All File Changes

v495_preview2 to v495_base (2026-03-02 to 2026-03-09) v495

• confs/hgwdev.hg.conf
  • lines changed 1, context: html, text, full: html, text
    3ac87d72e38e028b80b9171ae70466c6aeefde2f Sun Mar 8 01:11:16 2026 -0800
    Installing updated hg.conf files from UCSC servers
• docs/genomeBrowserGlossary.md
  • lines changed 486, context: html, text, full: html, text
    db04a602ccfef6857085f2a227eefc44e6051044 Wed Mar 4 18:40:53 2026 -0800
    adding new genome browser glossary page, refs #35259
  • lines changed 112, context: html, text, full: html, text
    3647084be920c90718eafc5b419ca2992ae65817 Thu Mar 5 10:37:37 2026 -0800
    Adding additional terms to the glossary page, refs #35259
• docs/page_template.md
  • lines changed 2, context: html, text, full: html, text
    2e404f055cc699b47719d19c9ff81682c065bb5e Mon Mar 2 17:57:57 2026 -0800
    Fixing a missing character in the lua rules for the docs markdown, refs #36894
• docs/staticPage.lua
  • lines changed 1, context: html, text, full: html, text
    2e404f055cc699b47719d19c9ff81682c065bb5e Mon Mar 2 17:57:57 2026 -0800
    Fixing a missing character in the lua rules for the docs markdown, refs #36894
  • lines changed 2, context: html, text, full: html, text
    adbb81edbcdfde3cde3c27f9756a6e18fd3abdb1 Mon Mar 9 09:27:41 2026 -0700
    Small fixes to the lua rules that were messing up the column spacing for markdown tables, and a double escaping when links were placed inside tables, refs #36894
• src/hg/hgBlat/hgBlat.c
  • lines changed 3, context: html, text, full: html, text
    754cf0e3c480484878009aa5ce6dd815f1126d0c Fri Mar 6 15:02:34 2026 -0800
    most public assembly hubs do not have blat/pcr servers available, so when a public hub has been selected from the 'recents' dropdown in the search bar on those cgis, submit their form so the backend can print a message to page telling the user we don't have blat/pcr availabel for those assemblies, refs #36535
• src/hg/hgConvert/hgConvert.c
  • lines changed 20, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
  • lines changed 2, context: html, text, full: html, text
    58c24abcdc7e2fe836db993243c6ac15fce457b5 Wed Mar 4 15:20:15 2026 -0800
    Fix more universal species search bugs: hgConvert re-factor meant two hidden form variables were created for the hglft_toDb variable, so remove one of them; make organism comparison case insensitive so 'human' matches 'Human', as genark results are typically lower case; append hubUrl to hgGateway gotohgTracks form so any searched genark hub shows up as a connected hub on hgHubConnect, refs #36535, #36232
  • lines changed 8, context: html, text, full: html, text
    5247d2f093c036439e46930a40607d2a47a05f25 Thu Mar 5 11:34:12 2026 -0800
    For hgConvert only, filter the popular genomes list in the toDb section by what liftover chains we have available for the fromDb, refs #36232
  • lines changed 14, context: html, text, full: html, text
    c7221bad6eda31fe88c6f9880276d8f993ff876e Thu Mar 5 12:37:14 2026 -0800
    Disable recent/popular species list selection in the hgConvert toDb dropdown if there are no chains available to them. Leave them in the list but unselectable, refs #36232
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 28, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
• src/hg/hgPcr/hgPcr.c
  • lines changed 2, context: html, text, full: html, text
    754cf0e3c480484878009aa5ce6dd815f1126d0c Fri Mar 6 15:02:34 2026 -0800
    most public assembly hubs do not have blat/pcr servers available, so when a public hub has been selected from the 'recents' dropdown in the search bar on those cgis, submit their form so the backend can print a message to page telling the user we don't have blat/pcr availabel for those assemblies, refs #36535
• src/hg/hgSearch/hgSearch.c
  • lines changed 31, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 5, context: html, text, full: html, text
    a3244b1059b27424713c97be5694c716d1b90172 Thu Mar 5 11:36:07 2026 -0800
    fixing bug in supertrack UI that appears when the track name has a dot in it, refs #36917, also uppercasing the visibilities, refs #37200
  • lines changed 5, context: html, text, full: html, text
    d4beb65c6ee1c8b31b134f949e03fa717f449af1 Mon Mar 9 08:26:56 2026 -0700
    Updating the text for the superTrack hgTrackUi, refs #36917
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    bcffaeb1cb9691429a39b40aaba346cec07f746d Mon Mar 2 18:36:01 2026 -0800
    Fix from code review. refs #37175,#37189
• src/hg/htdocs/goldenPath/help/barChart.html
  • lines changed 7, context: html, text, full: html, text
    fcd19999608dd4b9e0ca67016a838ca7dce1fd3f Thu Mar 5 09:46:22 2026 -0800
    Documenting the singleCellColumnNames trackDb setting, refs #37176
• src/hg/htdocs/goldenPath/help/heatmap.html
  • lines changed 232, context: html, text, full: html, text
    7095388baafcb7a9caac1086e9d737ea53b7151d Mon Mar 9 09:45:54 2026 -0700
    Docs tutorial for building a heatmap, refs #36176
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 2, context: html, text, full: html, text
    e1267c28ad3cdef044c73a85505da118d735815e Fri Mar 6 15:32:49 2026 -0800
    Making changes from code review. Mostly fixing typos, and creating a Methods section for the gnomAD coverage tracks, refs #37191
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 1, context: html, text, full: html, text
    e1267c28ad3cdef044c73a85505da118d735815e Fri Mar 6 15:32:49 2026 -0800
    Making changes from code review. Mostly fixing typos, and creating a Methods section for the gnomAD coverage tracks, refs #37191
• src/hg/htdocs/goldenPath/help/trackDb/changes.html
  • lines changed 24, context: html, text, full: html, text
    65a50016325861dc30c79f0992b65fb84a832dfe Mon Mar 9 09:58:28 2026 -0700
    trackDb docs for positional heatmaps, and linking in style settings, refs #36176, #36320
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 6, context: html, text, full: html, text
    fcd19999608dd4b9e0ca67016a838ca7dce1fd3f Thu Mar 5 09:46:22 2026 -0800
    Documenting the singleCellColumnNames trackDb setting, refs #37176
  • lines changed 39, context: html, text, full: html, text
    65a50016325861dc30c79f0992b65fb84a832dfe Mon Mar 9 09:58:28 2026 -0700
    trackDb docs for positional heatmaps, and linking in style settings, refs #36176, #36320
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 6, context: html, text, full: html, text
    fcd19999608dd4b9e0ca67016a838ca7dce1fd3f Thu Mar 5 09:46:22 2026 -0800
    Documenting the singleCellColumnNames trackDb setting, refs #37176
  • lines changed 63, context: html, text, full: html, text
    b708cb50f27e0480117869c4b44d69dcb3afeb40 Sat Mar 7 10:03:23 2026 -0800
    redoing intro for trackDb settings page, refs #37080
  • lines changed 32, context: html, text, full: html, text
    c22d2aab961e183d9765bb3913c3dc0807b4449e Sat Mar 7 11:15:47 2026 -0800
    minor tweaks based on feedback, refs #37080
  • lines changed 39, context: html, text, full: html, text
    65a50016325861dc30c79f0992b65fb84a832dfe Mon Mar 9 09:58:28 2026 -0700
    trackDb docs for positional heatmaps, and linking in style settings, refs #36176, #36320
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 11, context: html, text, full: html, text
    fcd19999608dd4b9e0ca67016a838ca7dce1fd3f Thu Mar 5 09:46:22 2026 -0800
    Documenting the singleCellColumnNames trackDb setting, refs #37176
  • lines changed 161, context: html, text, full: html, text
    65a50016325861dc30c79f0992b65fb84a832dfe Mon Mar 9 09:58:28 2026 -0700
    trackDb docs for positional heatmaps, and linking in style settings, refs #36176, #36320
• src/hg/htdocs/inc/hgSearch.html
  • lines changed 1, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
• src/hg/htdocs/store.html
  • lines changed 132, context: html, text, full: html, text
    4677e4639ee53f9c3556c2c195db517f7e4e1618 Fri Mar 6 16:08:14 2026 -0800
    Update to store after code review, did not change verb tense yet.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 17, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
• src/hg/hubApi/apiUtils.c
  • lines changed 8, context: html, text, full: html, text
    38576ff088798cb5e90741256ed0b5b20fde8346 Wed Mar 4 16:43:03 2026 -0800
    Claude recommended this change to the hub connection to avoid the error of a stale errorMessage in the hubStatus table
• src/hg/hubApi/dataApi.h
  • lines changed 3, context: html, text, full: html, text
    9c7de0bd83bc6e1876dc0b8b7091127629a07bf0 Thu Mar 5 14:32:25 2026 -0800
    Fix array size bounds check for /getData/track endpoint to actually limit to 100 requested tracks
• src/hg/hubApi/getData.c
  • lines changed 8, context: html, text, full: html, text
    9c7de0bd83bc6e1876dc0b8b7091127629a07bf0 Thu Mar 5 14:32:25 2026 -0800
    Fix array size bounds check for /getData/track endpoint to actually limit to 100 requested tracks
• src/hg/inc/hgFind.h
  • lines changed 6, context: html, text, full: html, text
    049e50b2293ce5e9102eef9177a7cb88b49d7a10 Wed Mar 4 14:14:03 2026 -0800
    Move chromosome:start-end parsing into it's own function in hgFind so we can call just that code from elsewhere. Add a defaultPosition check for assembly hub into hubCheck that verifies the requested chromosome exists for that assembly. Do not warn if the range is too large since we actually silently accept that anyways and clamp to the chromosome ends. refs #37126
• src/hg/js/autocompleteCat.js
  • lines changed 9, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
  • lines changed 6, context: html, text, full: html, text
    c7221bad6eda31fe88c6f9880276d8f993ff876e Thu Mar 5 12:37:14 2026 -0800
    Disable recent/popular species list selection in the hgConvert toDb dropdown if there are no chains available to them. Leave them in the list but unselectable, refs #36232
  • lines changed 3, context: html, text, full: html, text
    754cf0e3c480484878009aa5ce6dd815f1126d0c Fri Mar 6 15:02:34 2026 -0800
    most public assembly hubs do not have blat/pcr servers available, so when a public hub has been selected from the 'recents' dropdown in the search bar on those cgis, submit their form so the backend can print a message to page telling the user we don't have blat/pcr availabel for those assemblies, refs #36535
• src/hg/js/hgGateway.js
  • lines changed 5, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
  • lines changed 9, context: html, text, full: html, text
    58c24abcdc7e2fe836db993243c6ac15fce457b5 Wed Mar 4 15:20:15 2026 -0800
    Fix more universal species search bugs: hgConvert re-factor meant two hidden form variables were created for the hglft_toDb variable, so remove one of them; make organism comparison case insensitive so 'human' matches 'Human', as genark results are typically lower case; append hubUrl to hgGateway gotohgTracks form so any searched genark hub shows up as a connected hub on hgHubConnect, refs #36535, #36232
  • lines changed 9, context: html, text, full: html, text
    d84555710af610b002bd9492ca0702d622c00bc8 Thu Mar 5 11:07:17 2026 -0800
    Oops I overcorrected when fixing 3fb0b5d2a3d, which led to weird conditions where sometimes a genark hub would show up under 'Connected Hubs' depending on where you searched for the genark genome. When creating links to genarks, we only need the db= parameter, as fixUpDb in the cart code handles connecting to genarks transparently. So remove explicit hubUrl and genome parameters from genark links in the menu bar and in hgSearch ajax calls, refs #36535
  • lines changed 2, context: html, text, full: html, text
    754cf0e3c480484878009aa5ce6dd815f1126d0c Fri Mar 6 15:02:34 2026 -0800
    most public assembly hubs do not have blat/pcr servers available, so when a public hub has been selected from the 'recents' dropdown in the search bar on those cgis, submit their form so the backend can print a message to page telling the user we don't have blat/pcr availabel for those assemblies, refs #36535
• src/hg/js/hgSearch.js
  • lines changed 17, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
  • lines changed 4, context: html, text, full: html, text
    d84555710af610b002bd9492ca0702d622c00bc8 Thu Mar 5 11:07:17 2026 -0800
    Oops I overcorrected when fixing 3fb0b5d2a3d, which led to weird conditions where sometimes a genark hub would show up under 'Connected Hubs' depending on where you searched for the genark genome. When creating links to genarks, we only need the db= parameter, as fixUpDb in the cart code handles connecting to genarks transparently. So remove explicit hubUrl and genome parameters from genark links in the menu bar and in hgSearch ajax calls, refs #36535
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    83054537b0ec9ce3e74c6c20fc907c560406f836 Wed Mar 4 15:45:03 2026 -0800
    Fix typo found in code review, refs #37187
  • lines changed 9, context: html, text, full: html, text
    9db87ad5938d116af4d1e73f3e92cc29392df83c Thu Mar 5 14:58:24 2026 -0800
    Limit current tracks download feature to 100 tracks so we don't timeout out hubApi requests, refs #36858
• src/hg/js/react/lib/SpeciesSearch.jsx
  • lines changed 25, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
• src/hg/js/subCfg.js
  • lines changed 3, context: html, text, full: html, text
    a3244b1059b27424713c97be5694c716d1b90172 Thu Mar 5 11:36:07 2026 -0800
    fixing bug in supertrack UI that appears when the track name has a dot in it, refs #36917, also uppercasing the visibilities, refs #37200
  • lines changed 3, context: html, text, full: html, text
    c105602024944ec42576736467fcddd7337367d0 Thu Mar 5 15:38:05 2026 -0800
    fixing composite upcasing, refs #37200
• src/hg/js/utils.js
  • lines changed 59, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
  • lines changed 14, context: html, text, full: html, text
    d84555710af610b002bd9492ca0702d622c00bc8 Thu Mar 5 11:07:17 2026 -0800
    Oops I overcorrected when fixing 3fb0b5d2a3d, which led to weird conditions where sometimes a genark hub would show up under 'Connected Hubs' depending on where you searched for the genark genome. When creating links to genarks, we only need the db= parameter, as fixUpDb in the cart code handles connecting to genarks transparently. So remove explicit hubUrl and genome parameters from genark links in the menu bar and in hgSearch ajax calls, refs #36535
  • lines changed 9, context: html, text, full: html, text
    c7221bad6eda31fe88c6f9880276d8f993ff876e Thu Mar 5 12:37:14 2026 -0800
    Disable recent/popular species list selection in the hgConvert toDb dropdown if there are no chains available to them. Leave them in the list but unselectable, refs #36232
  • lines changed 16, context: html, text, full: html, text
    4fc775d4d4ce03a5e1236a5ce1e266b5a0a5e68e Fri Mar 6 11:13:42 2026 -0800
    database name in menubar links needs to include the hubUrl and hub_id when making a link to a non-genark assembly hub, refs #36535
  • lines changed 10, context: html, text, full: html, text
    24db314b5051da133465b7d5e0944aeba4bf25a0 Fri Mar 6 11:58:12 2026 -0800
    Make better labels when printing recent genomes to the menu bar. Don't print the default hg38/hg19/mm10/mm39/hs1 since they are already there by default, refs #36535
  • lines changed 9, context: html, text, full: html, text
    754cf0e3c480484878009aa5ce6dd815f1126d0c Fri Mar 6 15:02:34 2026 -0800
    most public assembly hubs do not have blat/pcr servers available, so when a public hub has been selected from the 'recents' dropdown in the search bar on those cgis, submit their form so the backend can print a message to page telling the user we don't have blat/pcr availabel for those assemblies, refs #36535
• src/hg/lib/hgFind.c
  • lines changed 190, context: html, text, full: html, text
    049e50b2293ce5e9102eef9177a7cb88b49d7a10 Wed Mar 4 14:14:03 2026 -0800
    Move chromosome:start-end parsing into it's own function in hgFind so we can call just that code from elsewhere. Add a defaultPosition check for assembly hub into hubCheck that verifies the requested chromosome exists for that assembly. Do not warn if the range is too large since we actually silently accept that anyways and clamp to the chromosome ends. refs #37126
• src/hg/lib/hui.c
  • lines changed 5, context: html, text, full: html, text
    a3244b1059b27424713c97be5694c716d1b90172 Thu Mar 5 11:36:07 2026 -0800
    fixing bug in supertrack UI that appears when the track name has a dot in it, refs #36917, also uppercasing the visibilities, refs #37200
  • lines changed 1, context: html, text, full: html, text
    3df73adf84cf0ecfbe9310c21682034c5e6ad7cc Sat Mar 7 09:47:33 2026 -0800
    Default polyA tail detection to off for BAM/CRAM tracks. The polyA detection was designed for mRNA/EST alignments and produces misleading asymmetric coloring on BAM reads due to strand-dependent checks in baseColorOverdrawQInsert. Users who need it for long-read cDNA/RNA sequencing can still enable it via the checkbox in hgTrackUi. refs #37133 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/lib/web.c
  • lines changed 28, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
  • lines changed 36, context: html, text, full: html, text
    a029a389a46082c6ab69d5053d5c17912dd72bf6 Thu Mar 5 12:18:56 2026 -0800
    Make menubar assembly link clicks add to recents list, refs #36535
  • lines changed 1, context: html, text, full: html, text
    397351b825b3ea9a7fb6ac7a2f64359166c9ba32 Thu Mar 5 12:25:51 2026 -0800
    Oops forgot the usual trackHubDatabase check, refs #36535
  • lines changed 10, context: html, text, full: html, text
    4fc775d4d4ce03a5e1236a5ce1e266b5a0a5e68e Fri Mar 6 11:13:42 2026 -0800
    database name in menubar links needs to include the hubUrl and hub_id when making a link to a non-genark assembly hub, refs #36535
  • lines changed 3, context: html, text, full: html, text
    24db314b5051da133465b7d5e0944aeba4bf25a0 Fri Mar 6 11:58:12 2026 -0800
    Make better labels when printing recent genomes to the menu bar. Don't print the default hg38/hg19/mm10/mm39/hs1 since they are already there by default, refs #36535
• src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv
  • lines changed 740, context: html, text, full: html, text
    4441651b9bd4e2995c45ea456b9864b588b83976 Wed Mar 4 12:05:56 2026 -0800
    BRC update refs #34337
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    203ec1e4bada4087ee20819ddf8d50b4b7c33a0c Mon Mar 2 18:56:52 2026 -0800
    Removing color lines (and itemRgb) for tracks that are table tracks and have the color designated in the itemRgb field of the file. This bug was introduced when we made itemRgb default, it's a weird interaction and they should not have had color settings designated, refs #37180
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra
  • lines changed 15, context: html, text, full: html, text
    99d7b5a5db773224bce4920bb92a3e278e1dabb0 Mon Mar 2 18:50:27 2026 -0800
    Removing color lines (and itemRgb) for tracks that are table tracks and have the color designated in the itemRgb field of the file. This bug was introduced when we made itemRgb default, it's a weird interaction and they should not have had color settings designated, refs #37183
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.release3.ra
  • lines changed 17, context: html, text, full: html, text
    99d7b5a5db773224bce4920bb92a3e278e1dabb0 Mon Mar 2 18:50:27 2026 -0800
    Removing color lines (and itemRgb) for tracks that are table tracks and have the color designated in the itemRgb field of the file. This bug was introduced when we made itemRgb default, it's a weird interaction and they should not have had color settings designated, refs #37183
• src/hg/makeDb/trackDb/human/hg38/coreCollection.html
  • lines changed 14, context: html, text, full: html, text
    28d44b10ce702bd6ef275947da83d5c11e96c746 Mon Mar 2 19:57:19 2026 -0800
    Making updates to the mm10 cCREs track from Zhiping feedback, changing the priorities to be by track name (alphabetically), removing roadmap project for mouse encode, credits, etc. Also a small edit to the released human track, refs #37131
• src/hg/makeDb/trackDb/human/hg38/genotypeArrays.html
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    244f263edff6b7cd99b09b170c722b0d04a12e45 Mon Mar 2 16:53:07 2026 -0800
    Feedback from CR, refs #37193
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
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    ff9ce4b1a9bddac4d716fb1de37b1e99bf4fe969 Fri Mar 6 14:34:51 2026 -0800
    Staging the gnomAD Coverage tracks on hgwbeta, refs #37036
• src/hg/makeDb/trackDb/human/hg38/gnomad3Coverage.html
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    e1267c28ad3cdef044c73a85505da118d735815e Fri Mar 6 15:32:49 2026 -0800
    Making changes from code review. Mostly fixing typos, and creating a Methods section for the gnomAD coverage tracks, refs #37191
• src/hg/makeDb/trackDb/human/hg38/gnomad4ExomeCoverage.html
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    e1267c28ad3cdef044c73a85505da118d735815e Fri Mar 6 15:32:49 2026 -0800
    Making changes from code review. Mostly fixing typos, and creating a Methods section for the gnomAD coverage tracks, refs #37191
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    203ec1e4bada4087ee20819ddf8d50b4b7c33a0c Mon Mar 2 18:56:52 2026 -0800
    Removing color lines (and itemRgb) for tracks that are table tracks and have the color designated in the itemRgb field of the file. This bug was introduced when we made itemRgb default, it's a weird interaction and they should not have had color settings designated, refs #37180
• src/hg/makeDb/trackDb/human/methylationAtlas.html
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    a120735fd0e3914968ffd26170946de5ab960135 Sat Mar 7 16:28:02 2026 -0800
    Reorganizing trackDb, updating name for files, updating shortLabels, updating the Human Methylation Atlas Summary and Human Methylation Atlas Signals track description pages, refs #36826
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    7648a54276c90c08ff73dc555fe051f92dd4f57d Sun Mar 8 18:20:00 2026 -0700
    Updating the Methylation Atlas summary subtracks section and adding a Cell/Tissue Type section, #36826
• src/hg/makeDb/trackDb/human/methylationAtlas.ra
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    a120735fd0e3914968ffd26170946de5ab960135 Sat Mar 7 16:28:02 2026 -0800
    Reorganizing trackDb, updating name for files, updating shortLabels, updating the Human Methylation Atlas Summary and Human Methylation Atlas Signals track description pages, refs #36826
• src/hg/makeDb/trackDb/human/methylationAtlasSignals.ra
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    a120735fd0e3914968ffd26170946de5ab960135 Sat Mar 7 16:28:02 2026 -0800
    Reorganizing trackDb, updating name for files, updating shortLabels, updating the Human Methylation Atlas Summary and Human Methylation Atlas Signals track description pages, refs #36826
• src/hg/makeDb/trackDb/human/trackDb.ra
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    a120735fd0e3914968ffd26170946de5ab960135 Sat Mar 7 16:28:02 2026 -0800
    Reorganizing trackDb, updating name for files, updating shortLabels, updating the Human Methylation Atlas Summary and Human Methylation Atlas Signals track description pages, refs #36826
• src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html
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    28d44b10ce702bd6ef275947da83d5c11e96c746 Mon Mar 2 19:57:19 2026 -0800
    Making updates to the mm10 cCREs track from Zhiping feedback, changing the priorities to be by track name (alphabetically), removing roadmap project for mouse encode, credits, etc. Also a small edit to the released human track, refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/coreCollection.html
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    28d44b10ce702bd6ef275947da83d5c11e96c746 Mon Mar 2 19:57:19 2026 -0800
    Making updates to the mm10 cCREs track from Zhiping feedback, changing the priorities to be by track name (alphabetically), removing roadmap project for mouse encode, credits, etc. Also a small edit to the released human track, refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/encode.cCREs.override.ra
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    28d44b10ce702bd6ef275947da83d5c11e96c746 Mon Mar 2 19:57:19 2026 -0800
    Making updates to the mm10 cCREs track from Zhiping feedback, changing the priorities to be by track name (alphabetically), removing roadmap project for mouse encode, credits, etc. Also a small edit to the released human track, refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/encode4.ccres.ra
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    28d44b10ce702bd6ef275947da83d5c11e96c746 Mon Mar 2 19:57:19 2026 -0800
    Making updates to the mm10 cCREs track from Zhiping feedback, changing the priorities to be by track name (alphabetically), removing roadmap project for mouse encode, credits, etc. Also a small edit to the released human track, refs #37131
• src/hg/utils/hubCheck/hubCheck.c
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    049e50b2293ce5e9102eef9177a7cb88b49d7a10 Wed Mar 4 14:14:03 2026 -0800
    Move chromosome:start-end parsing into it's own function in hgFind so we can call just that code from elsewhere. Add a defaultPosition check for assembly hub into hubCheck that verifies the requested chromosome exists for that assembly. Do not warn if the range is too large since we actually silently accept that anyways and clamp to the chromosome ends. refs #37126
• src/hg/utils/hubCheck/tests/expected/genomesConfigErrors.output.txt
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    049e50b2293ce5e9102eef9177a7cb88b49d7a10 Wed Mar 4 14:14:03 2026 -0800
    Move chromosome:start-end parsing into it's own function in hgFind so we can call just that code from elsewhere. Add a defaultPosition check for assembly hub into hubCheck that verifies the requested chromosome exists for that assembly. Do not warn if the range is too large since we actually silently accept that anyways and clamp to the chromosome ends. refs #37126
• src/hg/utils/hubCheck/tests/input/misconfigGenomes.txt
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    049e50b2293ce5e9102eef9177a7cb88b49d7a10 Wed Mar 4 14:14:03 2026 -0800
    Move chromosome:start-end parsing into it's own function in hgFind so we can call just that code from elsewhere. Add a defaultPosition check for assembly hub into hubCheck that verifies the requested chromosome exists for that assembly. Do not warn if the range is too large since we actually silently accept that anyways and clamp to the chromosome ends. refs #37126
• src/hg/utils/otto/clinGen/makeClinGenCspec.sh
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    4178716a1446bb583ac890e1304689b9d6a9ff1d Tue Mar 3 11:34:59 2026 -0800
    Fixing a logic bug found in code review, refs #37192
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    a8cc89fe8813508029edf57f0d7ed543c438f5e0 Tue Mar 3 11:41:17 2026 -0800
    Fixing other comments from code review, refs #37192
• src/hg/utils/otto/clinvar/clinVarToBed
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    5ecc240ed4c5b14d77c5903eefbff0c57b5f2135 Wed Mar 4 14:17:49 2026 -0800
    fixes after code review, refs #37195
• src/lib/cheapcgi.c
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    a3244b1059b27424713c97be5694c716d1b90172 Thu Mar 5 11:36:07 2026 -0800
    fixing bug in supertrack UI that appears when the track name has a dot in it, refs #36917, also uppercasing the visibilities, refs #37200

• lines changed: 3256
• files changed: 91