All File Changes

v480_base to v481_preview (2025-04-07 to 2025-04-14) v481

• src/hg/hgHubConnect/makefile
  • lines changed 5, context: html, text, full: html, text
    592607d89690cca775cdccde3b53ac98f1e84c86 Fri Apr 11 12:18:19 2025 -0700
    Add a beta target to the hgHubConnect hooks, refs Jonathan email
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    411ea25bd9d77d5d79b4bbebe136985dee7fa73d Mon Apr 14 11:34:05 2025 -0700
    add a little more context to the hgTrackUi Submit POST request
• src/hg/hgTracks/gvfTrack.c
  • lines changed 32, context: html, text, full: html, text
    736a3a779c20bf482ed252e5077f1c851c6a500f Thu Apr 10 10:51:26 2025 -0700
    add support for GVF in quickLift. Grab HTML from native db for quick lifted tracks.
• src/hg/hgTracks/lollyTrack.c
  • lines changed 27, context: html, text, full: html, text
    2fd02c5e1ce1bb989549b2e0069270ca8907efad Thu Apr 10 15:03:42 2025 -0700
    add bigLolly to quickLift support
• src/hg/hgTracks/quickLift.c
  • lines changed 47, context: html, text, full: html, text
    a47a1512c601832a59ecac5f667e2a884e4a6514 Sat Apr 12 10:36:56 2025 -0700
    allow quickLift highlight colors and limit to be set in hg.conf
• src/hg/hgTracks/simpleTracks.c
  • lines changed 72, context: html, text, full: html, text
    7f7a9a5579d7acec698c51dbf93f5030ce1a0439 Tue Apr 8 15:43:17 2025 -0700
    support genePred in quickLift
• src/hg/hgc/clinvarSubLolly.c
  • lines changed 33, context: html, text, full: html, text
    2fd02c5e1ce1bb989549b2e0069270ca8907efad Thu Apr 10 15:03:42 2025 -0700
    add bigLolly to quickLift support
  • lines changed 4, context: html, text, full: html, text
    9e5cc5d894b020d4e51b7b340f4e6441d0256388 Sat Apr 12 10:37:58 2025 -0700
    fix quickLifted clinvar submissions track
• src/hg/hgc/gvfClick.c
  • lines changed 28, context: html, text, full: html, text
    736a3a779c20bf482ed252e5077f1c851c6a500f Thu Apr 10 10:51:26 2025 -0700
    add support for GVF in quickLift. Grab HTML from native db for quick lifted tracks.
• src/hg/hgc/hgc.c
  • lines changed 13, context: html, text, full: html, text
    7f7a9a5579d7acec698c51dbf93f5030ce1a0439 Tue Apr 8 15:43:17 2025 -0700
    support genePred in quickLift
  • lines changed 29, context: html, text, full: html, text
    736a3a779c20bf482ed252e5077f1c851c6a500f Thu Apr 10 10:51:26 2025 -0700
    add support for GVF in quickLift. Grab HTML from native db for quick lifted tracks.
• src/hg/htdocs/goldenPath/history.html
  • lines changed 1, context: html, text, full: html, text
    6eef7f7745a3006b3ce9dbbb96145630e86acc5e Mon Mar 31 04:57:37 2025 -0700
    adding link to GI history page, rather than a link to the page itself, refs #35140
• src/hg/htdocs/inc/hgMyData.html
  • lines changed 6, context: html, text, full: html, text
    1ee60b0f512688d475db239e379fb10c86ce1528 Wed Apr 9 12:13:51 2025 -0700
    remove some copy from the hubspace UI as requested by QA. fix dates when set by the js to use the same format as returned by the server, fix a bug when deleting files that preventing the selected file information from going away, refs #31058
• src/hg/htdocs/indexMeetings.html
  • lines changed 6, context: html, text, full: html, text
    a371f097acf5c4e0c67c14d066475c6e18a5d210 Mon Apr 14 10:57:06 2025 -0700
    Removing the BioCuration conference from the meetings section on the index page, no Redmine
• src/hg/htdocs/license/index.html
  • lines changed 2, context: html, text, full: html, text
    859872a361f280de4b6b4d6ecbafebe7c8c30097 Thu Apr 10 04:40:36 2025 -0700
    after a question from the IBM SPSS team, clarify under which license the API falls, no redmine
• src/hg/htdocs/staff.html
  • lines changed 12, context: html, text, full: html, text
    81c31710b8f9ee4a30b578aa15186757bd7c61cd Fri Apr 11 14:37:55 2025 -0700
    Adding the student workers to the staff.html page, no Redmine.
• src/hg/htdocs/style/hgMyData.css
  • lines changed 5, context: html, text, full: html, text
    4157b5a16cd39c1f6af20dd321cb69e113574993 Tue Apr 8 16:55:52 2025 -0700
    Make the uppy window larger, add a search bar to the batch select options. TODO: make the batch change options present a plain option if there are differing metadata for each file, refs #31058
• src/hg/inc/genePred.h
  • lines changed 3, context: html, text, full: html, text
    7f7a9a5579d7acec698c51dbf93f5030ce1a0439 Tue Apr 8 15:43:17 2025 -0700
    support genePred in quickLift
• src/hg/inc/liftOver.h
  • lines changed 6, context: html, text, full: html, text
    7f7a9a5579d7acec698c51dbf93f5030ce1a0439 Tue Apr 8 15:43:17 2025 -0700
    support genePred in quickLift
• src/hg/js/hgCollection.js
  • lines changed 1, context: html, text, full: html, text
    8043b90858fce6a2f40909d793062cff4b431425 Fri Apr 11 15:09:50 2025 -0700
    Fixes missing uri encoding in url for ajax callback. fixes #34751
• src/hg/js/hgMyData.js
  • lines changed 88, context: html, text, full: html, text
    4157b5a16cd39c1f6af20dd321cb69e113574993 Tue Apr 8 16:55:52 2025 -0700
    Make the uppy window larger, add a search bar to the batch select options. TODO: make the batch change options present a plain option if there are differing metadata for each file, refs #31058
  • lines changed 16, context: html, text, full: html, text
    1ee60b0f512688d475db239e379fb10c86ce1528 Wed Apr 9 12:13:51 2025 -0700
    remove some copy from the hubspace UI as requested by QA. fix dates when set by the js to use the same format as returned by the server, fix a bug when deleting files that preventing the selected file information from going away, refs #31058
  • lines changed 20, context: html, text, full: html, text
    d4fe91a0b0657952985cc2cac9660ba9bb407f7b Wed Apr 9 12:58:32 2025 -0700
    add a back button to the hubspace ui when navigating into a subdirectory, refs #31058
  • lines changed 5, context: html, text, full: html, text
    2a5fc64aaf49a1c43f450ede86225d8e5955d8bb Fri Apr 11 10:25:08 2025 -0700
    Make hub.txt uploads work correctly in the hubSpace UI, refs #35383
  • lines changed 1, context: html, text, full: html, text
    8585d249099dfb41e8195d074f087746a736dd42 Mon Apr 14 12:32:19 2025 -0700
    Specify the file name that has an invalid parent hub name in hubspace UI error message, refs #35481
• src/hg/lib/genbank.c
  • lines changed 4, context: html, text, full: html, text
    7f7a9a5579d7acec698c51dbf93f5030ce1a0439 Tue Apr 8 15:43:17 2025 -0700
    support genePred in quickLift
• src/hg/lib/genePred.c
  • lines changed 6, context: html, text, full: html, text
    7f7a9a5579d7acec698c51dbf93f5030ce1a0439 Tue Apr 8 15:43:17 2025 -0700
    support genePred in quickLift
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    073f999294e187d3ced854717e467a17098972d7 Wed Apr 9 13:21:13 2025 -0700
    do not look for genome chrom names/sizes in a database when it is a GenArk hub refs #35479 #34043
• src/hg/lib/liftOver.c
  • lines changed 17, context: html, text, full: html, text
    7f7a9a5579d7acec698c51dbf93f5030ce1a0439 Tue Apr 8 15:43:17 2025 -0700
    support genePred in quickLift
• src/hg/lib/quickLift.c
  • lines changed 1, context: html, text, full: html, text
    7f7a9a5579d7acec698c51dbf93f5030ce1a0439 Tue Apr 8 15:43:17 2025 -0700
    support genePred in quickLift
• src/hg/lib/trackHub.c
  • lines changed 2, context: html, text, full: html, text
    7f7a9a5579d7acec698c51dbf93f5030ce1a0439 Tue Apr 8 15:43:17 2025 -0700
    support genePred in quickLift
  • lines changed 7, context: html, text, full: html, text
    736a3a779c20bf482ed252e5077f1c851c6a500f Thu Apr 10 10:51:26 2025 -0700
    add support for GVF in quickLift. Grab HTML from native db for quick lifted tracks.
  • lines changed 12, context: html, text, full: html, text
    2fd02c5e1ce1bb989549b2e0069270ca8907efad Thu Apr 10 15:03:42 2025 -0700
    add bigLolly to quickLift support
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 38, context: html, text, full: html, text
    d1013ef3c61b027b582a45612ebc3848fe480f3e Mon Apr 7 13:42:08 2025 -0700
    now sending to hgdownload3 refs #35402
  • lines changed 1, context: html, text, full: html, text
    6addae8d76b1b44013e1e27762268fb8a8d858b5 Thu Apr 10 12:35:47 2025 -0700
    correctly make the assemblyList.json for the VGP set refs #34370
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 10, context: html, text, full: html, text
    e9f4a4f731d395f02c435614640e58b0bf919e23 Tue Apr 8 14:29:52 2025 -0700
    BRC update and a couple user requests refs #29545
  • lines changed 1, context: html, text, full: html, text
    88a53ecf7f28a5c829fe46eac7297d16fbd8e2e6 Tue Apr 8 18:53:08 2025 -0700
    adding one per user request refs #29545
  • lines changed 24, context: html, text, full: html, text
    a36006a7ddfa0c559bdc43f9437eb476b53e0d52 Thu Apr 10 13:33:50 2025 -0700
    VGP update refs #29545
  • lines changed 9, context: html, text, full: html, text
    8448f5b01d0af06b0b56d5c40f62bac9e5ff202c Fri Apr 11 11:38:08 2025 -0700
    VGP update refs #29545
  • lines changed 1, context: html, text, full: html, text
    2fc83b5b9dc8e08b6f599f99453bde3569b920c2 Fri Apr 11 12:15:15 2025 -0700
    VGP update refs #29545
  • lines changed 10, context: html, text, full: html, text
    6116bdab443a8dc802081eeb6451dcd889ffa4b5 Sun Apr 13 22:08:28 2025 -0700
    VGP update refs #29545
  • lines changed 1, context: html, text, full: html, text
    82c53f775cbff69892c7d009cb27b3c93aba08c2 Mon Apr 14 09:00:37 2025 -0700
    VGP update with a new marmoset refs #29545
• src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
  • lines changed 10, context: html, text, full: html, text
    d1013ef3c61b027b582a45612ebc3848fe480f3e Mon Apr 7 13:42:08 2025 -0700
    now sending to hgdownload3 refs #35402
• src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
  • lines changed 1, context: html, text, full: html, text
    34ea5c1305694c5e84fc9072ee9a375879895038 Mon Apr 7 13:43:31 2025 -0700
    new low track count for BRC project refs #34337
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    e9f4a4f731d395f02c435614640e58b0bf919e23 Tue Apr 8 14:29:52 2025 -0700
    BRC update and a couple user requests refs #29545
  • lines changed 3, context: html, text, full: html, text
    8448f5b01d0af06b0b56d5c40f62bac9e5ff202c Fri Apr 11 11:38:08 2025 -0700
    VGP update refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    88a53ecf7f28a5c829fe46eac7297d16fbd8e2e6 Tue Apr 8 18:53:08 2025 -0700
    adding one per user request refs #29545
  • lines changed 5, context: html, text, full: html, text
    04d3c728227704f2064e5efcc00d358f3e9b7e40 Wed Apr 9 23:55:35 2025 -0700
    common name fixups for VGP update refs #29545
  • lines changed 5, context: html, text, full: html, text
    a36006a7ddfa0c559bdc43f9437eb476b53e0d52 Thu Apr 10 13:33:50 2025 -0700
    VGP update refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 17, context: html, text, full: html, text
    a36006a7ddfa0c559bdc43f9437eb476b53e0d52 Thu Apr 10 13:33:50 2025 -0700
    VGP update refs #29545
  • lines changed 1, context: html, text, full: html, text
    2fc83b5b9dc8e08b6f599f99453bde3569b920c2 Fri Apr 11 12:15:15 2025 -0700
    VGP update refs #29545
  • lines changed 3, context: html, text, full: html, text
    6116bdab443a8dc802081eeb6451dcd889ffa4b5 Sun Apr 13 22:08:28 2025 -0700
    VGP update refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    a36006a7ddfa0c559bdc43f9437eb476b53e0d52 Thu Apr 10 13:33:50 2025 -0700
    VGP update refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 1, context: html, text, full: html, text
    88a53ecf7f28a5c829fe46eac7297d16fbd8e2e6 Tue Apr 8 18:53:08 2025 -0700
    adding one per user request refs #29545
  • lines changed 16, context: html, text, full: html, text
    b6ed6ba4a6456f58fa60a91c04aaef0c36728a1d Wed Apr 9 23:52:39 2025 -0700
    VGP update refs #29545
  • lines changed 1, context: html, text, full: html, text
    4819435d71306cf2fd1d6e48b3c5d488e6eef752 Thu Apr 10 10:46:52 2025 -0700
    eliminate duplicate refs #29545
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    a36006a7ddfa0c559bdc43f9437eb476b53e0d52 Thu Apr 10 13:33:50 2025 -0700
    VGP update refs #29545
  • lines changed 2, context: html, text, full: html, text
    8448f5b01d0af06b0b56d5c40f62bac9e5ff202c Fri Apr 11 11:38:08 2025 -0700
    VGP update refs #29545
  • lines changed 1, context: html, text, full: html, text
    2fc83b5b9dc8e08b6f599f99453bde3569b920c2 Fri Apr 11 12:15:15 2025 -0700
    VGP update refs #29545
  • lines changed 5, context: html, text, full: html, text
    6116bdab443a8dc802081eeb6451dcd889ffa4b5 Sun Apr 13 22:08:28 2025 -0700
    VGP update refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    88a53ecf7f28a5c829fe46eac7297d16fbd8e2e6 Tue Apr 8 18:53:08 2025 -0700
    adding one per user request refs #29545
  • lines changed 12, context: html, text, full: html, text
    b6ed6ba4a6456f58fa60a91c04aaef0c36728a1d Wed Apr 9 23:52:39 2025 -0700
    VGP update refs #29545
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    a36006a7ddfa0c559bdc43f9437eb476b53e0d52 Thu Apr 10 13:33:50 2025 -0700
    VGP update refs #29545
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    8448f5b01d0af06b0b56d5c40f62bac9e5ff202c Fri Apr 11 11:38:08 2025 -0700
    VGP update refs #29545
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    2fc83b5b9dc8e08b6f599f99453bde3569b920c2 Fri Apr 11 12:15:15 2025 -0700
    VGP update refs #29545
  • lines changed 5, context: html, text, full: html, text
    6116bdab443a8dc802081eeb6451dcd889ffa4b5 Sun Apr 13 22:08:28 2025 -0700
    VGP update refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    577743f1021ebf4049429f8257ea3587f01856fd Wed Apr 9 23:54:26 2025 -0700
    common name fixups for VGP update refs #29545
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    a36006a7ddfa0c559bdc43f9437eb476b53e0d52 Thu Apr 10 13:33:50 2025 -0700
    VGP update refs #29545
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    8448f5b01d0af06b0b56d5c40f62bac9e5ff202c Fri Apr 11 11:38:08 2025 -0700
    VGP update refs #29545
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    6116bdab443a8dc802081eeb6451dcd889ffa4b5 Sun Apr 13 22:08:28 2025 -0700
    VGP update refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    e9f4a4f731d395f02c435614640e58b0bf919e23 Tue Apr 8 14:29:52 2025 -0700
    BRC update and a couple user requests refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    85933c16175043e83dcf1371fe7a475597e79cf3 Wed Apr 9 23:55:00 2025 -0700
    common name fixups for VGP update refs #29545
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    6116bdab443a8dc802081eeb6451dcd889ffa4b5 Sun Apr 13 22:08:28 2025 -0700
    VGP update refs #29545
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    82c53f775cbff69892c7d009cb27b3c93aba08c2 Mon Apr 14 09:00:37 2025 -0700
    VGP update with a new marmoset refs #29545
• src/hg/makeDb/doc/ucscGenes/hg19.gencodeV48lift37.sh
  • lines changed 23, context: html, text, full: html, text
    1ee63d464e71659db20c5c7933b3f3fa601f0b09 Sat Apr 12 17:20:54 2025 -0700
    Makedoc for hg19 knownGeneV48, refs #35187
• src/hg/makeDb/doc/ucscGenes/hg38.gencodeV48.sh
  • lines changed 38, context: html, text, full: html, text
    35499837cef4853e0a36b82db057c8675578ef0e Thu Apr 10 10:33:18 2025 -0700
    Makedoc for V48 knownGene on hg38, refs #35186
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
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    1785f3fa7c99f5cde3c4ad098681ba1a6675f3eb Wed Apr 9 23:53:46 2025 -0700
    common name fixups for VGP update refs #29545
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    a36006a7ddfa0c559bdc43f9437eb476b53e0d52 Thu Apr 10 13:33:50 2025 -0700
    VGP update refs #29545
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    8448f5b01d0af06b0b56d5c40f62bac9e5ff202c Fri Apr 11 11:38:08 2025 -0700
    VGP update refs #29545
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    1e11c079beed5fcc711c78345614f7367606a94b Sun Apr 13 22:09:36 2025 -0700
    VGP update refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv
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    9862e359bb0b2ee9c1f45331799d059f6a20e702 Wed Apr 9 23:48:38 2025 -0700
    VGP update refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
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    9862e359bb0b2ee9c1f45331799d059f6a20e702 Wed Apr 9 23:48:38 2025 -0700
    VGP update refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
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    9862e359bb0b2ee9c1f45331799d059f6a20e702 Wed Apr 9 23:48:38 2025 -0700
    VGP update refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
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    9862e359bb0b2ee9c1f45331799d059f6a20e702 Wed Apr 9 23:48:38 2025 -0700
    VGP update refs #29545
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
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    e9f4a4f731d395f02c435614640e58b0bf919e23 Tue Apr 8 14:29:52 2025 -0700
    BRC update and a couple user requests refs #29545
• src/hg/makeDb/trackDb/human/hg19/knownGene.alpha.ra
  • lines changed 46, context: html, text, full: html, text
    75711ca6eda92d718879304fde2251bcdedd8534 Sat Apr 12 17:18:29 2025 -0700
    V48lift37 knownGene trackDb, refs #35187
• src/hg/makeDb/trackDb/human/hg19/knownGeneArchive.ra
  • lines changed 26, context: html, text, full: html, text
    75711ca6eda92d718879304fde2251bcdedd8534 Sat Apr 12 17:18:29 2025 -0700
    V48lift37 knownGene trackDb, refs #35187
• src/hg/makeDb/trackDb/human/hg19/knownGeneV48lift37.html
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    75711ca6eda92d718879304fde2251bcdedd8534 Sat Apr 12 17:18:29 2025 -0700
    V48lift37 knownGene trackDb, refs #35187
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    75711ca6eda92d718879304fde2251bcdedd8534 Sat Apr 12 17:18:29 2025 -0700
    V48lift37 knownGene trackDb, refs #35187
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
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    36c22bace06f07f8d4f59ef8a18659e926f9d410 Thu Apr 10 10:30:30 2025 -0700
    Gencode V48 knownGene trackDb
• src/hg/makeDb/trackDb/human/hg38/knownGeneArchive.ra
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    36c22bace06f07f8d4f59ef8a18659e926f9d410 Thu Apr 10 10:30:30 2025 -0700
    Gencode V48 knownGene trackDb
• src/hg/makeDb/trackDb/human/hg38/knownGeneV48.html
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    36c22bace06f07f8d4f59ef8a18659e926f9d410 Thu Apr 10 10:30:30 2025 -0700
    Gencode V48 knownGene trackDb
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    36c22bace06f07f8d4f59ef8a18659e926f9d410 Thu Apr 10 10:30:30 2025 -0700
    Gencode V48 knownGene trackDb
• src/utils/qa/weeklybld/buildEnv.csh
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    d5a5a12f667f09d74b69c49e125ee2ecf17f39c2 Mon Apr 14 13:26:22 2025 -0700
    v481 preview1, refs #35440
• src/utils/qa/weeklybld/makeStrictBeta.csh
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    3e26b51b24970c933f50f13304ae5bb1ca5a8059 Tue Apr 8 13:29:26 2025 -0700
    Trying a parallel version of the final build tdb make to speed things up, refs #35489

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• files changed: 95