All File Changes

v479_base to v480_preview (2025-03-17 to 2025-03-24) v480

• docs/gb101.md
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    9dce2c252215de653e7674112ce47b0ca2f77eb9 Mon Mar 17 17:40:17 2025 -0700
    Adding a Sections bluebar, refs #34938
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    5d849143124f2f80667971d307f94fa9f9e01b79 Thu Mar 20 11:36:19 2025 -0700
    Updating 'Workthrough' to 'Walkthrough' for the gb101 tutorial, refs #34938
• src/hg/hgTrackUi/hgTrackUi.c
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    e323d595c241d03570d380d8c60de60e99c1c4ec Fri Mar 21 12:36:21 2025 -0700
    add support for bigDbSnp to quicklift
• src/hg/hgTracks/bigBedTrack.c
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    e323d595c241d03570d380d8c60de60e99c1c4ec Fri Mar 21 12:36:21 2025 -0700
    add support for bigDbSnp to quicklift
• src/hg/hgTracks/interactTrack.c
  • lines changed 199, context: html, text, full: html, text
    54a41e9d2247122e363b0ce29594d8aeddf7381e Mon Mar 24 09:50:10 2025 -0700
    Make interact hgc link boxes better, add an option to suppress them in trackDb, and finish implementing arcs everywhere. refs #30380
• src/hg/hgTracks/simpleTracks.c
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    9007158bac3746b1eb7f76513c8e8631e1ca1ca2 Fri Mar 21 13:18:22 2025 -0700
    add decipher SQL tracks to quickLift support
• src/hg/hgTracks/variation.c
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    e323d595c241d03570d380d8c60de60e99c1c4ec Fri Mar 21 12:36:21 2025 -0700
    add support for bigDbSnp to quicklift
• src/hg/hgTracks/variation.h
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    e323d595c241d03570d380d8c60de60e99c1c4ec Fri Mar 21 12:36:21 2025 -0700
    add support for bigDbSnp to quicklift
• src/hg/hgTracks/wigMafTrack.c
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    a56bcbb2f7e139c6b3edb2338df3d14fe50195b9 Wed Mar 19 09:10:56 2025 -0700
    don't limit groups to 20 but instead 1000
• src/hg/hgc/bigDbSnpClick.c
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    e323d595c241d03570d380d8c60de60e99c1c4ec Fri Mar 21 12:36:21 2025 -0700
    add support for bigDbSnp to quicklift
• src/hg/hgc/hgc.c
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    e323d595c241d03570d380d8c60de60e99c1c4ec Fri Mar 21 12:36:21 2025 -0700
    add support for bigDbSnp to quicklift
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 4, context: html, text, full: html, text
    54a41e9d2247122e363b0ce29594d8aeddf7381e Mon Mar 24 09:50:10 2025 -0700
    Make interact hgc link boxes better, add an option to suppress them in trackDb, and finish implementing arcs everywhere. refs #30380
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 4, context: html, text, full: html, text
    54a41e9d2247122e363b0ce29594d8aeddf7381e Mon Mar 24 09:50:10 2025 -0700
    Make interact hgc link boxes better, add an option to suppress them in trackDb, and finish implementing arcs everywhere. refs #30380
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 7, context: html, text, full: html, text
    54a41e9d2247122e363b0ce29594d8aeddf7381e Mon Mar 24 09:50:10 2025 -0700
    Make interact hgc link boxes better, add an option to suppress them in trackDb, and finish implementing arcs everywhere. refs #30380
• src/hg/htdocs/goldenPath/newsarch.html
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    7bfa786edcedd88aa5640771833895c204a601ac Tue Mar 18 11:42:43 2025 -0700
    Fixing some typos that Gerardo found in code review, refs #35399
• src/hg/htdocs/inc/hgMyData.html
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    e2002b80518d8b522ac768713cda4126cf3b5dc0 Thu Mar 20 12:21:10 2025 -0700
    Make wording changes to hubSpace UI. Make checkbox selection not recursive, fix bug in deselect all rows checkbox, refs #31058
• src/hg/htdocs/indexMeetings.html
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    2d8f60cbee43a060eeb6b48bb4e3c30332aaedb8 Mon Mar 17 15:51:54 2025 -0700
    Adding the biocuration 2025 meeting to the list. Fixing the listing so each meeting is not on a single HTML line, no Redmine.
• src/hg/htdocs/style/hgMyData.css
  • lines changed 6, context: html, text, full: html, text
    321bb7e5cd86f33caac0f1975fc1197c01d301a6 Tue Mar 18 12:39:55 2025 -0700
    More hubspace changes. Set height of selected file row to prevent page jumping, cgiEncode the actual ui values to display filenames correctly, make file uploads to an already existing hub actually display the files in that hub, make clicks on table rows more fine tuned: clicks on the checkbox select the file or all subdirectory files like before, but clicks anywhere else depend on the row that was clicked, if a regular row, just select, if a directory row, open the directory (and clear previous selections)
• src/hg/inc/hvGfx.h
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    2e8e0086e36251107884419892402f41f860ef03 Tue Mar 18 18:12:10 2025 -0700
    Fixing hvGfxCurve to correctly relocate the three points in reverse-complement, refs #35408
• src/hg/inc/interactUi.h
  • lines changed 3, context: html, text, full: html, text
    54a41e9d2247122e363b0ce29594d8aeddf7381e Mon Mar 24 09:50:10 2025 -0700
    Make interact hgc link boxes better, add an option to suppress them in trackDb, and finish implementing arcs everywhere. refs #30380
• src/hg/js/hgMyData.js
  • lines changed 65, context: html, text, full: html, text
    321bb7e5cd86f33caac0f1975fc1197c01d301a6 Tue Mar 18 12:39:55 2025 -0700
    More hubspace changes. Set height of selected file row to prevent page jumping, cgiEncode the actual ui values to display filenames correctly, make file uploads to an already existing hub actually display the files in that hub, make clicks on table rows more fine tuned: clicks on the checkbox select the file or all subdirectory files like before, but clicks anywhere else depend on the row that was clicked, if a regular row, just select, if a directory row, open the directory (and clear previous selections)
  • lines changed 16, context: html, text, full: html, text
    102c601cb4dfad3f72902f38cd28d2d0ce803528 Wed Mar 19 15:41:09 2025 -0700
    When files come in from hubtools, display the files and hub names decoded. Prevent hub names from having spaces in them, too tricky to get apache to play nice with those urls, refs #31058
  • lines changed 48, context: html, text, full: html, text
    e2002b80518d8b522ac768713cda4126cf3b5dc0 Thu Mar 20 12:21:10 2025 -0700
    Make wording changes to hubSpace UI. Make checkbox selection not recursive, fix bug in deselect all rows checkbox, refs #31058
  • lines changed 13, context: html, text, full: html, text
    0f1759077310950597e9c3da02fd41aea006ed98 Fri Mar 21 10:28:03 2025 -0700
    Remove the delete button when a hub.txt row was explicitly selected so users cannot delete them without deleting the entire hub, otherwise they can delete hub.txt files and then have no easy way to view their track files, refs #31058
• src/hg/js/utils.js
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    cde069ff775afde4092c01650eea5f9989d97997 Tue Mar 18 18:46:15 2025 -0700
    changes after code review, refs #35362
• src/hg/lib/hgHgvs.c
  • lines changed 65, context: html, text, full: html, text
    b17ae6ec773d69464d8c526d71040441c30da265 Wed Mar 12 12:54:15 2025 -0700
    Implicitly convert ENST accessions to ENSP accessions during hgvs search if the hgvs term is a p. term, refs #35335
• src/hg/lib/trackHub.c
  • lines changed 2, context: html, text, full: html, text
    e323d595c241d03570d380d8c60de60e99c1c4ec Fri Mar 21 12:36:21 2025 -0700
    add support for bigDbSnp to quicklift
  • lines changed 7, context: html, text, full: html, text
    9007158bac3746b1eb7f76513c8e8631e1ca1ca2 Fri Mar 21 13:18:22 2025 -0700
    add decipher SQL tracks to quickLift support
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    27ed593f3eaf9a64d69e68295411da0f2999cf84 Thu Mar 20 02:12:49 2025 -0700
    adding elephant grass per user request refs #29545
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    5fde777d726aa1599b49cb0ed3c20dadef9e85f5 Fri Mar 21 01:36:22 2025 -0700
    adding two per user request refs #29545
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    fca02abd676d5eceb29050caf72a16d958859224 Sat Mar 22 05:38:37 2025 -0700
    adding 1 per user request refs #29545
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    8fc2eaf789628409583e42e05e55609052c3f660 Sun Mar 23 18:05:23 2025 -0700
    VGP update and user request additions refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
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    5fde777d726aa1599b49cb0ed3c20dadef9e85f5 Fri Mar 21 01:36:22 2025 -0700
    adding two per user request refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    8fc2eaf789628409583e42e05e55609052c3f660 Sun Mar 23 18:05:23 2025 -0700
    VGP update and user request additions refs #29545
• src/hg/makeDb/doc/genarkOrg.txt
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    9007158bac3746b1eb7f76513c8e8631e1ca1ca2 Fri Mar 21 13:18:22 2025 -0700
    add decipher SQL tracks to quickLift support
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    8fc2eaf789628409583e42e05e55609052c3f660 Sun Mar 23 18:05:23 2025 -0700
    VGP update and user request additions refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
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    8fc2eaf789628409583e42e05e55609052c3f660 Sun Mar 23 18:05:23 2025 -0700
    VGP update and user request additions refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
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    8fc2eaf789628409583e42e05e55609052c3f660 Sun Mar 23 18:05:23 2025 -0700
    VGP update and user request additions refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
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    fca02abd676d5eceb29050caf72a16d958859224 Sat Mar 22 05:38:37 2025 -0700
    adding 1 per user request refs #29545
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    8fc2eaf789628409583e42e05e55609052c3f660 Sun Mar 23 18:05:23 2025 -0700
    VGP update and user request additions refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
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    27ed593f3eaf9a64d69e68295411da0f2999cf84 Thu Mar 20 02:12:49 2025 -0700
    adding elephant grass per user request refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
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    8fc2eaf789628409583e42e05e55609052c3f660 Sun Mar 23 18:05:23 2025 -0700
    VGP update and user request additions refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
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    8fc2eaf789628409583e42e05e55609052c3f660 Sun Mar 23 18:05:23 2025 -0700
    VGP update and user request additions refs #29545
• src/hg/makeDb/trackDb/human/hg19/denovoDb.html
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    7bfa786edcedd88aa5640771833895c204a601ac Tue Mar 18 11:42:43 2025 -0700
    Fixing some typos that Gerardo found in code review, refs #35399
• src/hg/makeDb/trackDb/human/hg19/denovoDb.ra
  • lines changed 1, context: html, text, full: html, text
    b80e1f01ac695c043c2581dee15dd3a3acf97842 Tue Mar 18 13:26:57 2025 -0700
    Adding penantIcons for the denovo-db track, refs #28790
• src/hg/makeDb/trackDb/tagTypes.tab
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    54a41e9d2247122e363b0ce29594d8aeddf7381e Mon Mar 24 09:50:10 2025 -0700
    Make interact hgc link boxes better, add an option to suppress them in trackDb, and finish implementing arcs everywhere. refs #30380
• src/hg/utils/bedPartition/bedPartition.c
  • lines changed 67, context: html, text, full: html, text
    30b1ed267a38a0136b3463d3638ce108bfb62960 Tue Mar 18 17:29:07 2025 -0700
    bedPartition: add -minPartitionItems, -partMergeDist, and statistics output
• src/hg/utils/bedPartition/tests/expected/test1.out
  • lines changed 5, context: html, text, full: html, text
    30b1ed267a38a0136b3463d3638ce108bfb62960 Tue Mar 18 17:29:07 2025 -0700
    bedPartition: add -minPartitionItems, -partMergeDist, and statistics output
• src/hg/utils/bedPartition/tests/expected/test2.out
  • lines changed 5, context: html, text, full: html, text
    30b1ed267a38a0136b3463d3638ce108bfb62960 Tue Mar 18 17:29:07 2025 -0700
    bedPartition: add -minPartitionItems, -partMergeDist, and statistics output
• src/hg/utils/bedPartition/tests/expected/test2.ranges.bed
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    30b1ed267a38a0136b3463d3638ce108bfb62960 Tue Mar 18 17:29:07 2025 -0700
    bedPartition: add -minPartitionItems, -partMergeDist, and statistics output
• src/hg/utils/bedPartition/tests/expected/test3.out
  • lines changed 5, context: html, text, full: html, text
    30b1ed267a38a0136b3463d3638ce108bfb62960 Tue Mar 18 17:29:07 2025 -0700
    bedPartition: add -minPartitionItems, -partMergeDist, and statistics output
• src/hg/utils/bedPartition/tests/expected/test3.ranges.bed
  • lines changed 4, context: html, text, full: html, text
    30b1ed267a38a0136b3463d3638ce108bfb62960 Tue Mar 18 17:29:07 2025 -0700
    bedPartition: add -minPartitionItems, -partMergeDist, and statistics output
• src/hg/utils/bedPartition/tests/makefile
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    30b1ed267a38a0136b3463d3638ce108bfb62960 Tue Mar 18 17:29:07 2025 -0700
    bedPartition: add -minPartitionItems, -partMergeDist, and statistics output
• src/utils/qa/check_Tables_Metadata.py
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    502c72373f7959e6195860cbc2b5a1aa09aaa600 Fri Mar 21 20:03:13 2025 -0700
    Code review edits, refs #35396
• src/utils/qa/hgTracksTiming.py
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    9efd3ec91a0196806fd934222628b48ad501d937 Wed Mar 19 16:39:42 2025 -0700
    Updating hgTracksRandom with a QA script that logs server response times, and tracks performance. Refs #32284
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    5c927671ebda7c1f56363bc29286646f4928a8c8 Wed Mar 19 16:44:18 2025 -0700
    Fixing typo.
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    97d6863c524ea374b1f29d96ce17dc0e8530507a Thu Mar 20 09:28:10 2025 -0700
    10s proved to be too short, raising it to 15s to before it complains about hgTracks being down. Refs #32284
• src/utils/qa/makefile
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    9efd3ec91a0196806fd934222628b48ad501d937 Wed Mar 19 16:39:42 2025 -0700
    Updating hgTracksRandom with a QA script that logs server response times, and tracks performance. Refs #32284
• src/utils/qa/weeklybld/buildEnv.csh
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    5bc489acead0169ab6ce3fcf0754fdf1cceb5d7d Mon Mar 24 11:36:48 2025 -0700
    v480 preview1, refs #35332

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• files changed: 59