faa52e34d94302e Fri May 8 10:31:34 2026 -0700
    Block hgTables output for QuickLift tracks and hide QuickLift groups, refs #37519 QuickLift remaps tracks from another assembly on the fly for display, but the underlying bigBed data is in the source assembly's coordinates, so output queries against the destination assembly's region return no results (or, with a whole-genome query, dump source-assembly data with source coordinates). Detect quickLiftUrl on the selected track and errAbort from doTopSubmit and doSummaryStats with a clear message. Also filter groups whose label starts with "QuickLift" out of the Group dropdown in hgTables, and clear the cart's group var if it was pointing at a QuickLift group. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 7, context: html, text, full: html, text
    e7cf756b7ca8283e86d6cef92289b26831391c15 Tue May 5 11:48:51 2026 -0700
    Reduce gap between superTrack Filters heading and first filter row. refs #37426
• src/hg/hgTracks/config.c
  • lines changed 1, context: html, text, full: html, text
    60527238f7fe8afc89824e93b0d8780f1bcf65ad Wed May 6 14:38:50 2026 -0700
    Rename my variants to my annotations where appropriate, refs #33808
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    60527238f7fe8afc89824e93b0d8780f1bcf65ad Wed May 6 14:38:50 2026 -0700
    Rename my variants to my annotations where appropriate, refs #33808
  • lines changed 1, context: html, text, full: html, text
    61117792d4e14c4f3daeb754964893f50592356d Wed May 6 19:10:46 2026 -0700
    Use Font Awesome info-circle for chromAlias icon and soften styling, refs #29201 Replace the unicode &#9432; (CIRCLED LATIN SMALL LETTER I) with the Font Awesome fa-info-circle icon to fix pixelated/inconsistent rendering in Chrome and Edge — the unicode glyph falls back to platform symbol fonts that produce low-quality bitmap glyphs at small sizes. The FA glyph is vector and renders identically across browsers. Also soften the icon color to #aaa, drop font-size to 95%, and tighten right margin to 0.1em.
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    b2b58edce8b1d75567737b05e21ba9103073c69d Mon May 4 12:11:37 2026 -0700
    Fix myVariants tracks to load via a hardcoded query rather than hRangeQuery because the tableName is already qualified with the database. Remove dead code after refactor. Fix table browser output for myVariants tracks for various options, refs #33808
• src/hg/hgTracks/myVariantsTrack.c
  • lines changed 33, context: html, text, full: html, text
    b2b58edce8b1d75567737b05e21ba9103073c69d Mon May 4 12:11:37 2026 -0700
    Fix myVariants tracks to load via a hardcoded query rather than hRangeQuery because the tableName is already qualified with the database. Remove dead code after refactor. Fix table browser output for myVariants tracks for various options, refs #33808
  • lines changed 1, context: html, text, full: html, text
    bd0d63cb1a33174b6f43b32a48fddad7850d0acc Mon May 4 14:05:56 2026 -0700
    Remove em-dashes and fix myVariants custom tracks to use encoded usernames in their track names and trash files instead of raw usernames, refs #33808
  • lines changed 104, context: html, text, full: html, text
    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgc/bigBedClick.c
  • lines changed 10, context: html, text, full: html, text
    01badfbaa97a6547c7b938f79d48e454f1f09dce Wed May 6 14:23:26 2026 -0700
    hgc bigBed: only emit <BR> and set found after passing all filters, refs #36335
• src/hg/hgc/hgc.c
  • lines changed 10, context: html, text, full: html, text
    2654a3d85847492877e5d2b48d921a292e991771 Thu May 7 09:40:26 2026 -0700
    hgConvert quickLift: fix subtrack selection, hgc Predicted Protein / CDS FASTA links Three remaining issues on this ticket: (vii) After "+ Select all subtracks" on hg38 refSeqComposite then quickLifting to hs1, only RefSeq Curated rendered. dumpTdbAndChildren built buffer="<track>_sel" but then read cart[tdb->track] (the visibility, not the checkbox state); the visibility is never "1", so every subtrack emitted "parent <comp> off" and only trackDb-default-on subtracks rendered. Read cart[buffer] and accept any cartUsualBoolean-true value ("on" or positive int). Predicted Protein blank page on quickLifted refGene: getGenePredForPositionSql passed the hub-prefixed tdb->table to quickLiftSql, which then queried the source DB (hg38) for a "hub_NNN_refGene" table that doesn't exist. Strip the prefix with trackHubSkipHubName before the source-DB query. Also, doRefGene was overriding pepName to rl->mrnaAcc for every quickLifted item, so for non-coding NR_* the mrnaAcc matched gbSeq and we offered a Predicted Protein link that htcTranslatedPredMRna can only abort on. Only override pepName for coding mRNAs; non-coding falls through to the existing "Non-protein coding gene..." message. CDS FASTA "Unknown database hub_NNN_<db>": addPalLink generates an hgPal URL with no db=, so hgPal tries to open the destination hub-virtual db and dies. palInfo coords are in destination space anyway while the multiZ alignment lives in source coords, so skip addPalLink for quickLifted tracks. refs #36125 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgc/mafClick.c
  • lines changed 30, context: html, text, full: html, text
    7a4080b1727435d2c348f5d672823d80411eb1d6 Mon May 4 15:01:47 2026 -0700
    fix hgc click on mafWig track when GCx accessions are in use with speciesLabels
  • lines changed 32, context: html, text, full: html, text
    0a05f3e3c58ea53afa036c0d0be18d4eb79e11b5 Mon May 4 15:28:20 2026 -0700
    enable B links for maf clicks to GenArk browsers
• src/hg/hgc/myVariantsClick.c
  • lines changed 3, context: html, text, full: html, text
    60527238f7fe8afc89824e93b0d8780f1bcf65ad Wed May 6 14:38:50 2026 -0700
    Rename my variants to my annotations where appropriate, refs #33808
  • lines changed 87, context: html, text, full: html, text
    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/facetedComposite.html
  • lines changed 114, context: html, text, full: html, text
    9e3b6ed0cea49664cac3413a3136ff262ee2b581 Mon May 11 10:01:04 2026 -0700
    Working on faceted composite docs page, refs #36320
• src/hg/htdocs/inc/myVariantsDesc.html
  • lines changed 51, context: html, text, full: html, text
    fa0ff693583dbd90241f3bd3b2dce6eafd974d6a Mon May 4 14:17:20 2026 -0700
    Add a basic description page for myVariants tracks, refs #38808
• src/hg/htdocs/indexMeetings.html
  • lines changed 26, context: html, text, full: html, text
    c2e393e9426c225608ab90840d2c593f29a1a37f Thu May 7 12:22:25 2026 -0700
    Remove past HGM and CSHL meetings from indexMeetings page and rebalance columns. No RM.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 3, context: html, text, full: html, text
    61117792d4e14c4f3daeb754964893f50592356d Wed May 6 19:10:46 2026 -0700
    Use Font Awesome info-circle for chromAlias icon and soften styling, refs #29201 Replace the unicode &#9432; (CIRCLED LATIN SMALL LETTER I) with the Font Awesome fa-info-circle icon to fix pixelated/inconsistent rendering in Chrome and Edge — the unicode glyph falls back to platform symbol fonts that produce low-quality bitmap glyphs at small sizes. The FA glyph is vector and renders identically across browsers. Also soften the icon color to #aaa, drop font-size to 95%, and tighten right margin to 0.1em.
• src/hg/inc/myVariants.h
  • lines changed 29, context: html, text, full: html, text
    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/inc/userdata.h
  • lines changed 10, context: html, text, full: html, text
    46a7db400ddc1280555e0bc32ed09311e19efc65 Thu May 7 10:53:58 2026 -0700
    Reword some hubSpace assembly hub error message. Make the duration of some error message notifications longer, change some text around input about why certain inputs are disabled in certain situations, refs #37411
• src/hg/js/hgMyData.js
  • lines changed 101, context: html, text, full: html, text
    30a4424ce1b185ef0e6e95969e0b688d686dfb8d Wed May 6 11:52:40 2026 -0700
    HubSpace assembly hub fixes: fixes 1,5,6,8 and prettify error messages, refs #37411
  • lines changed 30, context: html, text, full: html, text
    46a7db400ddc1280555e0bc32ed09311e19efc65 Thu May 7 10:53:58 2026 -0700
    Reword some hubSpace assembly hub error message. Make the duration of some error message notifications longer, change some text around input about why certain inputs are disabled in certain situations, refs #37411
• src/hg/js/hgTracks.js
  • lines changed 11, context: html, text, full: html, text
    60527238f7fe8afc89824e93b0d8780f1bcf65ad Wed May 6 14:38:50 2026 -0700
    Rename my variants to my annotations where appropriate, refs #33808
  • lines changed 4, context: html, text, full: html, text
    c6c395f3e8c38023107bab00507ee605f140ecf8 Thu May 7 11:00:09 2026 -0700
    More variant|item to annotation labeling changes. One 'item' is left in because it seems more appropriate as the placeholder text, refs #33808
  • lines changed 1, context: html, text, full: html, text
    6eaa03a52d1610050bcacf6e3a56c3086677574d Thu May 7 11:02:34 2026 -0700
    Change create to add in the highlight menu for creating a myVariants item, refs #33808
  • lines changed 3, context: html, text, full: html, text
    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    8cdfd0efc540471112f850be74da7b87a8bd9b1e Fri May 8 13:48:54 2026 -0700
    Fix zoom to exon/codon option not appearing for genePreds/bigGenePreds/bigBeds. This broke because of tooltip code that now moves tooltip text into a data-tooltip attribute instead of leaving the text in the title attribute, refs #37521
• src/hg/js/liftRequest.js
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    735a45a2ff3e444fe9d668584ad5d221046f0417 Wed May 6 09:02:07 2026 -0700
    correctly reset form after display of existing alignment refs #31811
• src/hg/js/utils.js
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    8cdfd0efc540471112f850be74da7b87a8bd9b1e Fri May 8 13:48:54 2026 -0700
    Fix zoom to exon/codon option not appearing for genePreds/bigGenePreds/bigBeds. This broke because of tooltip code that now moves tooltip text into a data-tooltip attribute instead of leaving the text in the title attribute, refs #37521
• src/hg/lib/customFactory.c
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    fa0ff693583dbd90241f3bd3b2dce6eafd974d6a Mon May 4 14:17:20 2026 -0700
    Add a basic description page for myVariants tracks, refs #38808
• src/hg/lib/myVariants.c
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    bd0d63cb1a33174b6f43b32a48fddad7850d0acc Mon May 4 14:05:56 2026 -0700
    Remove em-dashes and fix myVariants custom tracks to use encoded usernames in their track names and trash files instead of raw usernames, refs #33808
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    60527238f7fe8afc89824e93b0d8780f1bcf65ad Wed May 6 14:38:50 2026 -0700
    Rename my variants to my annotations where appropriate, refs #33808
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    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/lib/trackHub.c
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    e214ffa17d2231d1a7413af72c539c1d3bfa0af2 Wed May 6 13:36:15 2026 -0700
    hgConvert quickLift: still lift hidden composite siblings c4e77d5 stopped validating hidden subtracks to keep them out of the "failed to lift" warning, but that also dropped them from the generated quickLift hub, so a composite came across with only its visible subtracks. Validate every sibling again so all liftable ones make it into the hub; pass a NULL badList for hidden siblings so non-liftable ones still don't show up in the user-facing complaint. Verified with refSeqComposite (default vis: only ncbiRefSeqCurated visible): pre-fix hub contained only ncbiRefSeqCurated; post-fix hub contains all 10 RefSeq subtracks with hidden ones marked "parent refSeqComposite off". cons100way badList unchanged: hidden phastCons100way (wig, non-liftable) is silenced on both. refs #36125 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    2654a3d85847492877e5d2b48d921a292e991771 Thu May 7 09:40:26 2026 -0700
    hgConvert quickLift: fix subtrack selection, hgc Predicted Protein / CDS FASTA links Three remaining issues on this ticket: (vii) After "+ Select all subtracks" on hg38 refSeqComposite then quickLifting to hs1, only RefSeq Curated rendered. dumpTdbAndChildren built buffer="<track>_sel" but then read cart[tdb->track] (the visibility, not the checkbox state); the visibility is never "1", so every subtrack emitted "parent <comp> off" and only trackDb-default-on subtracks rendered. Read cart[buffer] and accept any cartUsualBoolean-true value ("on" or positive int). Predicted Protein blank page on quickLifted refGene: getGenePredForPositionSql passed the hub-prefixed tdb->table to quickLiftSql, which then queried the source DB (hg38) for a "hub_NNN_refGene" table that doesn't exist. Strip the prefix with trackHubSkipHubName before the source-DB query. Also, doRefGene was overriding pepName to rl->mrnaAcc for every quickLifted item, so for non-coding NR_* the mrnaAcc matched gbSeq and we offered a Predicted Protein link that htcTranslatedPredMRna can only abort on. Only override pepName for coding mRNAs; non-coding falls through to the existing "Non-protein coding gene..." message. CDS FASTA "Unknown database hub_NNN_<db>": addPalLink generates an hgPal URL with no db=, so hgPal tries to open the destination hub-virtual db and dies. palInfo coords are in destination space anyway while the multiZ alignment lives in source coords, so skip addPalLink for quickLifted tracks. refs #36125 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/clinPred/clinPredToWig.py
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    f350ebff8f2cc1e0772032e59e926b5e45b374cd Tue May 5 16:18:28 2026 -0700
    Adding ClinPred missense pathogenicity score track on hg19 and hg38. refs #37510 ClinPred (Alirezaie et al, AJHG 2018) joins the predictionScoresSuper supertrack as a composite of four bigWigs, one per alternate base, with a per-position color overlay (red for score >= 0.5 likely pathogenic, blue for < 0.5 likely benign). Adds clinPredToWig.py to convert the upstream score table to wig, a clinPred branch in makeWigColorByRevelCadd.py for the color overlay step, and reciprocal relatedTracks entries to REVEL, CADD, PrimateAI-3D, and AlphaMissense. Also adds Display Conventions and Credits entries in predictionScoresSuper.html for ClinPred, PrimateAI-3D, and PromoterAI.
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
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    ad49432690b003435d90afb3f8636a2d4ed5d616 Fri May 8 14:48:58 2026 -0700
    adding a few per user requests
• src/hg/makeDb/doc/hg19.txt
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    f350ebff8f2cc1e0772032e59e926b5e45b374cd Tue May 5 16:18:28 2026 -0700
    Adding ClinPred missense pathogenicity score track on hg19 and hg38. refs #37510 ClinPred (Alirezaie et al, AJHG 2018) joins the predictionScoresSuper supertrack as a composite of four bigWigs, one per alternate base, with a per-position color overlay (red for score >= 0.5 likely pathogenic, blue for < 0.5 likely benign). Adds clinPredToWig.py to convert the upstream score table to wig, a clinPred branch in makeWigColorByRevelCadd.py for the color overlay step, and reciprocal relatedTracks entries to REVEL, CADD, PrimateAI-3D, and AlphaMissense. Also adds Display Conventions and Credits entries in predictionScoresSuper.html for ClinPred, PrimateAI-3D, and PromoterAI.
• src/hg/makeDb/doc/hg38/cactus447.txt
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    32b87a2e38fd80d8c3f0c1ffcf536f903bbf29c6 Tue May 5 15:28:59 2026 -0700
    Removing lines from the makedoc since these tracks are now done, and not currently running, refs #28259
• src/hg/makeDb/doc/hg38/clinPred.txt
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    f350ebff8f2cc1e0772032e59e926b5e45b374cd Tue May 5 16:18:28 2026 -0700
    Adding ClinPred missense pathogenicity score track on hg19 and hg38. refs #37510 ClinPred (Alirezaie et al, AJHG 2018) joins the predictionScoresSuper supertrack as a composite of four bigWigs, one per alternate base, with a per-position color overlay (red for score >= 0.5 likely pathogenic, blue for < 0.5 likely benign). Adds clinPredToWig.py to convert the upstream score table to wig, a clinPred branch in makeWigColorByRevelCadd.py for the color overlay step, and reciprocal relatedTracks entries to REVEL, CADD, PrimateAI-3D, and AlphaMissense. Also adds Display Conventions and Credits entries in predictionScoresSuper.html for ClinPred, PrimateAI-3D, and PromoterAI.
• src/hg/makeDb/doc/hg38/mei.txt
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    00e086afbcb8296c6aef946c13eeb777f34bac02 Mon May 11 07:03:10 2026 -0700
    mei: new track for HGSVC3 mobile element insertions on hg38 and hs1 12,642 MEIs on hg38, 12,919 on hs1, from the HGSVC3 callset (Logsdon et al. 2025). Single shared trackDb stanza in human/mei.ra with $D substitution. Okabe-Ito colors, INS-svLen:carrierCount item names, inserted DNA in an insertSeq field. Cross-link to lrSv via relatedTracks.ra. refs #37524
• src/hg/makeDb/doc/hg38/multiz30way.txt
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    32b87a2e38fd80d8c3f0c1ffcf536f903bbf29c6 Tue May 5 15:28:59 2026 -0700
    Removing lines from the makedoc since these tracks are now done, and not currently running, refs #28259
• src/hg/makeDb/doc/hg38/varFreqs.txt
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    986c4ede954e44904eb314772fb2cf83a48d307c Wed May 6 06:24:47 2026 -0700
    varFreqs: lift GenomeAsia (gasp + gaspIndel) GRCh37 -> hg38 Both subtracks were served at /gbdb/hg38/ but the upstream callset is GRCh37 (caught in QA, see #36642 note 2026-05-04). Lifted with CrossMap using hg19ToHg38.over.chain.gz; recipe matches tishkoff180 / mxbFreq. gasp (SNVs): 66,236,516 -> 66,222,771 (99.98%; 6,240 unmapped + 7,505 alt/random) gaspIndel: 4,415,156 -> 4,410,871 (99.90%; 3,332 unmapped + 953 alt/random) New driver script: scripts/varFreqs/gaspLift.sh. gaspIndel bigDataUrl renamed from All.indels.annot.cont_withmaf.vcf.gz to ga100k.indels.vcf.gz (old name was a verbatim copy of the upstream download name). varFreqsAll combined bigBed regenerated to fold in the corrected coordinates (36.5 GB, 1,166,451,644 items, 125 fields). refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    65da29c9d74d4dd832ab7f16899ad3b209b92da4 Wed May 6 08:43:57 2026 -0700
    varFreqs: 5 vcfToBigBed.py fixes + add NPM Singapore to combined track vcfToBigBed.py and mergeAndAnnotate.sh moved into kent (they were hive-only); the build is now reproducible from a fresh kent checkout. Five vcfToBigBed.py fixes (all caught by Lou's QA pass on #36642): - normalize_consequence(): bcftools csq emits "&"-joined compound terms like "stop_gained&frameshift" which exact-match-failed the old 8-bucket consequence filter and orphaned ~8.5M records. Rewrites "&" to "," so a single record can match multiple buckets, and appends ",others" to any token list with no named-filter token. Trackdb gains 4 buckets (3' UTR, 5' UTR, Non-coding, Other) and switches to filterType.consequence multipleListOr. - Source-attribution bug: the old check only inspected the unified AC/AF slot. AllOfUs ships only per-population fields ("." in the unified slot), so all 67M+ AllOfUs variants got no source attribution -- ~43M rows in the previous bigBed had an empty "sources" column. Fix scans per-population slots before declaring "no data". - parse_bcsq() returns "" instead of "." for aaChange/dnaChange on non-coding variants, so the mouseOver and detail page render a clean blank line. - maxAF format: "{:.6g}" -> "{:.6f}" so very small AFs render as "0.000003" instead of "3.31347e-06". - autoSql `table varFreqs` -> `table varFreqsAll` (matches the bigBed filename; required for hgIntegrator wiring). NPM Singapore (SG10K_Health, 9.7k WGS) added to databases.tsv, files.txt, populations.tsv (SgChinese / SgMalay / SgIndian) and the trackDb filter UI. NPM individual subtrack stays tableBrowser off (license); folded into varFreqsAll same as finngen / kova / mgrb / swefreq / tishkoff180. varFreqsAll bigBed rebuild is in progress at /hive/data/genomes/hg38/ bed/varFreqs/all/; will land in /gbdb when the bedToBigBed step completes. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/hs1/mei.txt
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    00e086afbcb8296c6aef946c13eeb777f34bac02 Mon May 11 07:03:10 2026 -0700
    mei: new track for HGSVC3 mobile element insertions on hg38 and hs1 12,642 MEIs on hg38, 12,919 on hs1, from the HGSVC3 callset (Logsdon et al. 2025). Single shared trackDb stanza in human/mei.ra with $D substitution. Okabe-Ito colors, INS-svLen:carrierCount item names, inserted DNA in an insertSeq field. Cross-link to lrSv via relatedTracks.ra. refs #37524
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    ad49432690b003435d90afb3f8636a2d4ed5d616 Fri May 8 14:48:58 2026 -0700
    adding a few per user requests
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
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    904f12950eb738c0fba248f3c78a9b0c2d93419c Fri May 8 14:02:21 2026 -0700
    adding an older assembly for P. vivax for BRC refs #34377
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
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    904f12950eb738c0fba248f3c78a9b0c2d93419c Fri May 8 14:02:21 2026 -0700
    adding an older assembly for P. vivax for BRC refs #34377
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
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    ad49432690b003435d90afb3f8636a2d4ed5d616 Fri May 8 14:48:58 2026 -0700
    adding a few per user requests
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
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    ad49432690b003435d90afb3f8636a2d4ed5d616 Fri May 8 14:48:58 2026 -0700
    adding a few per user requests
• src/hg/makeDb/doc/vgp577way/vgp577way.txt
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    16bf6ea9e265c3d36d2485cccb9a6ad45a1646d0 Wed May 6 12:05:34 2026 -0700
    additional comments refs #34370
• src/hg/makeDb/scripts/mei/meiHgsvc3.as
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    00e086afbcb8296c6aef946c13eeb777f34bac02 Mon May 11 07:03:10 2026 -0700
    mei: new track for HGSVC3 mobile element insertions on hg38 and hs1 12,642 MEIs on hg38, 12,919 on hs1, from the HGSVC3 callset (Logsdon et al. 2025). Single shared trackDb stanza in human/mei.ra with $D substitution. Okabe-Ito colors, INS-svLen:carrierCount item names, inserted DNA in an insertSeq field. Cross-link to lrSv via relatedTracks.ra. refs #37524
• src/hg/makeDb/scripts/mei/meiHgsvc3CsvToBed.py
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    00e086afbcb8296c6aef946c13eeb777f34bac02 Mon May 11 07:03:10 2026 -0700
    mei: new track for HGSVC3 mobile element insertions on hg38 and hs1 12,642 MEIs on hg38, 12,919 on hs1, from the HGSVC3 callset (Logsdon et al. 2025). Single shared trackDb stanza in human/mei.ra with $D substitution. Okabe-Ito colors, INS-svLen:carrierCount item names, inserted DNA in an insertSeq field. Cross-link to lrSv via relatedTracks.ra. refs #37524
• src/hg/makeDb/scripts/varFreqs/databases.tsv
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    ec5c73f4dc3ef4beae16fa1c12b7e5bf872bb73d Tue May 5 15:04:39 2026 -0700
    varFreqs: fix gaspIndel bigDataUrl after Max's GenomeAsia hg38 lift; add Tishkoff180 to combined-track filter UI; sync databases.tsv with deployed bigBed; minor description-page corrections. refs #36642 GenomeAsia hg38 lift (May 5 2026, by Max): - gaspIndel.bigDataUrl was pointing at the old GRCh37 filename "All.indels.annot.cont_withmaf.vcf.gz" which was renamed to "ga100k.indels.vcf.gz" during the lift; this left the gaspIndel track broken on the sandbox until the trackdb stanza was updated to match. - gasp/gaspIndel dataVersion strings updated from "Pilot 2019 (GRCh37 - to be lifted)" to "Pilot 2019 (lifted to hg38, May 2026)". - databases.tsv: also updated GenomeAsiaIndel path to ga100k.indels.vcf.gz so the next varFreqsAll rebuild reads from the lifted file. Tishkoff180 in varFreqsAll.bb but unfilterable (fresh-eyes audit finding): - Added Tishkoff180 to filterValues.sources and added filterByRange.Tishkoff180AF / Tishkoff180AC entries. - Added Tishkoff180 (and SVatalog) rows to databases.tsv to match the deployed bigBed (which already has those columns). Description-page corrections: - varFreqsAll.html: "20 population databases" -> "25 source databases" (matches actual count); HGDP+1kG bullet "European" -> "Non-Finnish European" to disambiguate from Finnish (gnomAD's nfe). - varFreqs.html: GenomeAsia row in the Available Datasets table updated from 3 to 7 sub-populations (NEA/SEA/SAS plus the previously hidden OCE/AMR/AFR/WER) so the table matches what the data exposes once Max's rebuild populates the new filter columns. - KOVA longLabel: "1.9k WGS+3.5k WES" -> "1.9k WGS+3.4k WES" (3.4k is correct per Lee 2017 and kova.html).
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    986c4ede954e44904eb314772fb2cf83a48d307c Wed May 6 06:24:47 2026 -0700
    varFreqs: lift GenomeAsia (gasp + gaspIndel) GRCh37 -> hg38 Both subtracks were served at /gbdb/hg38/ but the upstream callset is GRCh37 (caught in QA, see #36642 note 2026-05-04). Lifted with CrossMap using hg19ToHg38.over.chain.gz; recipe matches tishkoff180 / mxbFreq. gasp (SNVs): 66,236,516 -> 66,222,771 (99.98%; 6,240 unmapped + 7,505 alt/random) gaspIndel: 4,415,156 -> 4,410,871 (99.90%; 3,332 unmapped + 953 alt/random) New driver script: scripts/varFreqs/gaspLift.sh. gaspIndel bigDataUrl renamed from All.indels.annot.cont_withmaf.vcf.gz to ga100k.indels.vcf.gz (old name was a verbatim copy of the upstream download name). varFreqsAll combined bigBed regenerated to fold in the corrected coordinates (36.5 GB, 1,166,451,644 items, 125 fields). refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    65da29c9d74d4dd832ab7f16899ad3b209b92da4 Wed May 6 08:43:57 2026 -0700
    varFreqs: 5 vcfToBigBed.py fixes + add NPM Singapore to combined track vcfToBigBed.py and mergeAndAnnotate.sh moved into kent (they were hive-only); the build is now reproducible from a fresh kent checkout. Five vcfToBigBed.py fixes (all caught by Lou's QA pass on #36642): - normalize_consequence(): bcftools csq emits "&"-joined compound terms like "stop_gained&frameshift" which exact-match-failed the old 8-bucket consequence filter and orphaned ~8.5M records. Rewrites "&" to "," so a single record can match multiple buckets, and appends ",others" to any token list with no named-filter token. Trackdb gains 4 buckets (3' UTR, 5' UTR, Non-coding, Other) and switches to filterType.consequence multipleListOr. - Source-attribution bug: the old check only inspected the unified AC/AF slot. AllOfUs ships only per-population fields ("." in the unified slot), so all 67M+ AllOfUs variants got no source attribution -- ~43M rows in the previous bigBed had an empty "sources" column. Fix scans per-population slots before declaring "no data". - parse_bcsq() returns "" instead of "." for aaChange/dnaChange on non-coding variants, so the mouseOver and detail page render a clean blank line. - maxAF format: "{:.6g}" -> "{:.6f}" so very small AFs render as "0.000003" instead of "3.31347e-06". - autoSql `table varFreqs` -> `table varFreqsAll` (matches the bigBed filename; required for hgIntegrator wiring). NPM Singapore (SG10K_Health, 9.7k WGS) added to databases.tsv, files.txt, populations.tsv (SgChinese / SgMalay / SgIndian) and the trackDb filter UI. NPM individual subtrack stays tableBrowser off (license); folded into varFreqsAll same as finngen / kova / mgrb / swefreq / tishkoff180. varFreqsAll bigBed rebuild is in progress at /hive/data/genomes/hg38/ bed/varFreqs/all/; will land in /gbdb when the bedToBigBed step completes. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/gaspLift.sh
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    986c4ede954e44904eb314772fb2cf83a48d307c Wed May 6 06:24:47 2026 -0700
    varFreqs: lift GenomeAsia (gasp + gaspIndel) GRCh37 -> hg38 Both subtracks were served at /gbdb/hg38/ but the upstream callset is GRCh37 (caught in QA, see #36642 note 2026-05-04). Lifted with CrossMap using hg19ToHg38.over.chain.gz; recipe matches tishkoff180 / mxbFreq. gasp (SNVs): 66,236,516 -> 66,222,771 (99.98%; 6,240 unmapped + 7,505 alt/random) gaspIndel: 4,415,156 -> 4,410,871 (99.90%; 3,332 unmapped + 953 alt/random) New driver script: scripts/varFreqs/gaspLift.sh. gaspIndel bigDataUrl renamed from All.indels.annot.cont_withmaf.vcf.gz to ga100k.indels.vcf.gz (old name was a verbatim copy of the upstream download name). varFreqsAll combined bigBed regenerated to fold in the corrected coordinates (36.5 GB, 1,166,451,644 items, 125 fields). refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/mergeAndAnnotate.sh
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    65da29c9d74d4dd832ab7f16899ad3b209b92da4 Wed May 6 08:43:57 2026 -0700
    varFreqs: 5 vcfToBigBed.py fixes + add NPM Singapore to combined track vcfToBigBed.py and mergeAndAnnotate.sh moved into kent (they were hive-only); the build is now reproducible from a fresh kent checkout. Five vcfToBigBed.py fixes (all caught by Lou's QA pass on #36642): - normalize_consequence(): bcftools csq emits "&"-joined compound terms like "stop_gained&frameshift" which exact-match-failed the old 8-bucket consequence filter and orphaned ~8.5M records. Rewrites "&" to "," so a single record can match multiple buckets, and appends ",others" to any token list with no named-filter token. Trackdb gains 4 buckets (3' UTR, 5' UTR, Non-coding, Other) and switches to filterType.consequence multipleListOr. - Source-attribution bug: the old check only inspected the unified AC/AF slot. AllOfUs ships only per-population fields ("." in the unified slot), so all 67M+ AllOfUs variants got no source attribution -- ~43M rows in the previous bigBed had an empty "sources" column. Fix scans per-population slots before declaring "no data". - parse_bcsq() returns "" instead of "." for aaChange/dnaChange on non-coding variants, so the mouseOver and detail page render a clean blank line. - maxAF format: "{:.6g}" -> "{:.6f}" so very small AFs render as "0.000003" instead of "3.31347e-06". - autoSql `table varFreqs` -> `table varFreqsAll` (matches the bigBed filename; required for hgIntegrator wiring). NPM Singapore (SG10K_Health, 9.7k WGS) added to databases.tsv, files.txt, populations.tsv (SgChinese / SgMalay / SgIndian) and the trackDb filter UI. NPM individual subtrack stays tableBrowser off (license); folded into varFreqsAll same as finngen / kova / mgrb / swefreq / tishkoff180. varFreqsAll bigBed rebuild is in progress at /hive/data/genomes/hg38/ bed/varFreqs/all/; will land in /gbdb when the bedToBigBed step completes. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/populations.tsv
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    f674b74547b883a2054c4771533d753266e07c06 Mon May 4 16:21:54 2026 -0700
    QA pass on varFreqs supertrack: relabel HGDP+1kG and AllOfUs per-population fields to match data semantics, expose all 7 GenomeAsia populations in filter UI, normalize labels and capitalization, add Methods + References to description page, and flag GenomeAsia GRCh37 coordinate mismatch via dataVersion. refs #36642 trackDb (varFreqs.ra): - HGDP+1kG per-population AC/AF labels relabeled from "gnomAD HGDP+1kG <pop>" to "gnomAD v3.1.2 <pop> (full release)" since the values come from the full ~76k-genome gnomAD release, not the 4,094-genome HGDP+1kG cohort. - AllOfUs per-population AC/AF labels appended with "(local ancestry)" to clarify these are local-ancestry-stratified haplotype frequencies (Ioannidis lab pipeline), not the AllOfUs paper's global Rye categories. - Added 8 new filter entries for GenomeAsia OCE/AMR/AFR/WER (data has 7 population groups; trackUI previously exposed only 3). - shortLabel shortenings: alfaVcf, finngen, gasp, gaspIndel, kova, saudi, schema, colorsDbSnv, tishkoff180. - longLabel shortenings: ga4kSnv, colorsDbSnv, svatalogSnv, tishkoff180. - Capitalization fixes: SFARI Spark to SFARI SPARK, Japan ToMMO to Japan ToMMo, NHLBI TOPMED to NHLBI TOPMed. - dataVersion added on 6 subtracks that lacked it (gasp, gaspIndel, indigenomes, saudi, ga4kSnv, svatalogSnv); gasp/gaspIndel flagged "Pilot 2019 (GRCh37 - to be lifted)" for visibility of the open hg19 issue. - Default visibility flipped: non-summary subtracks now dense, summary varFreqsAll now pack. Container stays hide. Description page (varFreqs.html): - Added References section with 21 primary publications for the source cohorts. - Added "Notes on Specific Sub-tracks" explaining the HGDP+1kG cohort vs full-release distinction and the AllOfUs locAncFreq semantics. - Added Methods section describing per-subtrack and combined-track build pipelines, with links to the GitHub scripts directory and makedoc. - Encoded genome@soe.ucsc.edu with encodeEmail.pl. - Corrected "more than 1.2 billion variants" to "1.17 billion" (actual varFreqsAll.bb itemCount: 1,169,063,801). - Normalized body-text quotes to &quot; entities. - AllOfUs and HGDP+1kG rows in the datasets table now flag the semantic distinction inline. Build config (scripts/varFreqs/populations.tsv): - Added 4 GenomeAsia rows (OCE, AMR, AFR, WER) so the next varFreqsAll bigBed rebuild will populate the new filter columns. - Fixed HGDP1kG nfe label "European" to "Non-Finnish European" to match the trackdb relabel.
  • lines changed 4, context: html, text, full: html, text
    65da29c9d74d4dd832ab7f16899ad3b209b92da4 Wed May 6 08:43:57 2026 -0700
    varFreqs: 5 vcfToBigBed.py fixes + add NPM Singapore to combined track vcfToBigBed.py and mergeAndAnnotate.sh moved into kent (they were hive-only); the build is now reproducible from a fresh kent checkout. Five vcfToBigBed.py fixes (all caught by Lou's QA pass on #36642): - normalize_consequence(): bcftools csq emits "&"-joined compound terms like "stop_gained&frameshift" which exact-match-failed the old 8-bucket consequence filter and orphaned ~8.5M records. Rewrites "&" to "," so a single record can match multiple buckets, and appends ",others" to any token list with no named-filter token. Trackdb gains 4 buckets (3' UTR, 5' UTR, Non-coding, Other) and switches to filterType.consequence multipleListOr. - Source-attribution bug: the old check only inspected the unified AC/AF slot. AllOfUs ships only per-population fields ("." in the unified slot), so all 67M+ AllOfUs variants got no source attribution -- ~43M rows in the previous bigBed had an empty "sources" column. Fix scans per-population slots before declaring "no data". - parse_bcsq() returns "" instead of "." for aaChange/dnaChange on non-coding variants, so the mouseOver and detail page render a clean blank line. - maxAF format: "{:.6g}" -> "{:.6f}" so very small AFs render as "0.000003" instead of "3.31347e-06". - autoSql `table varFreqs` -> `table varFreqsAll` (matches the bigBed filename; required for hgIntegrator wiring). NPM Singapore (SG10K_Health, 9.7k WGS) added to databases.tsv, files.txt, populations.tsv (SgChinese / SgMalay / SgIndian) and the trackDb filter UI. NPM individual subtrack stays tableBrowser off (license); folded into varFreqsAll same as finngen / kova / mgrb / swefreq / tishkoff180. varFreqsAll bigBed rebuild is in progress at /hive/data/genomes/hg38/ bed/varFreqs/all/; will land in /gbdb when the bedToBigBed step completes. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/vcfToBigBed.py
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    65da29c9d74d4dd832ab7f16899ad3b209b92da4 Wed May 6 08:43:57 2026 -0700
    varFreqs: 5 vcfToBigBed.py fixes + add NPM Singapore to combined track vcfToBigBed.py and mergeAndAnnotate.sh moved into kent (they were hive-only); the build is now reproducible from a fresh kent checkout. Five vcfToBigBed.py fixes (all caught by Lou's QA pass on #36642): - normalize_consequence(): bcftools csq emits "&"-joined compound terms like "stop_gained&frameshift" which exact-match-failed the old 8-bucket consequence filter and orphaned ~8.5M records. Rewrites "&" to "," so a single record can match multiple buckets, and appends ",others" to any token list with no named-filter token. Trackdb gains 4 buckets (3' UTR, 5' UTR, Non-coding, Other) and switches to filterType.consequence multipleListOr. - Source-attribution bug: the old check only inspected the unified AC/AF slot. AllOfUs ships only per-population fields ("." in the unified slot), so all 67M+ AllOfUs variants got no source attribution -- ~43M rows in the previous bigBed had an empty "sources" column. Fix scans per-population slots before declaring "no data". - parse_bcsq() returns "" instead of "." for aaChange/dnaChange on non-coding variants, so the mouseOver and detail page render a clean blank line. - maxAF format: "{:.6g}" -> "{:.6f}" so very small AFs render as "0.000003" instead of "3.31347e-06". - autoSql `table varFreqs` -> `table varFreqsAll` (matches the bigBed filename; required for hgIntegrator wiring). NPM Singapore (SG10K_Health, 9.7k WGS) added to databases.tsv, files.txt, populations.tsv (SgChinese / SgMalay / SgIndian) and the trackDb filter UI. NPM individual subtrack stays tableBrowser off (license); folded into varFreqsAll same as finngen / kova / mgrb / swefreq / tishkoff180. varFreqsAll bigBed rebuild is in progress at /hive/data/genomes/hg38/ bed/varFreqs/all/; will land in /gbdb when the bedToBigBed step completes. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/wigColorByColors/makeWigColorByRevelCadd.py
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    f350ebff8f2cc1e0772032e59e926b5e45b374cd Tue May 5 16:18:28 2026 -0700
    Adding ClinPred missense pathogenicity score track on hg19 and hg38. refs #37510 ClinPred (Alirezaie et al, AJHG 2018) joins the predictionScoresSuper supertrack as a composite of four bigWigs, one per alternate base, with a per-position color overlay (red for score >= 0.5 likely pathogenic, blue for < 0.5 likely benign). Adds clinPredToWig.py to convert the upstream score table to wig, a clinPred branch in makeWigColorByRevelCadd.py for the color overlay step, and reciprocal relatedTracks entries to REVEL, CADD, PrimateAI-3D, and AlphaMissense. Also adds Display Conventions and Credits entries in predictionScoresSuper.html for ClinPred, PrimateAI-3D, and PromoterAI.
• src/hg/makeDb/trackDb/buildRelatedTracks
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    4aa12e0290f91453769f0be4fc5f86ca932fda52 Fri May 8 09:51:50 2026 -0700
    fortify against cron job usage full path to kent commands refs #31811
• src/hg/makeDb/trackDb/buildTrix
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    a0cc27521dca2ea6d5fe90fb27eef33826dfecba Fri May 8 09:56:48 2026 -0700
    fortify against cron job usage full path to kent commands refs #31811
• src/hg/makeDb/trackDb/checkMetaDb
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    55ed63b493027583cbd68e954b9ced58d608fba8 Fri May 8 10:15:15 2026 -0700
    fortify against cron job usage full path to kent commands refs #31811
• src/hg/makeDb/trackDb/hubTxtFromGenArk.pl
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    55ed63b493027583cbd68e954b9ced58d608fba8 Fri May 8 10:15:15 2026 -0700
    fortify against cron job usage full path to kent commands refs #31811
• src/hg/makeDb/trackDb/human/abraom.html
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    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/alfaVcf.html
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    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
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    c16022c991b55ffe9bb620746a6101346c920a67 Tue May 5 14:23:44 2026 -0700
    QA: claim cross-checks on varFreqs description pages; correct 1 internal contradiction and update 3 supertrack references to current/canonical papers. refs #36642 alfaVcf.html: the Description claimed "15.5 million rs sites" while the Methods (and the actual VCF, 163,487,286 records) reflected the post-conversion content. Updated the Description to "163 million variants (146 million SNPs and 17 million indels)" so Description and Methods now agree, and removed the outdated ClinVar count. varFreqs.html (supertrack References): - ABraOM: replaced Naslavsky 2017 Hum Mutat (the 609-individual exome paper) with Naslavsky 2022 Nat Commun (the 1,171-WGS paper), which is the flagship for the data we actually serve and is what abraom.html cites. - Mexico Biobank: added Sohail 2023 Nature ("Mexican Biobank advances population and medical genomics of diverse ancestries"), which is the descriptor paper for the 6,011-individual MEGA-array dataset; the supertrack page previously had no MexBB citation. - ToMMo: replaced Tadaka 2021 NAR (jMorp updates in 2020) with Tadaka 2024 NAR (jMorp Multi-Omics Reference Panel update report 2023), the more recent jMorp release note that tommo60kjpn.html already cites. Other claims spot-checked against the VCF and verified consistent: TopMed (header NS=150,899 matches the page; 868,581,653 records matches exactly), GenomeAsia (~65M / actual 66.2M; 1,739 individuals from 219 populations confirmed), GA4K (552 samples / AN=1,104 / 36.2M variants all verified), SVatalog (8.8M / actual 8,814,835), Tishkoff (33.6M / actual 33,600,472), Saudi (302 individuals / 25.5M variants).
• src/hg/makeDb/trackDb/human/allofus.html
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    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/clinPred.html
  • lines changed 126, context: html, text, full: html, text
    f350ebff8f2cc1e0772032e59e926b5e45b374cd Tue May 5 16:18:28 2026 -0700
    Adding ClinPred missense pathogenicity score track on hg19 and hg38. refs #37510 ClinPred (Alirezaie et al, AJHG 2018) joins the predictionScoresSuper supertrack as a composite of four bigWigs, one per alternate base, with a per-position color overlay (red for score >= 0.5 likely pathogenic, blue for < 0.5 likely benign). Adds clinPredToWig.py to convert the upstream score table to wig, a clinPred branch in makeWigColorByRevelCadd.py for the color overlay step, and reciprocal relatedTracks entries to REVEL, CADD, PrimateAI-3D, and AlphaMissense. Also adds Display Conventions and Credits entries in predictionScoresSuper.html for ClinPred, PrimateAI-3D, and PromoterAI.
• src/hg/makeDb/trackDb/human/clinPred.ra
  • lines changed 70, context: html, text, full: html, text
    f350ebff8f2cc1e0772032e59e926b5e45b374cd Tue May 5 16:18:28 2026 -0700
    Adding ClinPred missense pathogenicity score track on hg19 and hg38. refs #37510 ClinPred (Alirezaie et al, AJHG 2018) joins the predictionScoresSuper supertrack as a composite of four bigWigs, one per alternate base, with a per-position color overlay (red for score >= 0.5 likely pathogenic, blue for < 0.5 likely benign). Adds clinPredToWig.py to convert the upstream score table to wig, a clinPred branch in makeWigColorByRevelCadd.py for the color overlay step, and reciprocal relatedTracks entries to REVEL, CADD, PrimateAI-3D, and AlphaMissense. Also adds Display Conventions and Credits entries in predictionScoresSuper.html for ClinPred, PrimateAI-3D, and PromoterAI.
• src/hg/makeDb/trackDb/human/colorsDbSnv.html
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    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/gasp.html
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    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
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    986c4ede954e44904eb314772fb2cf83a48d307c Wed May 6 06:24:47 2026 -0700
    varFreqs: lift GenomeAsia (gasp + gaspIndel) GRCh37 -> hg38 Both subtracks were served at /gbdb/hg38/ but the upstream callset is GRCh37 (caught in QA, see #36642 note 2026-05-04). Lifted with CrossMap using hg19ToHg38.over.chain.gz; recipe matches tishkoff180 / mxbFreq. gasp (SNVs): 66,236,516 -> 66,222,771 (99.98%; 6,240 unmapped + 7,505 alt/random) gaspIndel: 4,415,156 -> 4,410,871 (99.90%; 3,332 unmapped + 953 alt/random) New driver script: scripts/varFreqs/gaspLift.sh. gaspIndel bigDataUrl renamed from All.indels.annot.cont_withmaf.vcf.gz to ga100k.indels.vcf.gz (old name was a verbatim copy of the upstream download name). varFreqsAll combined bigBed regenerated to fold in the corrected coordinates (36.5 GB, 1,166,451,644 items, 125 fields). refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/gregor.html
  • lines changed 10, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/hg38/cactus447way.html
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    eeb891a1a770321ce23b4a6304d92f53bf0af243 Tue May 5 13:53:54 2026 -0700
    Adding SSREV phyloP content to the cons30way and cactus447way description pages: new SSREV explanation in cons30way, rewrite of the cactus447way intro to list all four phyloP subtracks correctly, a new phyloP Methods subsection, the Pollard 2010 reference, and a missing <li> in the download list, refs #28259
• src/hg/makeDb/trackDb/human/hg38/cons30way.html
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    5bf4519a366ba72f5ab328f50052ea8b64996229 Tue May 5 13:24:47 2026 -0700
    Fixing broken links and fixing typos found by Claude, refs #28259
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    eeb891a1a770321ce23b4a6304d92f53bf0af243 Tue May 5 13:53:54 2026 -0700
    Adding SSREV phyloP content to the cons30way and cactus447way description pages: new SSREV explanation in cons30way, rewrite of the cactus447way intro to list all four phyloP subtracks correctly, a new phyloP Methods subsection, the Pollard 2010 reference, and a missing <li> in the download list, refs #28259
• src/hg/makeDb/trackDb/human/hg38/gencNcOrfs.html
  • lines changed 18, context: html, text, full: html, text
    80a9c846173cd82685ec66c298090085f8720c1b Fri May 8 16:29:07 2026 -0700
    Fixing reference issues found by Claude. Fixing the capitalization of GENCODE, refs #35101
• src/hg/makeDb/trackDb/human/hg38/metamorf.html
  • lines changed 55, context: html, text, full: html, text
    80a9c846173cd82685ec66c298090085f8720c1b Fri May 8 16:29:07 2026 -0700
    Fixing reference issues found by Claude. Fixing the capitalization of GENCODE, refs #35101
• src/hg/makeDb/trackDb/human/hg38/mpraVarDb.html
  • lines changed 17, context: html, text, full: html, text
    5d554d5ba53a383b1805bd4d3958a3aa2dce1cbb Tue May 5 14:33:19 2026 -0700
    Replace &nbsp; with regular spaces in mpraVarDb.html per CR feedback. refs #37504
• src/hg/makeDb/trackDb/human/hg38/ncOrfs.html
  • lines changed 6, context: html, text, full: html, text
    80a9c846173cd82685ec66c298090085f8720c1b Fri May 8 16:29:07 2026 -0700
    Fixing reference issues found by Claude. Fixing the capitalization of GENCODE, refs #35101
• src/hg/makeDb/trackDb/human/hg38/ncOrfs.ra
  • lines changed 7, context: html, text, full: html, text
    41ca3ca7e61769458b94f925a0696284ddc44192 Fri May 8 16:15:46 2026 -0700
    Updating long and shortLabels to be less than 22 characters, refs #35101
  • lines changed 96, context: html, text, full: html, text
    8b1ebf72b693afd8705c36af91d85e9596d1654f Mon May 11 08:31:13 2026 -0700
    adding kozak strengths to ncOrfs, refs #35101, this is only the tdb part
• src/hg/makeDb/trackDb/human/hg38/openprot.html
  • lines changed 18, context: html, text, full: html, text
    80a9c846173cd82685ec66c298090085f8720c1b Fri May 8 16:29:07 2026 -0700
    Fixing reference issues found by Claude. Fixing the capitalization of GENCODE, refs #35101
• src/hg/makeDb/trackDb/human/hg38/trackDb.30way.ra
  • lines changed 1, context: html, text, full: html, text
    63c4992e866795e17433a11d8696eab70ad1e9d1 Tue May 5 10:51:35 2026 -0700
    Fixing typo (SSREF --> SSREV). Updating short and longLabels, refs #28259
  • lines changed 2, context: html, text, full: html, text
    434a78bb9336d3dfbc788083d03f76bcf643803a Tue May 5 13:17:40 2026 -0700
    Adding the logoMaf line and updating the view limits for the SSREV tracks, refs #28259
• src/hg/makeDb/trackDb/human/hg38/trackDb.447way.ra
  • lines changed 3, context: html, text, full: html, text
    63c4992e866795e17433a11d8696eab70ad1e9d1 Tue May 5 10:51:35 2026 -0700
    Fixing typo (SSREF --> SSREV). Updating short and longLabels, refs #28259
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.ra
  • lines changed 1, context: html, text, full: html, text
    bf1405be33b01b7dbde397647de61eefe87e07a5 Sun May 10 16:48:50 2026 -0700
    wgEncodeReg4TfPeaks description page cleanup (em-dashes, AI phrasing, decorator and Shade-of-lowest setting notes, FactorBook/SCREEN linkouts, alphabetical refs) and detailsDynamicTable label fix ("experiments support this rPeak" -> "Experiments supporting this rPeak"). refs #34923
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html
  • lines changed 56, context: html, text, full: html, text
    bf1405be33b01b7dbde397647de61eefe87e07a5 Sun May 10 16:48:50 2026 -0700
    wgEncodeReg4TfPeaks description page cleanup (em-dashes, AI phrasing, decorator and Shade-of-lowest setting notes, FactorBook/SCREEN linkouts, alphabetical refs) and detailsDynamicTable label fix ("experiments support this rPeak" -> "Experiments supporting this rPeak"). refs #34923
  • lines changed 2, context: html, text, full: html, text
    c21fe9e8af0a00bb887b068b67d81846af40cdd4 Sun May 10 17:23:53 2026 -0700
    Removing Decoration settings sentence from wgEncodeReg4TfPeaks description page since the decorations only use block style. refs #34923
• src/hg/makeDb/trackDb/human/hgdp1kFreq.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/hrc.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/indigenomes.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/lrSv.html
  • lines changed 29, context: html, text, full: html, text
    ac18a42f0dafb4febaaeaebcd53fe75df9b83234 Mon May 11 08:29:14 2026 -0700
    lrSv: add Coverage column, drop redundant Sequencing column, rename SVs to SV count Coverage values pulled from the per-subtrack methods sections and the underlying papers (Han 17x, deCODE 17x, GA4K 27x, HPRC 60x HiFi + 30x ONT, etc.). Sequencing technology is now folded into the Coverage cells. Also cross-links to the new HGSVC3 Mobile Insertions tracks. refs #36642
• src/hg/makeDb/trackDb/human/mei.html
  • lines changed 74, context: html, text, full: html, text
    00e086afbcb8296c6aef946c13eeb777f34bac02 Mon May 11 07:03:10 2026 -0700
    mei: new track for HGSVC3 mobile element insertions on hg38 and hs1 12,642 MEIs on hg38, 12,919 on hs1, from the HGSVC3 callset (Logsdon et al. 2025). Single shared trackDb stanza in human/mei.ra with $D substitution. Okabe-Ito colors, INS-svLen:carrierCount item names, inserted DNA in an insertSeq field. Cross-link to lrSv via relatedTracks.ra. refs #37524
• src/hg/makeDb/trackDb/human/mei.ra
  • lines changed 46, context: html, text, full: html, text
    00e086afbcb8296c6aef946c13eeb777f34bac02 Mon May 11 07:03:10 2026 -0700
    mei: new track for HGSVC3 mobile element insertions on hg38 and hs1 12,642 MEIs on hg38, 12,919 on hs1, from the HGSVC3 callset (Logsdon et al. 2025). Single shared trackDb stanza in human/mei.ra with $D substitution. Okabe-Ito colors, INS-svLen:carrierCount item names, inserted DNA in an insertSeq field. Cross-link to lrSv via relatedTracks.ra. refs #37524
• src/hg/makeDb/trackDb/human/meiHgsvc3.html
  • lines changed 158, context: html, text, full: html, text
    00e086afbcb8296c6aef946c13eeb777f34bac02 Mon May 11 07:03:10 2026 -0700
    mei: new track for HGSVC3 mobile element insertions on hg38 and hs1 12,642 MEIs on hg38, 12,919 on hs1, from the HGSVC3 callset (Logsdon et al. 2025). Single shared trackDb stanza in human/mei.ra with $D substitution. Okabe-Ito colors, INS-svLen:carrierCount item names, inserted DNA in an insertSeq field. Cross-link to lrSv via relatedTracks.ra. refs #37524
• src/hg/makeDb/trackDb/human/mgrb.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/npm.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/predictionScoresSuper.html
  • lines changed 47, context: html, text, full: html, text
    f350ebff8f2cc1e0772032e59e926b5e45b374cd Tue May 5 16:18:28 2026 -0700
    Adding ClinPred missense pathogenicity score track on hg19 and hg38. refs #37510 ClinPred (Alirezaie et al, AJHG 2018) joins the predictionScoresSuper supertrack as a composite of four bigWigs, one per alternate base, with a per-position color overlay (red for score >= 0.5 likely pathogenic, blue for < 0.5 likely benign). Adds clinPredToWig.py to convert the upstream score table to wig, a clinPred branch in makeWigColorByRevelCadd.py for the color overlay step, and reciprocal relatedTracks entries to REVEL, CADD, PrimateAI-3D, and AlphaMissense. Also adds Display Conventions and Credits entries in predictionScoresSuper.html for ClinPred, PrimateAI-3D, and PromoterAI.
• src/hg/makeDb/trackDb/human/predictionScoresSuper.ra
  • lines changed 1, context: html, text, full: html, text
    f350ebff8f2cc1e0772032e59e926b5e45b374cd Tue May 5 16:18:28 2026 -0700
    Adding ClinPred missense pathogenicity score track on hg19 and hg38. refs #37510 ClinPred (Alirezaie et al, AJHG 2018) joins the predictionScoresSuper supertrack as a composite of four bigWigs, one per alternate base, with a per-position color overlay (red for score >= 0.5 likely pathogenic, blue for < 0.5 likely benign). Adds clinPredToWig.py to convert the upstream score table to wig, a clinPred branch in makeWigColorByRevelCadd.py for the color overlay step, and reciprocal relatedTracks entries to REVEL, CADD, PrimateAI-3D, and AlphaMissense. Also adds Display Conventions and Credits entries in predictionScoresSuper.html for ClinPred, PrimateAI-3D, and PromoterAI.
• src/hg/makeDb/trackDb/human/saudi.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/schema.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/sfariSparkExomes.html
  • lines changed 2, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/sgdpFreq.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/tommo60kjpn.html
  • lines changed 1, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/topmed.html
  • lines changed 12, context: html, text, full: html, text
    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
• src/hg/makeDb/trackDb/human/trackDb.ra
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    00e086afbcb8296c6aef946c13eeb777f34bac02 Mon May 11 07:03:10 2026 -0700
    mei: new track for HGSVC3 mobile element insertions on hg38 and hs1 12,642 MEIs on hg38, 12,919 on hs1, from the HGSVC3 callset (Logsdon et al. 2025). Single shared trackDb stanza in human/mei.ra with $D substitution. Okabe-Ito colors, INS-svLen:carrierCount item names, inserted DNA in an insertSeq field. Cross-link to lrSv via relatedTracks.ra. refs #37524
• src/hg/makeDb/trackDb/human/varFreqs.html
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    f674b74547b883a2054c4771533d753266e07c06 Mon May 4 16:21:54 2026 -0700
    QA pass on varFreqs supertrack: relabel HGDP+1kG and AllOfUs per-population fields to match data semantics, expose all 7 GenomeAsia populations in filter UI, normalize labels and capitalization, add Methods + References to description page, and flag GenomeAsia GRCh37 coordinate mismatch via dataVersion. refs #36642 trackDb (varFreqs.ra): - HGDP+1kG per-population AC/AF labels relabeled from "gnomAD HGDP+1kG <pop>" to "gnomAD v3.1.2 <pop> (full release)" since the values come from the full ~76k-genome gnomAD release, not the 4,094-genome HGDP+1kG cohort. - AllOfUs per-population AC/AF labels appended with "(local ancestry)" to clarify these are local-ancestry-stratified haplotype frequencies (Ioannidis lab pipeline), not the AllOfUs paper's global Rye categories. - Added 8 new filter entries for GenomeAsia OCE/AMR/AFR/WER (data has 7 population groups; trackUI previously exposed only 3). - shortLabel shortenings: alfaVcf, finngen, gasp, gaspIndel, kova, saudi, schema, colorsDbSnv, tishkoff180. - longLabel shortenings: ga4kSnv, colorsDbSnv, svatalogSnv, tishkoff180. - Capitalization fixes: SFARI Spark to SFARI SPARK, Japan ToMMO to Japan ToMMo, NHLBI TOPMED to NHLBI TOPMed. - dataVersion added on 6 subtracks that lacked it (gasp, gaspIndel, indigenomes, saudi, ga4kSnv, svatalogSnv); gasp/gaspIndel flagged "Pilot 2019 (GRCh37 - to be lifted)" for visibility of the open hg19 issue. - Default visibility flipped: non-summary subtracks now dense, summary varFreqsAll now pack. Container stays hide. Description page (varFreqs.html): - Added References section with 21 primary publications for the source cohorts. - Added "Notes on Specific Sub-tracks" explaining the HGDP+1kG cohort vs full-release distinction and the AllOfUs locAncFreq semantics. - Added Methods section describing per-subtrack and combined-track build pipelines, with links to the GitHub scripts directory and makedoc. - Encoded genome@soe.ucsc.edu with encodeEmail.pl. - Corrected "more than 1.2 billion variants" to "1.17 billion" (actual varFreqsAll.bb itemCount: 1,169,063,801). - Normalized body-text quotes to &quot; entities. - AllOfUs and HGDP+1kG rows in the datasets table now flag the semantic distinction inline. Build config (scripts/varFreqs/populations.tsv): - Added 4 GenomeAsia rows (OCE, AMR, AFR, WER) so the next varFreqsAll bigBed rebuild will populate the new filter columns. - Fixed HGDP1kG nfe label "European" to "Non-Finnish European" to match the trackdb relabel.
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    c16022c991b55ffe9bb620746a6101346c920a67 Tue May 5 14:23:44 2026 -0700
    QA: claim cross-checks on varFreqs description pages; correct 1 internal contradiction and update 3 supertrack references to current/canonical papers. refs #36642 alfaVcf.html: the Description claimed "15.5 million rs sites" while the Methods (and the actual VCF, 163,487,286 records) reflected the post-conversion content. Updated the Description to "163 million variants (146 million SNPs and 17 million indels)" so Description and Methods now agree, and removed the outdated ClinVar count. varFreqs.html (supertrack References): - ABraOM: replaced Naslavsky 2017 Hum Mutat (the 609-individual exome paper) with Naslavsky 2022 Nat Commun (the 1,171-WGS paper), which is the flagship for the data we actually serve and is what abraom.html cites. - Mexico Biobank: added Sohail 2023 Nature ("Mexican Biobank advances population and medical genomics of diverse ancestries"), which is the descriptor paper for the 6,011-individual MEGA-array dataset; the supertrack page previously had no MexBB citation. - ToMMo: replaced Tadaka 2021 NAR (jMorp updates in 2020) with Tadaka 2024 NAR (jMorp Multi-Omics Reference Panel update report 2023), the more recent jMorp release note that tommo60kjpn.html already cites. Other claims spot-checked against the VCF and verified consistent: TopMed (header NS=150,899 matches the page; 868,581,653 records matches exactly), GenomeAsia (~65M / actual 66.2M; 1,739 individuals from 219 populations confirmed), GA4K (552 samples / AN=1,104 / 36.2M variants all verified), SVatalog (8.8M / actual 8,814,835), Tishkoff (33.6M / actual 33,600,472), Saudi (302 individuals / 25.5M variants).
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    ec5c73f4dc3ef4beae16fa1c12b7e5bf872bb73d Tue May 5 15:04:39 2026 -0700
    varFreqs: fix gaspIndel bigDataUrl after Max's GenomeAsia hg38 lift; add Tishkoff180 to combined-track filter UI; sync databases.tsv with deployed bigBed; minor description-page corrections. refs #36642 GenomeAsia hg38 lift (May 5 2026, by Max): - gaspIndel.bigDataUrl was pointing at the old GRCh37 filename "All.indels.annot.cont_withmaf.vcf.gz" which was renamed to "ga100k.indels.vcf.gz" during the lift; this left the gaspIndel track broken on the sandbox until the trackdb stanza was updated to match. - gasp/gaspIndel dataVersion strings updated from "Pilot 2019 (GRCh37 - to be lifted)" to "Pilot 2019 (lifted to hg38, May 2026)". - databases.tsv: also updated GenomeAsiaIndel path to ga100k.indels.vcf.gz so the next varFreqsAll rebuild reads from the lifted file. Tishkoff180 in varFreqsAll.bb but unfilterable (fresh-eyes audit finding): - Added Tishkoff180 to filterValues.sources and added filterByRange.Tishkoff180AF / Tishkoff180AC entries. - Added Tishkoff180 (and SVatalog) rows to databases.tsv to match the deployed bigBed (which already has those columns). Description-page corrections: - varFreqsAll.html: "20 population databases" -> "25 source databases" (matches actual count); HGDP+1kG bullet "European" -> "Non-Finnish European" to disambiguate from Finnish (gnomAD's nfe). - varFreqs.html: GenomeAsia row in the Available Datasets table updated from 3 to 7 sub-populations (NEA/SEA/SAS plus the previously hidden OCE/AMR/AFR/WER) so the table matches what the data exposes once Max's rebuild populates the new filter columns. - KOVA longLabel: "1.9k WGS+3.5k WES" -> "1.9k WGS+3.4k WES" (3.4k is correct per Lee 2017 and kova.html).
• src/hg/makeDb/trackDb/human/varFreqs.ra
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    f674b74547b883a2054c4771533d753266e07c06 Mon May 4 16:21:54 2026 -0700
    QA pass on varFreqs supertrack: relabel HGDP+1kG and AllOfUs per-population fields to match data semantics, expose all 7 GenomeAsia populations in filter UI, normalize labels and capitalization, add Methods + References to description page, and flag GenomeAsia GRCh37 coordinate mismatch via dataVersion. refs #36642 trackDb (varFreqs.ra): - HGDP+1kG per-population AC/AF labels relabeled from "gnomAD HGDP+1kG <pop>" to "gnomAD v3.1.2 <pop> (full release)" since the values come from the full ~76k-genome gnomAD release, not the 4,094-genome HGDP+1kG cohort. - AllOfUs per-population AC/AF labels appended with "(local ancestry)" to clarify these are local-ancestry-stratified haplotype frequencies (Ioannidis lab pipeline), not the AllOfUs paper's global Rye categories. - Added 8 new filter entries for GenomeAsia OCE/AMR/AFR/WER (data has 7 population groups; trackUI previously exposed only 3). - shortLabel shortenings: alfaVcf, finngen, gasp, gaspIndel, kova, saudi, schema, colorsDbSnv, tishkoff180. - longLabel shortenings: ga4kSnv, colorsDbSnv, svatalogSnv, tishkoff180. - Capitalization fixes: SFARI Spark to SFARI SPARK, Japan ToMMO to Japan ToMMo, NHLBI TOPMED to NHLBI TOPMed. - dataVersion added on 6 subtracks that lacked it (gasp, gaspIndel, indigenomes, saudi, ga4kSnv, svatalogSnv); gasp/gaspIndel flagged "Pilot 2019 (GRCh37 - to be lifted)" for visibility of the open hg19 issue. - Default visibility flipped: non-summary subtracks now dense, summary varFreqsAll now pack. Container stays hide. Description page (varFreqs.html): - Added References section with 21 primary publications for the source cohorts. - Added "Notes on Specific Sub-tracks" explaining the HGDP+1kG cohort vs full-release distinction and the AllOfUs locAncFreq semantics. - Added Methods section describing per-subtrack and combined-track build pipelines, with links to the GitHub scripts directory and makedoc. - Encoded genome@soe.ucsc.edu with encodeEmail.pl. - Corrected "more than 1.2 billion variants" to "1.17 billion" (actual varFreqsAll.bb itemCount: 1,169,063,801). - Normalized body-text quotes to &quot; entities. - AllOfUs and HGDP+1kG rows in the datasets table now flag the semantic distinction inline. Build config (scripts/varFreqs/populations.tsv): - Added 4 GenomeAsia rows (OCE, AMR, AFR, WER) so the next varFreqsAll bigBed rebuild will populate the new filter columns. - Fixed HGDP1kG nfe label "European" to "Non-Finnish European" to match the trackdb relabel.
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    ec5c73f4dc3ef4beae16fa1c12b7e5bf872bb73d Tue May 5 15:04:39 2026 -0700
    varFreqs: fix gaspIndel bigDataUrl after Max's GenomeAsia hg38 lift; add Tishkoff180 to combined-track filter UI; sync databases.tsv with deployed bigBed; minor description-page corrections. refs #36642 GenomeAsia hg38 lift (May 5 2026, by Max): - gaspIndel.bigDataUrl was pointing at the old GRCh37 filename "All.indels.annot.cont_withmaf.vcf.gz" which was renamed to "ga100k.indels.vcf.gz" during the lift; this left the gaspIndel track broken on the sandbox until the trackdb stanza was updated to match. - gasp/gaspIndel dataVersion strings updated from "Pilot 2019 (GRCh37 - to be lifted)" to "Pilot 2019 (lifted to hg38, May 2026)". - databases.tsv: also updated GenomeAsiaIndel path to ga100k.indels.vcf.gz so the next varFreqsAll rebuild reads from the lifted file. Tishkoff180 in varFreqsAll.bb but unfilterable (fresh-eyes audit finding): - Added Tishkoff180 to filterValues.sources and added filterByRange.Tishkoff180AF / Tishkoff180AC entries. - Added Tishkoff180 (and SVatalog) rows to databases.tsv to match the deployed bigBed (which already has those columns). Description-page corrections: - varFreqsAll.html: "20 population databases" -> "25 source databases" (matches actual count); HGDP+1kG bullet "European" -> "Non-Finnish European" to disambiguate from Finnish (gnomAD's nfe). - varFreqs.html: GenomeAsia row in the Available Datasets table updated from 3 to 7 sub-populations (NEA/SEA/SAS plus the previously hidden OCE/AMR/AFR/WER) so the table matches what the data exposes once Max's rebuild populates the new filter columns. - KOVA longLabel: "1.9k WGS+3.5k WES" -> "1.9k WGS+3.4k WES" (3.4k is correct per Lee 2017 and kova.html).
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    8790628157f14caae701bfc3d793150127c13812 Tue May 5 16:27:53 2026 -0700
    varFreqs: add a 7-line mouseOver to the varFreqsAll combined track exposing variant identity, AA change, var type, consequence, max AF, total AC, and source databases. refs #36642 Replaces a previously commented-out 2-field mouseOver with a labeled 7-line tooltip designed to answer the questions a user typically has on hover: what is this variant, what protein change does it cause, which consequence bucket, how rare is it, how many alleles, and which population databases call it. The fields are the existing AutoSql columns on varFreqsAll.bb so no data rebuild is required.
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    dfee6d0940b88f5e537a436263bcb7f8bea5d3a8 Tue May 5 16:42:04 2026 -0700
    varFreqs: fix varFreqsAll mouseOver to use HTML (<br> + <b>) instead of \n. refs #36642 The previous commit 8790628157f used \n for line breaks, which is not what UCSC trackdb mouseOver supports — the trackDb tooltip renders the value as HTML, so newlines need to be <br> tags. Verified live in the sandbox: data-tooltip on each <area> now correctly renders with bolded labels and line breaks. Also bolds the field labels (Var, AA change, Var type, Conseq, Max AF, Total AC, Sources) for readability, matching the convention seen in uniprot.ra and other tracks.
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    986c4ede954e44904eb314772fb2cf83a48d307c Wed May 6 06:24:47 2026 -0700
    varFreqs: lift GenomeAsia (gasp + gaspIndel) GRCh37 -> hg38 Both subtracks were served at /gbdb/hg38/ but the upstream callset is GRCh37 (caught in QA, see #36642 note 2026-05-04). Lifted with CrossMap using hg19ToHg38.over.chain.gz; recipe matches tishkoff180 / mxbFreq. gasp (SNVs): 66,236,516 -> 66,222,771 (99.98%; 6,240 unmapped + 7,505 alt/random) gaspIndel: 4,415,156 -> 4,410,871 (99.90%; 3,332 unmapped + 953 alt/random) New driver script: scripts/varFreqs/gaspLift.sh. gaspIndel bigDataUrl renamed from All.indels.annot.cont_withmaf.vcf.gz to ga100k.indels.vcf.gz (old name was a verbatim copy of the upstream download name). varFreqsAll combined bigBed regenerated to fold in the corrected coordinates (36.5 GB, 1,166,451,644 items, 125 fields). refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    65da29c9d74d4dd832ab7f16899ad3b209b92da4 Wed May 6 08:43:57 2026 -0700
    varFreqs: 5 vcfToBigBed.py fixes + add NPM Singapore to combined track vcfToBigBed.py and mergeAndAnnotate.sh moved into kent (they were hive-only); the build is now reproducible from a fresh kent checkout. Five vcfToBigBed.py fixes (all caught by Lou's QA pass on #36642): - normalize_consequence(): bcftools csq emits "&"-joined compound terms like "stop_gained&frameshift" which exact-match-failed the old 8-bucket consequence filter and orphaned ~8.5M records. Rewrites "&" to "," so a single record can match multiple buckets, and appends ",others" to any token list with no named-filter token. Trackdb gains 4 buckets (3' UTR, 5' UTR, Non-coding, Other) and switches to filterType.consequence multipleListOr. - Source-attribution bug: the old check only inspected the unified AC/AF slot. AllOfUs ships only per-population fields ("." in the unified slot), so all 67M+ AllOfUs variants got no source attribution -- ~43M rows in the previous bigBed had an empty "sources" column. Fix scans per-population slots before declaring "no data". - parse_bcsq() returns "" instead of "." for aaChange/dnaChange on non-coding variants, so the mouseOver and detail page render a clean blank line. - maxAF format: "{:.6g}" -> "{:.6f}" so very small AFs render as "0.000003" instead of "3.31347e-06". - autoSql `table varFreqs` -> `table varFreqsAll` (matches the bigBed filename; required for hgIntegrator wiring). NPM Singapore (SG10K_Health, 9.7k WGS) added to databases.tsv, files.txt, populations.tsv (SgChinese / SgMalay / SgIndian) and the trackDb filter UI. NPM individual subtrack stays tableBrowser off (license); folded into varFreqsAll same as finngen / kova / mgrb / swefreq / tishkoff180. varFreqsAll bigBed rebuild is in progress at /hive/data/genomes/hg38/ bed/varFreqs/all/; will land in /gbdb when the bedToBigBed step completes. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/varFreqsAll.html
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    38bafc856320cf5360e0482faeee72b78f2ea963 Tue May 5 14:13:30 2026 -0700
    QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set.
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    ec5c73f4dc3ef4beae16fa1c12b7e5bf872bb73d Tue May 5 15:04:39 2026 -0700
    varFreqs: fix gaspIndel bigDataUrl after Max's GenomeAsia hg38 lift; add Tishkoff180 to combined-track filter UI; sync databases.tsv with deployed bigBed; minor description-page corrections. refs #36642 GenomeAsia hg38 lift (May 5 2026, by Max): - gaspIndel.bigDataUrl was pointing at the old GRCh37 filename "All.indels.annot.cont_withmaf.vcf.gz" which was renamed to "ga100k.indels.vcf.gz" during the lift; this left the gaspIndel track broken on the sandbox until the trackdb stanza was updated to match. - gasp/gaspIndel dataVersion strings updated from "Pilot 2019 (GRCh37 - to be lifted)" to "Pilot 2019 (lifted to hg38, May 2026)". - databases.tsv: also updated GenomeAsiaIndel path to ga100k.indels.vcf.gz so the next varFreqsAll rebuild reads from the lifted file. Tishkoff180 in varFreqsAll.bb but unfilterable (fresh-eyes audit finding): - Added Tishkoff180 to filterValues.sources and added filterByRange.Tishkoff180AF / Tishkoff180AC entries. - Added Tishkoff180 (and SVatalog) rows to databases.tsv to match the deployed bigBed (which already has those columns). Description-page corrections: - varFreqsAll.html: "20 population databases" -> "25 source databases" (matches actual count); HGDP+1kG bullet "European" -> "Non-Finnish European" to disambiguate from Finnish (gnomAD's nfe). - varFreqs.html: GenomeAsia row in the Available Datasets table updated from 3 to 7 sub-populations (NEA/SEA/SAS plus the previously hidden OCE/AMR/AFR/WER) so the table matches what the data exposes once Max's rebuild populates the new filter columns. - KOVA longLabel: "1.9k WGS+3.5k WES" -> "1.9k WGS+3.4k WES" (3.4k is correct per Lee 2017 and kova.html).
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    65da29c9d74d4dd832ab7f16899ad3b209b92da4 Wed May 6 08:43:57 2026 -0700
    varFreqs: 5 vcfToBigBed.py fixes + add NPM Singapore to combined track vcfToBigBed.py and mergeAndAnnotate.sh moved into kent (they were hive-only); the build is now reproducible from a fresh kent checkout. Five vcfToBigBed.py fixes (all caught by Lou's QA pass on #36642): - normalize_consequence(): bcftools csq emits "&"-joined compound terms like "stop_gained&frameshift" which exact-match-failed the old 8-bucket consequence filter and orphaned ~8.5M records. Rewrites "&" to "," so a single record can match multiple buckets, and appends ",others" to any token list with no named-filter token. Trackdb gains 4 buckets (3' UTR, 5' UTR, Non-coding, Other) and switches to filterType.consequence multipleListOr. - Source-attribution bug: the old check only inspected the unified AC/AF slot. AllOfUs ships only per-population fields ("." in the unified slot), so all 67M+ AllOfUs variants got no source attribution -- ~43M rows in the previous bigBed had an empty "sources" column. Fix scans per-population slots before declaring "no data". - parse_bcsq() returns "" instead of "." for aaChange/dnaChange on non-coding variants, so the mouseOver and detail page render a clean blank line. - maxAF format: "{:.6g}" -> "{:.6f}" so very small AFs render as "0.000003" instead of "3.31347e-06". - autoSql `table varFreqs` -> `table varFreqsAll` (matches the bigBed filename; required for hgIntegrator wiring). NPM Singapore (SG10K_Health, 9.7k WGS) added to databases.tsv, files.txt, populations.tsv (SgChinese / SgMalay / SgIndian) and the trackDb filter UI. NPM individual subtrack stays tableBrowser off (license); folded into varFreqsAll same as finngen / kova / mgrb / swefreq / tishkoff180. varFreqsAll bigBed rebuild is in progress at /hive/data/genomes/hg38/ bed/varFreqs/all/; will land in /gbdb when the bedToBigBed step completes. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/loadTracks
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    be8c719942e930d2f4846f231297120d03b4826d Fri May 8 08:15:49 2026 -0700
    fortify against cron job usage full path to hgsql command refs #31811
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    d25bea3289a29e2c24fa84bd84285ecb4a0d1188 Fri May 8 09:14:31 2026 -0700
    fortify against cron job usage full path to kent commands refs #31811
• src/hg/makeDb/trackDb/makeMetaDb
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    55ed63b493027583cbd68e954b9ced58d608fba8 Fri May 8 10:15:15 2026 -0700
    fortify against cron job usage full path to kent commands refs #31811
• src/hg/makeDb/trackDb/makeTrixLinks
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    55ed63b493027583cbd68e954b9ced58d608fba8 Fri May 8 10:15:15 2026 -0700
    fortify against cron job usage full path to kent commands refs #31811
• src/hg/makeDb/trackDb/makefile
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    329cf5cc379f5158995d59530a51aafd51dd11cb Fri May 8 09:23:23 2026 -0700
    fortify against cron job usage full path to kent commands refs #31811
• src/hg/makeDb/trackDb/maybeBuildHub
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    78377989820616cc99f1e3aca34aca1cd27bafa2 Fri May 8 10:00:45 2026 -0700
    fortify against cron job usage full path to kent commands refs #31811
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
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    08402ed691ea91d15ad8fd3daf8b7f8d3578a8d8 Thu May 7 10:53:11 2026 -0700
    VGP 577-way track enabled refs #34370
• src/hg/makeDb/trackDb/mouse/mm39/vgp577way.trackDb.ra
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    08402ed691ea91d15ad8fd3daf8b7f8d3578a8d8 Thu May 7 10:53:11 2026 -0700
    VGP 577-way track enabled refs #34370
• src/hg/makeDb/trackDb/relatedTracks.ra
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    f350ebff8f2cc1e0772032e59e926b5e45b374cd Tue May 5 16:18:28 2026 -0700
    Adding ClinPred missense pathogenicity score track on hg19 and hg38. refs #37510 ClinPred (Alirezaie et al, AJHG 2018) joins the predictionScoresSuper supertrack as a composite of four bigWigs, one per alternate base, with a per-position color overlay (red for score >= 0.5 likely pathogenic, blue for < 0.5 likely benign). Adds clinPredToWig.py to convert the upstream score table to wig, a clinPred branch in makeWigColorByRevelCadd.py for the color overlay step, and reciprocal relatedTracks entries to REVEL, CADD, PrimateAI-3D, and AlphaMissense. Also adds Display Conventions and Credits entries in predictionScoresSuper.html for ClinPred, PrimateAI-3D, and PromoterAI.
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    00e086afbcb8296c6aef946c13eeb777f34bac02 Mon May 11 07:03:10 2026 -0700
    mei: new track for HGSVC3 mobile element insertions on hg38 and hs1 12,642 MEIs on hg38, 12,919 on hs1, from the HGSVC3 callset (Logsdon et al. 2025). Single shared trackDb stanza in human/mei.ra with $D substitution. Okabe-Ito colors, INS-svLen:carrierCount item names, inserted DNA in an insertSeq field. Cross-link to lrSv via relatedTracks.ra. refs #37524
• src/hg/makeDb/trackDb/worm/ce11/ce11.GCA_000180635.4.chainNet.ra
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    c10a3a45de693f5470abb7ba36b6a1567cbca67c Thu May 7 13:01:04 2026 -0700
    chainNet trackDb for ce11 GCA_000180635.4, otto liftOver
• src/hg/makeDb/trackDb/worm/ce11/ce11.danRer11.chainNet.ra
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    3e52b82695dfd0b5f63b3f5d1505f600647e7143 Mon May 11 09:20:54 2026 -0700
    chainNet trackDb for ce11 danRer11, otto liftOver
• src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
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    c10a3a45de693f5470abb7ba36b6a1567cbca67c Thu May 7 13:01:04 2026 -0700
    chainNet trackDb for ce11 GCA_000180635.4, otto liftOver
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    3e52b82695dfd0b5f63b3f5d1505f600647e7143 Mon May 11 09:20:54 2026 -0700
    chainNet trackDb for ce11 danRer11, otto liftOver
• src/hg/makeDb/trackDb/zebrafish/danRer11/danRer11.GCA_052040795.1.chainNet.ra
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    11f37d009d2ccde22aea894922d55addb6802b07 Fri May 8 09:09:20 2026 -0700
    chainNet trackDb for danRer11 GCA_052040795.1, otto liftOver
• src/hg/makeDb/trackDb/zebrafish/danRer11/danRer11.ce11.chainNet.ra
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    ca8a1a9cc6ae1705396dd14c82ed7e11ccfe9017 Mon May 11 09:20:46 2026 -0700
    chainNet trackDb for danRer11 ce11, otto liftOver
• src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra
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    11f37d009d2ccde22aea894922d55addb6802b07 Fri May 8 09:09:20 2026 -0700
    chainNet trackDb for danRer11 GCA_052040795.1, otto liftOver
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    ca8a1a9cc6ae1705396dd14c82ed7e11ccfe9017 Mon May 11 09:20:46 2026 -0700
    chainNet trackDb for danRer11 ce11, otto liftOver
• src/hg/mouseStuff/chainToMaf/tests/makefile
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    2da9964103135a26ecc753c4afbb33dea7a9324c Tue May 5 19:52:29 2026 -0700
    added for chainToMaf suggested by Hiram
• src/hg/utils/automation/aliasTextToBed.pl
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    78be2a814ea9a2f97515f8937b8d1480893b2822 Fri May 8 12:02:51 2026 -0700
    add plasmoDB as a naming scheme
• src/hg/utils/automation/asmHubChainNetTrackDb.sh
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    128037dded4246f2963b7ef08e8f4f1085a6c4eb Thu May 7 14:51:38 2026 -0700
    cron safe full path to hgsql refs #31811
• src/hg/utils/otto/userRequests/chainNetTrackDb.pl
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    80cbd6bce96d71ce3e03be94934cbff7b4521a4b Thu May 7 13:14:24 2026 -0700
    the trackDb update process for UCSC database assemblies refs #31811
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    46f246dc334a47ded8a439de133f6d94ef9dae81 Thu May 7 14:40:00 2026 -0700
    now working correctly with UCSC database assemblies for pushing the lift.over file out to hgdownload refs #31811
• src/hg/utils/otto/userRequests/ottoRequestPush.py
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    46f246dc334a47ded8a439de133f6d94ef9dae81 Thu May 7 14:40:00 2026 -0700
    now working correctly with UCSC database assemblies for pushing the lift.over file out to hgdownload refs #31811
• src/hg/utils/otto/userRequests/ottoRequestView.cgi
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    46f246dc334a47ded8a439de133f6d94ef9dae81 Thu May 7 14:40:00 2026 -0700
    now working correctly with UCSC database assemblies for pushing the lift.over file out to hgdownload refs #31811
• src/hg/utils/otto/userRequests/ottoRequestWatch.sh
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    46f246dc334a47ded8a439de133f6d94ef9dae81 Thu May 7 14:40:00 2026 -0700
    now working correctly with UCSC database assemblies for pushing the lift.over file out to hgdownload refs #31811
• src/hg/utils/phyloTrees/findScores.pl
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    2fe7f1d880ccd04daa45aa69719e963981ee3470 Thu May 7 13:36:43 2026 -0700
    updated to work with the galaxy workflow .yaml file refs #31811
• src/hg/utils/rts/rtsUpdate
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    1b38723574b05053668a698a9856652a077fce2f Mon May 4 14:48:55 2026 -0700
    First draft of rtsUpdate, a utility to streamline pushing Recommended Track Set sessions from a curator session through dev -> beta -> RR. Replaces the manual download-and-resave-on-every-mirror process. Each step is gated by an interactive confirmation; RR push has an additional --i-confirm-rr flag and a 5-second pause. Cart contents written via MySQL _binary 0xHEX literals for binary safety; sessionName regex-validated; WHERE clauses are exact-equality only. The kent tree (rts/<db>/<sessionName>) is the canonical backup, tracked by git. Not yet exercised against a live update. refs #32768
• src/inc/cheapcgi.h
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    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/lib/cheapcgi.c
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    d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
    Fixes from code review, refs #37500 - Revalidate shared myVariants tracks against hgcentral on every read path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no longer trusted. New myVariantsResolveSharedTrack helper. - Scope shared-track UPDATE statements by share->project/db so a recipient can't edit rows outside the granted scope. - Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the hgTracks.js highlight Add-Annotation POST. - HTML-escape owner-controlled fields in the canEdit branch of doMyVariantsDetails (Chromosome, Project, project select options, hidden text input). - Validate targetUser against gbMembers when creating a share; return a clear 400 on typos. - Replace the concat(id,' ',name)='%s' lookup with parsed-id + name verification. - Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form uses spectrum.js (already loaded for the create dialog). - Strip _hidden_* columns from hgTables field lists for shared tracks, both the display path and the selected-fields read path. - Make the per-assembly invariant explicit: myVariantsLoadItems and doMyVariantsDetails bail out if share->db != current database. - Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral round-trips on genome-wide hgTables queries. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/lib/jsonParse.c
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    1da15f230f81e48dd030f04649f186688cefd933 Thu May 7 11:58:06 2026 -0700
    Fix incorrect strncpy call in jsonParse with a better snippage of the input string that avoids a strncpy altogether, refs #37500

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