All File Changes

v481_preview2 to v481_base (2025-04-21 to 2025-04-28) v481

• confs/hgwdev.hg.conf
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    a4a7c2f31da990454d58fe5cf08879c1e89ef029 Sun Apr 27 01:11:12 2025 -0700
    Installing updated hg.conf files from UCSC servers
• src/fuse/makefile
  • lines changed 22, context: html, text, full: html, text
    836b73dcf9a90141ad0923009f03d2494fdd18ca Tue Apr 22 15:17:05 2025 -0700
    Replaced shell loops in build paths of makefile to use rules. This should address issues where errors in some rules are not reported (#35339) and also increase speed of builds using multiple cores
• src/hg/cgilib/annoFormatVep.c
  • lines changed 10, context: html, text, full: html, text
    66cfabe5850f11b52956866d59e9c55ecaa799ce Thu Apr 24 15:03:57 2025 -0700
    Fix a couple things found by valgrind. Using memmove instead of safecpy when ranges can overlap is safer, but using safecpy didn't seem to be causing bugs. However, failing to clip to length of codonNew when uppercasing caused memory corruption that caused eventual failure reported in #35577. valgrind rules.
• src/hg/encode3/makefile
  • lines changed 34, context: html, text, full: html, text
    836b73dcf9a90141ad0923009f03d2494fdd18ca Tue Apr 22 15:17:05 2025 -0700
    Replaced shell loops in build paths of makefile to use rules. This should address issues where errors in some rules are not reported (#35339) and also increase speed of builds using multiple cores
• src/hg/gar/makefile
  • lines changed 10, context: html, text, full: html, text
    0ba17462c2e7b3f97e2bcac98b278057886281d5 Fri Apr 25 16:26:06 2025 +0200
    adding GBIC mode for OSX, no ticket yet, waiting for GBIC for arm on linux update ticket
• src/hg/hgConvert/hgConvert.c
  • lines changed 2, context: html, text, full: html, text
    88ad1e962497e5d4d2a0d6514aa64970d042a8d8 Thu Apr 24 13:46:01 2025 -0700
    forgot a check-in
• src/hg/hgCustom/hgCustom.c
  • lines changed 5, context: html, text, full: html, text
    8bd8d6c944fa53c3d456b1f78b5faa6ea2251942 Fri Apr 25 10:33:43 2025 -0700
    Modifying the new text about updating data via URL on hgCustom, refs #20985
• src/hg/hgGateway/hgGateway.c
  • lines changed 10, context: html, text, full: html, text
    73dbd7cdaa77baf709b8900c92d4eee474c5309d Fri Apr 25 20:23:04 2025 -0700
    Updating files for the Gateway interactive tutorial, refs #35464
• src/hg/hgGene/hgGene.c
  • lines changed 7, context: html, text, full: html, text
    4ae34371cb47aaf48f640e0043ec00717092cbd6 Tue Apr 22 12:34:33 2025 -0700
    a few tweaks to get hgGene to work with quickLift
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 2, context: html, text, full: html, text
    1a5ac904a3b854204a706cec107024581405d4de Thu Apr 24 13:37:24 2025 -0700
    Updating the missing description page for track warning and adding a sentence with a Hub Track Database Definition page link, refs #32998
• src/hg/hgSession/hgSession.c
  • lines changed 6, context: html, text, full: html, text
    dcabcf3e37e0b1e3c71b6a98358c1fb844ca3b8a Tue Apr 22 12:26:11 2025 -0700
    sessions save a copy of the quickLift hub.
• src/hg/hgTracks/config.c
  • lines changed 12, context: html, text, full: html, text
    90d488f2fa8de173d8e2fd3b999de732e885dac5 Wed Apr 23 16:37:28 2025 -0700
    add more legible fonts refs #35571
• src/hg/hgTracks/encode.c
  • lines changed 44, context: html, text, full: html, text
    f998ca175cbeb8b9761a6452468c365699fe2723 Thu Apr 24 12:04:37 2025 -0700
    add quickLift support for narrowPeak
• src/hg/hgTracks/simpleTracks.c
  • lines changed 6, context: html, text, full: html, text
    a2c9728424a8d22c1ae93ae37c4a5f1fd4095e62 Thu Apr 24 11:45:15 2025 -0700
    add quickLift support for pubs* tracks
  • lines changed 2, context: html, text, full: html, text
    d11abe9d8636b197e2742e5d5b8da4fee2742234 Thu Apr 24 13:37:24 2025 -0700
    oops, typo
• src/hg/hgc/hgc.c
  • lines changed 26, context: html, text, full: html, text
    e1988a798585c610e2399538a900fd57cfa83d63 Tue Apr 22 11:19:22 2025 -0700
    Fixes VCF does not work on extended case-color options in Get DNA for vcf, vcfTabix, and vcfPhasedTrio. fixes #16386
  • lines changed 1, context: html, text, full: html, text
    a2c9728424a8d22c1ae93ae37c4a5f1fd4095e62 Thu Apr 24 11:45:15 2025 -0700
    add quickLift support for pubs* tracks
• src/hg/hgc/hgc.h
  • lines changed 8, context: html, text, full: html, text
    e1988a798585c610e2399538a900fd57cfa83d63 Tue Apr 22 11:19:22 2025 -0700
    Fixes VCF does not work on extended case-color options in Get DNA for vcf, vcfTabix, and vcfPhasedTrio. fixes #16386
• src/hg/hgc/pubs.c
  • lines changed 6, context: html, text, full: html, text
    a2c9728424a8d22c1ae93ae37c4a5f1fd4095e62 Thu Apr 24 11:45:15 2025 -0700
    add quickLift support for pubs* tracks
• src/hg/hgc/vcfClick.c
  • lines changed 53, context: html, text, full: html, text
    e1988a798585c610e2399538a900fd57cfa83d63 Tue Apr 22 11:19:22 2025 -0700
    Fixes VCF does not work on extended case-color options in Get DNA for vcf, vcfTabix, and vcfPhasedTrio. fixes #16386
  • lines changed 8, context: html, text, full: html, text
    f00d46c3edc5ac3916e8e0c7bb0fbe5e4915145d Tue Apr 22 15:56:51 2025 -0700
    Fixes minor bug vcf extended color dna download. refs #16386
• src/hg/hgcentralTidy/hgcentralTidy.c
  • lines changed 1, context: html, text, full: html, text
    b0b9e204768e7c478ec39977858910e9d478c979 Mon Apr 21 11:21:30 2025 -0700
    fixing new gcc warning in hgcentralTidy.c, no redmine
  • lines changed 1, context: html, text, full: html, text
    27ef3088295431a5fdadf5def360a14151ac574f Mon Apr 21 12:12:26 2025 -0700
    last fix for Jonathans contribution for verbose, however this was not a bug that mattered much since it was in the verbose statement. I have updated the exec in /cluster/bin/x86_64/ wwith the latest compiling version.
  • lines changed 14, context: html, text, full: html, text
    ce90ee5ec5f7377937451a8c8eb93a7dc33731de Tue Apr 22 13:56:24 2025 -0700
    hgcentralTidy.c cleaner - added -skipDel option and verbose=4 for seeing sql delete statements detail. dryRun skips too many details.
  • lines changed 7, context: html, text, full: html, text
    783eee083cb8f18c4235ce6655e0f6bc18c09d5e Thu Apr 24 04:48:00 2025 -0700
    making hgcentraltidy more aggressive for single use userDb rows, refs #35554
  • lines changed 8, context: html, text, full: html, text
    7c23ae36017c35ef4f20b3725454c71100860c46 Thu Apr 24 07:04:20 2025 -0700
    making sure that robo1RangeEnd includes today, so the cleaner will touch rows from today, refs #35554
  • lines changed 5, context: html, text, full: html, text
    74693f4a03751622a098ed60a2a38c256c66b216 Fri Apr 25 16:40:20 2025 -0700
    Fixing small off by one error specify the days range. refs #35554
  • lines changed 33, context: html, text, full: html, text
    823555550e19e556ca7f3ac9ebcc9793f0c39668 Fri Apr 25 19:56:46 2025 -0700
    Since it was confusing not to have the end included in the range, fixed binary search to specify flag if you want the beginning or the end of the range. THis allows the natural expression of day 0 instead of -1.
• src/hg/htdocs/FAQ/FAQcustom.html
  • lines changed 11, context: html, text, full: html, text
    822194a76aaec283cb1699653d5ad3433c7e44ba Thu Apr 24 16:20:58 2025 -0700
    adding FAQ entry about special characters in labels, adding links to that FAQ to short/longLabel entries in trackDbDoc, and fixing minor formatting error with maxWindowCoverage section, refs #35003
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 102, context: html, text, full: html, text
    90206b0ea2036dba8693fa886347d9368dce8efb Tue Apr 22 14:38:39 2025 -0700
    Documenting a frequently asked question, how to filter by biotype when using GENCODE, NCBI RefSeq, or Ensembl, refs #24243
  • lines changed 1, context: html, text, full: html, text
    d253d039a1a4157faaaae030b254bf4fcbb1fd07 Thu Apr 24 14:51:40 2025 -0700
    Adding a link at the top of the page to the new FAQ, refs #24243
• src/hg/htdocs/goldenPath/help/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    0ba17462c2e7b3f97e2bcac98b278057886281d5 Fri Apr 25 16:26:06 2025 +0200
    adding GBIC mode for OSX, no ticket yet, waiting for GBIC for arm on linux update ticket
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 7, context: html, text, full: html, text
    822194a76aaec283cb1699653d5ad3433c7e44ba Thu Apr 24 16:20:58 2025 -0700
    adding FAQ entry about special characters in labels, adding links to that FAQ to short/longLabel entries in trackDbDoc, and fixing minor formatting error with maxWindowCoverage section, refs #35003
• src/hg/htdocs/images/Search_box.png
  • lines changed 0, context: html, text, full: html, text
    3561f06a8cf64f82e23e3b70e29d618244c7319f Mon Apr 28 09:37:47 2025 -0700
    Adding images for the Gateway interactive tutorial, refs #35464
• src/hg/htdocs/images/assembly_details.png
  • lines changed 0, context: html, text, full: html, text
    3561f06a8cf64f82e23e3b70e29d618244c7319f Mon Apr 28 09:37:47 2025 -0700
    Adding images for the Gateway interactive tutorial, refs #35464
• src/hg/htdocs/images/assembly_request.png
  • lines changed 0, context: html, text, full: html, text
    3561f06a8cf64f82e23e3b70e29d618244c7319f Mon Apr 28 09:37:47 2025 -0700
    Adding images for the Gateway interactive tutorial, refs #35464
• src/hg/htdocs/images/assembly_version.png
  • lines changed 0, context: html, text, full: html, text
    3561f06a8cf64f82e23e3b70e29d618244c7319f Mon Apr 28 09:37:47 2025 -0700
    Adding images for the Gateway interactive tutorial, refs #35464
• src/hg/htdocs/images/gatewayPageAnnotated.jpg
  • lines changed 0, context: html, text, full: html, text
    3561f06a8cf64f82e23e3b70e29d618244c7319f Mon Apr 28 09:37:47 2025 -0700
    Adding images for the Gateway interactive tutorial, refs #35464
• src/hg/htdocs/images/popular_species.png
  • lines changed 0, context: html, text, full: html, text
    3561f06a8cf64f82e23e3b70e29d618244c7319f Mon Apr 28 09:37:47 2025 -0700
    Adding images for the Gateway interactive tutorial, refs #35464
• src/hg/htdocs/images/request_page.png
  • lines changed 0, context: html, text, full: html, text
    3561f06a8cf64f82e23e3b70e29d618244c7319f Mon Apr 28 09:37:47 2025 -0700
    Adding images for the Gateway interactive tutorial, refs #35464
• src/hg/htdocs/images/sequences_list.png
  • lines changed 0, context: html, text, full: html, text
    3561f06a8cf64f82e23e3b70e29d618244c7319f Mon Apr 28 09:37:47 2025 -0700
    Adding images for the Gateway interactive tutorial, refs #35464
• src/hg/htdocs/images/species_tree.png
  • lines changed 0, context: html, text, full: html, text
    3561f06a8cf64f82e23e3b70e29d618244c7319f Mon Apr 28 09:37:47 2025 -0700
    Adding images for the Gateway interactive tutorial, refs #35464
• src/hg/htdocs/images/view_sequence.png
  • lines changed 0, context: html, text, full: html, text
    3561f06a8cf64f82e23e3b70e29d618244c7319f Mon Apr 28 09:37:47 2025 -0700
    Adding images for the Gateway interactive tutorial, refs #35464
• src/hg/htdocs/license/index.html
  • lines changed 17, context: html, text, full: html, text
    913c8bf3ad9c78d50e3df3e4bec48a0ccf4134af Thu Apr 24 16:14:26 2025 -0700
    Adding license info for two new accessibility fonts, refs #35571
• src/hg/htdocs/makefile
  • lines changed 1, context: html, text, full: html, text
    0ba17462c2e7b3f97e2bcac98b278057886281d5 Fri Apr 25 16:26:06 2025 +0200
    adding GBIC mode for OSX, no ticket yet, waiting for GBIC for arm on linux update ticket
  • lines changed 8, context: html, text, full: html, text
    4261cec435a67f5a86a9dd5268aef9bdab66e84d Fri Apr 25 15:42:59 2025 -0700
    falling back to find in makefile if gitFiles is not present, which is the case for all mirrors
  • lines changed 5, context: html, text, full: html, text
    23042424a3f60f3a861e2f9c4f32f65ca1b23fd6 Sat Apr 26 02:24:47 2025 +0200
    making htdocs make work on OSX
• src/hg/hubApi/tests/expected/list22.gz
  • lines changed 0, context: html, text, full: html, text
    43a557569d3db3c7f5b301e1c0c87d83556d10ee Wed Apr 23 12:34:07 2025 -0700
    updating expected for hubApi tests
• src/hg/hubApi/tests/expected/list26.gz
  • lines changed 0, context: html, text, full: html, text
    43a557569d3db3c7f5b301e1c0c87d83556d10ee Wed Apr 23 12:34:07 2025 -0700
    updating expected for hubApi tests
• src/hg/hubApi/tests/expected/list27.gz
  • lines changed 0, context: html, text, full: html, text
    43a557569d3db3c7f5b301e1c0c87d83556d10ee Wed Apr 23 12:34:07 2025 -0700
    updating expected for hubApi tests
• src/hg/hubApi/tests/expected/redmine23733.gz
  • lines changed 0, context: html, text, full: html, text
    43a557569d3db3c7f5b301e1c0c87d83556d10ee Wed Apr 23 12:34:07 2025 -0700
    updating expected for hubApi tests
• src/hg/inc/cart.h
  • lines changed 2, context: html, text, full: html, text
    dcabcf3e37e0b1e3c71b6a98358c1fb844ca3b8a Tue Apr 22 12:26:11 2025 -0700
    sessions save a copy of the quickLift hub.
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    7d9e5c172d1b2ae2de50b00f344e199006b8ffab Sun Apr 27 23:24:19 2025 -0700
    Fixed mangled composite track UI when score filtering is disabled. This caused form and table begin/end mismatches. Also a little bit of movement of some inconsistent code to make it easier to understand where score fitler config is called.
• src/hg/inc/quickLift.h
  • lines changed 2, context: html, text, full: html, text
    dcabcf3e37e0b1e3c71b6a98358c1fb844ca3b8a Tue Apr 22 12:26:11 2025 -0700
    sessions save a copy of the quickLift hub.
• src/hg/inc/trackHub.h
  • lines changed 1, context: html, text, full: html, text
    22f3b1b0c2d7ea49cbe84baa32fab19205027010 Thu Apr 24 13:40:02 2025 -0700
    work on vetted and not liftable list
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    e225fe12308746322ff2f9c98e457e5fdeaadf20 Mon Apr 28 11:16:36 2025 -0700
    New version number v481
• src/hg/js/makefile
  • lines changed 3, context: html, text, full: html, text
    836b73dcf9a90141ad0923009f03d2494fdd18ca Tue Apr 22 15:17:05 2025 -0700
    Replaced shell loops in build paths of makefile to use rules. This should address issues where errors in some rules are not reported (#35339) and also increase speed of builds using multiple cores
• src/hg/js/tutorials/gatewayTutorial.js
  • lines changed 289, context: html, text, full: html, text
    73dbd7cdaa77baf709b8900c92d4eee474c5309d Fri Apr 25 20:23:04 2025 -0700
    Updating files for the Gateway interactive tutorial, refs #35464
• src/hg/lib/cart.c
  • lines changed 29, context: html, text, full: html, text
    dcabcf3e37e0b1e3c71b6a98358c1fb844ca3b8a Tue Apr 22 12:26:11 2025 -0700
    sessions save a copy of the quickLift hub.
  • lines changed 6, context: html, text, full: html, text
    783eee083cb8f18c4235ce6655e0f6bc18c09d5e Thu Apr 24 04:48:00 2025 -0700
    making hgcentraltidy more aggressive for single use userDb rows, refs #35554
• src/hg/lib/featureBits.c
  • lines changed 23, context: html, text, full: html, text
    e1988a798585c610e2399538a900fd57cfa83d63 Tue Apr 22 11:19:22 2025 -0700
    Fixes VCF does not work on extended case-color options in Get DNA for vcf, vcfTabix, and vcfPhasedTrio. fixes #16386
• src/hg/lib/hubConnect.c
  • lines changed 5, context: html, text, full: html, text
    dcabcf3e37e0b1e3c71b6a98358c1fb844ca3b8a Tue Apr 22 12:26:11 2025 -0700
    sessions save a copy of the quickLift hub.
• src/hg/lib/hui.c
  • lines changed 46, context: html, text, full: html, text
    7d9e5c172d1b2ae2de50b00f344e199006b8ffab Sun Apr 27 23:24:19 2025 -0700
    Fixed mangled composite track UI when score filtering is disabled. This caused form and table begin/end mismatches. Also a little bit of movement of some inconsistent code to make it easier to understand where score fitler config is called.
• src/hg/lib/sessionData.c
  • lines changed 6, context: html, text, full: html, text
    dcabcf3e37e0b1e3c71b6a98358c1fb844ca3b8a Tue Apr 22 12:26:11 2025 -0700
    sessions save a copy of the quickLift hub.
• src/hg/lib/trackHub.c
  • lines changed 43, context: html, text, full: html, text
    22f3b1b0c2d7ea49cbe84baa32fab19205027010 Thu Apr 24 13:40:02 2025 -0700
    work on vetted and not liftable list
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 34, context: html, text, full: html, text
    b980c29c9c0b7b6ea51a398bc0c5e780b37cae79 Thu Apr 24 14:50:19 2025 -0700
    refseq update refs #29545
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    c0bca292cfa2bb068ba4989d26af72070eb1a7e1 Sun Apr 27 22:00:38 2025 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    b980c29c9c0b7b6ea51a398bc0c5e780b37cae79 Thu Apr 24 14:50:19 2025 -0700
    refseq update refs #29545
• src/hg/makeDb/doc/bosTau9/genarkQuickLift.txt
  • lines changed 26, context: html, text, full: html, text
    dcabcf3e37e0b1e3c71b6a98358c1fb844ca3b8a Tue Apr 22 12:26:11 2025 -0700
    sessions save a copy of the quickLift hub.
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    060deb4df162b799f73c1df831996af516a23505 Tue Apr 22 10:29:58 2025 -0700
    adding one for VGP update refs #34370
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    b980c29c9c0b7b6ea51a398bc0c5e780b37cae79 Thu Apr 24 14:50:19 2025 -0700
    refseq update refs #29545
• src/hg/makeDb/doc/hg38/pseudogenes.txt
  • lines changed 35, context: html, text, full: html, text
    a95486084d48d3739b6d995a11f2cea55754f10c Fri Apr 18 12:16:18 2025 -0700
    better labeling and searching of Yale pseudogene track
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 21, context: html, text, full: html, text
    b980c29c9c0b7b6ea51a398bc0c5e780b37cae79 Thu Apr 24 14:50:19 2025 -0700
    refseq update refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 8, context: html, text, full: html, text
    b980c29c9c0b7b6ea51a398bc0c5e780b37cae79 Thu Apr 24 14:50:19 2025 -0700
    refseq update refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 8, context: html, text, full: html, text
    b980c29c9c0b7b6ea51a398bc0c5e780b37cae79 Thu Apr 24 14:50:19 2025 -0700
    refseq update refs #29545
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    8c3d9a3c81b2c1d472df3e4a9f90b9f1fa395eea Mon Apr 28 10:39:32 2025 -0700
    update to VGP freeze1 status refs #34370
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    b980c29c9c0b7b6ea51a398bc0c5e780b37cae79 Thu Apr 24 14:50:19 2025 -0700
    refseq update refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    b980c29c9c0b7b6ea51a398bc0c5e780b37cae79 Thu Apr 24 14:50:19 2025 -0700
    refseq update refs #29545
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    c0bca292cfa2bb068ba4989d26af72070eb1a7e1 Sun Apr 27 22:00:38 2025 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    5fcbbf99999c63d0c9cee57aa2010a7ec33eda75 Mon Apr 28 10:39:05 2025 -0700
    update to VGP freeze1 status refs #34370
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    b980c29c9c0b7b6ea51a398bc0c5e780b37cae79 Thu Apr 24 14:50:19 2025 -0700
    refseq update refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    b86ea0ed5a0cc938032d96a84356dcab7c37aa61 Tue Apr 22 10:41:08 2025 -0700
    adding one on the secondary list refs #34370
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    0bc9658008db86cf023e7894561f8ca86ca1cbad Mon Apr 28 10:38:04 2025 -0700
    update to freeze1 status refs #34370
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    0bc9658008db86cf023e7894561f8ca86ca1cbad Mon Apr 28 10:38:04 2025 -0700
    update to freeze1 status refs #34370
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    b86ea0ed5a0cc938032d96a84356dcab7c37aa61 Tue Apr 22 10:41:08 2025 -0700
    adding one on the secondary list refs #34370
  • lines changed 1, context: html, text, full: html, text
    0bc9658008db86cf023e7894561f8ca86ca1cbad Mon Apr 28 10:38:04 2025 -0700
    update to freeze1 status refs #34370
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
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    70e5b4c72c9a7c1177fea5ea1a8a7ca33486eb3f Tue Apr 22 12:08:14 2025 -0700
    adding one on the secondary list refs #34370
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    d8f2fd7fb27037ca7c15b90af4bad94a93d00069 Tue Apr 22 14:40:04 2025 -0700
    eliminate obsolete entries refs #34370
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    da0c05d0f33bf639264fa24aef63e25e6bab8216 Mon Apr 28 10:43:11 2025 -0700
    update to freeze1 status refs #34370
• src/hg/makeDb/outside/pseudogenes/pseudoPipeParents.py
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    a95486084d48d3739b6d995a11f2cea55754f10c Fri Apr 18 12:16:18 2025 -0700
    better labeling and searching of Yale pseudogene track
• src/hg/makeDb/outside/pseudogenes/pseudoPipeToBed.py
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    a95486084d48d3739b6d995a11f2cea55754f10c Fri Apr 18 12:16:18 2025 -0700
    better labeling and searching of Yale pseudogene track
• src/hg/makeDb/trackDb/human/hg38/encode4.ra
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    5910da9c6e6b700ca703191267cb9c8b942500ef Fri Apr 18 13:17:16 2025 -0700
    changing encode4 into long read transcript supertrack
• src/hg/makeDb/trackDb/human/hg38/long_read_transcripts.ra
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    5910da9c6e6b700ca703191267cb9c8b942500ef Fri Apr 18 13:17:16 2025 -0700
    changing encode4 into long read transcript supertrack
• src/hg/makeDb/trackDb/human/hg38/pseudogenes.ra
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    a95486084d48d3739b6d995a11f2cea55754f10c Fri Apr 18 12:16:18 2025 -0700
    better labeling and searching of Yale pseudogene track
• src/hg/makeDb/trackDb/human/hg38/recount3.ra
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    e54532b351e64aac1909932b1d78f48954fbef3f Wed Apr 23 11:18:22 2025 -0700
    fix track names in recount3.ra
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    5910da9c6e6b700ca703191267cb9c8b942500ef Fri Apr 18 13:17:16 2025 -0700
    changing encode4 into long read transcript supertrack
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    1e7d9c6de553533f62c9b818868663f7f6f82531 Thu Apr 24 11:43:44 2025 -0700
    including alpha on un-QA'd tracks
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    1e7d9c6de553533f62c9b818868663f7f6f82531 Thu Apr 24 11:43:44 2025 -0700
    including alpha on un-QA'd tracks
• src/hg/makeDb/trackDb/recount3.html
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    dc5d2fedb09bf9a1ea4ea9d9348f5cbfe7a21a82 Wed Apr 23 11:08:39 2025 -0700
    fix typos in recount3.html
• src/hg/makefile
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    836b73dcf9a90141ad0923009f03d2494fdd18ca Tue Apr 22 15:17:05 2025 -0700
    Replaced shell loops in build paths of makefile to use rules. This should address issues where errors in some rules are not reported (#35339) and also increase speed of builds using multiple cores
• src/hg/near/hgNear/hgNear.c
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    df0b444ffb7c4b4f6ec8e745ad0e0f22b46cd15f Thu Apr 24 02:29:22 2025 -0700
    Found hgNear as a highly executed CGI on RR, added botDelay. No rm.
• src/hg/snp/makefile
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    836b73dcf9a90141ad0923009f03d2494fdd18ca Tue Apr 22 15:17:05 2025 -0700
    Replaced shell loops in build paths of makefile to use rules. This should address issues where errors in some rules are not reported (#35339) and also increase speed of builds using multiple cores
• src/hg/txGene/makefile
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    836b73dcf9a90141ad0923009f03d2494fdd18ca Tue Apr 22 15:17:05 2025 -0700
    Replaced shell loops in build paths of makefile to use rules. This should address issues where errors in some rules are not reported (#35339) and also increase speed of builds using multiple cores
• src/hg/txGraph/makefile
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    836b73dcf9a90141ad0923009f03d2494fdd18ca Tue Apr 22 15:17:05 2025 -0700
    Replaced shell loops in build paths of makefile to use rules. This should address issues where errors in some rules are not reported (#35339) and also increase speed of builds using multiple cores
• src/hg/utils/hubCheck/hubCheck.c
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    641fedbb2b65a9b9fe8ae820b80bf844b41f773b Wed Apr 23 13:38:29 2025 -0700
    Adding more information and a link for hubCheckâ€'s missing description page for track warning, refs #32998
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    5ec8b7da58a074c66ba4cd8edfa0d229614ec866 Wed Apr 23 15:43:45 2025 -0700
    Forgot to include the html setting anchor, refs #32998
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    1a5ac904a3b854204a706cec107024581405d4de Thu Apr 24 13:37:24 2025 -0700
    Updating the missing description page for track warning and adding a sentence with a Hub Track Database Definition page link, refs #32998
• src/inc/cgiLoader.mk
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    836b73dcf9a90141ad0923009f03d2494fdd18ca Tue Apr 22 15:17:05 2025 -0700
    Replaced shell loops in build paths of makefile to use rules. This should address issues where errors in some rules are not reported (#35339) and also increase speed of builds using multiple cores
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    0ba17462c2e7b3f97e2bcac98b278057886281d5 Fri Apr 25 16:26:06 2025 +0200
    adding GBIC mode for OSX, no ticket yet, waiting for GBIC for arm on linux update ticket
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    fbc8d393d023d018b71322e8717a8079d80c2d3c Sat Apr 26 00:38:02 2025 +0200
    trying to fix mysterious merge conflict, as I didnt touch this file at all
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    e4014fd82b3819875269703e6a9d7f441299e3a4 Sat Apr 26 02:05:25 2025 +0200
    fixing a small OSX problem in GBIC, no redmine
• src/inc/common.mk
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    0ba17462c2e7b3f97e2bcac98b278057886281d5 Fri Apr 25 16:26:06 2025 +0200
    adding GBIC mode for OSX, no ticket yet, waiting for GBIC for arm on linux update ticket
• src/inc/srcVersion.h
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    e225fe12308746322ff2f9c98e457e5fdeaadf20 Mon Apr 28 11:16:36 2025 -0700
    New version number v481
• src/makefile
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    836b73dcf9a90141ad0923009f03d2494fdd18ca Tue Apr 22 15:17:05 2025 -0700
    Replaced shell loops in build paths of makefile to use rules. This should address issues where errors in some rules are not reported (#35339) and also increase speed of builds using multiple cores
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    f716b228d26ba0908c6bfeca4b01d428cb0efd42 Wed Apr 23 11:56:42 2025 -0700
    fixed make loop removal problem with top level run of make userApps [hiram owed lunch]
• src/product/installer/browserSetup.sh
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    0ba17462c2e7b3f97e2bcac98b278057886281d5 Fri Apr 25 16:26:06 2025 +0200
    adding GBIC mode for OSX, no ticket yet, waiting for GBIC for arm on linux update ticket
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    5ed524964ecfcf748f22f5823ef4e945212ac132 Fri Apr 25 16:38:33 2025 -0700
    adding support for Linux on ARM to GBIC, refs #29651, refs #29468
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    25c64ec48e9bbf3f5fb2aad878cf1b7dcce6d50b Mon Apr 28 16:06:03 2025 +0200
    building htdocs now in gbic for ARM
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    e132560389050652178d61d4a6006f86bbe5ea4c Mon Apr 28 16:13:27 2025 +0200
    GBIC: detecting mysql directory in case the user moved it, after current ML ticket. working around OSX weirdness with /gbdb. No redmine yet
• src/utils/qa/weeklybld/buildEnv.csh
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    4cd84d8c7391284eff46c9f2fe0527a719ea7f58 Mon Apr 28 11:16:09 2025 -0700
    v481 final build, refs #35512
• src/utils/userApps/makefile
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    836b73dcf9a90141ad0923009f03d2494fdd18ca Tue Apr 22 15:17:05 2025 -0700
    Replaced shell loops in build paths of makefile to use rules. This should address issues where errors in some rules are not reported (#35339) and also increase speed of builds using multiple cores

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