All File Changes

v484_base to v485_preview (2025-06-30 to 2025-07-07) v485

• confs/asia.hg.conf
  • lines changed 4, context: html, text, full: html, text
    96bae9c033a0e3043f88456daf9d3b6d238cb09e Sun Jul 6 01:11:14 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 10, context: html, text, full: html, text
    96bae9c033a0e3043f88456daf9d3b6d238cb09e Sun Jul 6 01:11:14 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 10, context: html, text, full: html, text
    96bae9c033a0e3043f88456daf9d3b6d238cb09e Sun Jul 6 01:11:14 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 13, context: html, text, full: html, text
    96bae9c033a0e3043f88456daf9d3b6d238cb09e Sun Jul 6 01:11:14 2025 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgBlat/hgBlat.c
  • lines changed 2, context: html, text, full: html, text
    72ecd89a5f2f0f37b07e54e25f4bc3718ab11682 Thu Jul 3 16:54:18 2025 -0700
    Updating the text to reflect the new limitations to hgBlat programmatic access. Refs #36028
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    b6759f9c765a20b162e146b23df06bff1b92eb1b Fri Jul 4 04:52:07 2025 -0700
    making hgBlat submit button same height as the other buttons, no redmine
• src/hg/hgConvert/hgConvert.c
  • lines changed 25, context: html, text, full: html, text
    51dfe6b3d4acfb1caafbee15bfdba3ea1f18fd43 Mon Jun 30 15:55:01 2025 -0700
    ongoing work on liftOver
• src/hg/hgFileSearch/hgFileSearch.c
  • lines changed 13, context: html, text, full: html, text
    2b063dcabdbbab34f4e93795f5d45b8c20a9ca6d Wed Jul 2 22:43:03 2025 -0700
    Add botdelay to hgFileSearch. Fixes #27537
• src/hg/hgTracks/barChartTrack.c
  • lines changed 4, context: html, text, full: html, text
    1c671b88fa7165c11637bafd70979a98b010f141 Fri Jul 4 08:21:20 2025 -0700
    fixing barchart bug, refs #36034
• src/hg/hgTracks/chainTrack.c
  • lines changed 3, context: html, text, full: html, text
    51dfe6b3d4acfb1caafbee15bfdba3ea1f18fd43 Mon Jun 30 15:55:01 2025 -0700
    ongoing work on liftOver
• src/hg/hgTracks/quickLift.c
  • lines changed 42, context: html, text, full: html, text
    d947dcc75b04fd0dc921c0eb02ed988d7b4819f0 Mon Jun 30 16:00:56 2025 -0700
    let genark hubs appear in hgConvert if we can figure out their UCSC org
• src/hg/hgTracks/simpleTracks.c
  • lines changed 5, context: html, text, full: html, text
    6522783fc78516c342ea5f09a3326bbc81875600 Thu Jul 3 02:00:22 2025 -0700
    Revert "make the decorator glyphs a little smaller on high zoom levels, refs #35750" This reverts commit 5ec0112a1ac3e2714a3e44d83bd9fffb225b8eb4.
• src/hg/hgTracks/vcfTrack.c
  • lines changed 15, context: html, text, full: html, text
    8aa101e7204bb6da91e3264469489e0eba6f6552 Sat Jul 5 00:33:14 2025 -0700
    Fixes erroneous code in vcfTrack.c when parallelFetch.threads=0. Tested on vcfTabix and vcfPhasedTrio in database or bigDataUrl setting or hub or ct for both .threads=0 and threads=N. fixes #36030
• src/hg/hgc/gencodeClick.c
  • lines changed 1, context: html, text, full: html, text
    e8cae79f2423f4ffc6852d2de611af4a60971810 Tue Jul 1 22:16:53 2025 -0700
    fixed bug where GENCODE Versions hgc had incorrect upper bounds for gene location click though
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 7, context: html, text, full: html, text
    72ecd89a5f2f0f37b07e54e25f4bc3718ab11682 Thu Jul 3 16:54:18 2025 -0700
    Updating the text to reflect the new limitations to hgBlat programmatic access. Refs #36028
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 1, context: html, text, full: html, text
    affd7eec361fd45c52bb5658910e7d4456f421a7 Wed Jul 2 16:23:16 2025 -0700
    Feedback from CR, refs #36014
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    affd7eec361fd45c52bb5658910e7d4456f421a7 Wed Jul 2 16:23:16 2025 -0700
    Feedback from CR, refs #36014
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    5e03648c60553bf87f9399b4dd070e5ef79a8074 Tue Jul 1 12:38:28 2025 -0700
    Code review edits, refs #36009
• src/hg/inc/genark.h
  • lines changed 8, context: html, text, full: html, text
    d947dcc75b04fd0dc921c0eb02ed988d7b4819f0 Mon Jun 30 16:00:56 2025 -0700
    let genark hubs appear in hgConvert if we can figure out their UCSC org
• src/hg/lib/asmEquivalent.c
  • lines changed 1, context: html, text, full: html, text
    478f9fe57277877ef7ef8e445a312ec9788a1b48 Wed Jul 2 22:26:33 2025 -0700
    the check for the successful hAllocConn will never get there as it will crash with the attempted connection refs #36030
• src/hg/lib/cart.c
  • lines changed 8, context: html, text, full: html, text
    b16a54cb0209ba472e8a5e2e8babd7438640deb8 Wed Jul 2 05:47:22 2025 -0700
    fix view/edit button on hgSession after captcha changes, refs #36024
  • lines changed 35, context: html, text, full: html, text
    bec8b07ad2d602943c4ae62323e3f411380f7ec8 Wed Jul 2 05:59:43 2025 -0700
    small cart.c changes for readability and cleanup. No redmine.
  • lines changed 12, context: html, text, full: html, text
    64cd6f16d5f331608214b97a2454adaec32d974a Wed Jul 2 06:40:13 2025 -0700
    small improvements after feedback from Brian, refs #36024
• src/hg/lib/customFactory.c
  • lines changed 1, context: html, text, full: html, text
    c640cdee51c537e715a7d4bf331f3ef71fd58849 Tue Jul 1 14:49:59 2025 -0700
    fix comment in response to code review
• src/hg/lib/genark.c
  • lines changed 82, context: html, text, full: html, text
    d947dcc75b04fd0dc921c0eb02ed988d7b4819f0 Mon Jun 30 16:00:56 2025 -0700
    let genark hubs appear in hgConvert if we can figure out their UCSC org
• src/hg/lib/hdb.c
  • lines changed 28, context: html, text, full: html, text
    d947dcc75b04fd0dc921c0eb02ed988d7b4819f0 Mon Jun 30 16:00:56 2025 -0700
    let genark hubs appear in hgConvert if we can figure out their UCSC org
• src/hg/lib/hubConnect.c
  • lines changed 3, context: html, text, full: html, text
    51dfe6b3d4acfb1caafbee15bfdba3ea1f18fd43 Mon Jun 30 15:55:01 2025 -0700
    ongoing work on liftOver
• src/hg/lib/trackHub.c
  • lines changed 7, context: html, text, full: html, text
    51dfe6b3d4acfb1caafbee15bfdba3ea1f18fd43 Mon Jun 30 15:55:01 2025 -0700
    ongoing work on liftOver
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 50, context: html, text, full: html, text
    d5a014d673b87e3818fd67a6458eae70e1b0c169 Mon Jun 30 15:46:08 2025 -0700
    finish off the HPRC update refs #35415
  • lines changed 1, context: html, text, full: html, text
    a2d13b7983fe1ae6696a7dcfe77e34ac64b7f6a9 Thu Jul 3 19:04:12 2025 -0700
    add one per user request refs #29545
  • lines changed 4, context: html, text, full: html, text
    e4408769134157e7443af0059351f2f562a95a41 Sun Jul 6 13:17:02 2025 -0700
    adding several per user request refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    e4408769134157e7443af0059351f2f562a95a41 Sun Jul 6 13:17:02 2025 -0700
    adding several per user request refs #29545
• src/hg/makeDb/doc/hg19.txt
  • lines changed 4, context: html, text, full: html, text
    18bdb7e650b738210115316787b9691f4d4c6969 Fri Jul 4 05:21:50 2025 -0700
    adding bionano tracks to hg19 and hg38, refs #36033
• src/hg/makeDb/doc/hg38/exomeProbesets.txt
  • lines changed 3, context: html, text, full: html, text
    18bdb7e650b738210115316787b9691f4d4c6969 Fri Jul 4 05:21:50 2025 -0700
    adding bionano tracks to hg19 and hg38, refs #36033
• src/hg/makeDb/doc/hprcAsmHub/hprc.orderList.tsv
  • lines changed 464, context: html, text, full: html, text
    ec4be1f046b60cc6fa453938884ece42327e130a Mon Jun 30 20:47:25 2025 -0700
    updated to 464 latest edition of HPRC refs 35415
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    a2d13b7983fe1ae6696a7dcfe77e34ac64b7f6a9 Thu Jul 3 19:04:12 2025 -0700
    add one per user request refs #29545
  • lines changed 2, context: html, text, full: html, text
    e4408769134157e7443af0059351f2f562a95a41 Sun Jul 6 13:17:02 2025 -0700
    adding several per user request refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 16, context: html, text, full: html, text
    90251c6317fe6ed1f8675d5759e924034f1c8456 Mon Jun 30 16:39:04 2025 -0700
    finish off the HPRC update refs move obsolets to legacy #35415
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 16, context: html, text, full: html, text
    90251c6317fe6ed1f8675d5759e924034f1c8456 Mon Jun 30 16:39:04 2025 -0700
    finish off the HPRC update refs move obsolets to legacy #35415
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 50, context: html, text, full: html, text
    d5a014d673b87e3818fd67a6458eae70e1b0c169 Mon Jun 30 15:46:08 2025 -0700
    finish off the HPRC update refs #35415
  • lines changed 464, context: html, text, full: html, text
    90251c6317fe6ed1f8675d5759e924034f1c8456 Mon Jun 30 16:39:04 2025 -0700
    finish off the HPRC update refs move obsolets to legacy #35415
• src/hg/makeDb/doc/rheMac10/mgap.txt
  • lines changed 6, context: html, text, full: html, text
    fb1f5e7813084d80c19ff0e394457b5ff1b59386 Fri Jul 4 03:36:19 2025 -0700
    adding mgap track, refs #36032
• src/hg/makeDb/trackDb/human/civic.ra
  • lines changed 1, context: html, text, full: html, text
    553f892edf37a754bcf2ae6975be07e8cf8e608d Tue Jul 1 16:28:15 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/decipher.ra
  • lines changed 1, context: html, text, full: html, text
    a520bf95164b64737722c4a6250552fd43e5dd1b Tue Jul 1 14:48:08 2025 -0700
    Fixing a typo in the DECIPHER CNV track that was preventing the mouseOver text from appearing, refs #36001
  • lines changed 2, context: html, text, full: html, text
    7ed7d9175b7b6cec121e069a7501fd6c087faff8 Tue Jul 1 15:11:06 2025 -0700
    Using the new mouseOver trackDb setting for the DECIPHER CNV track, refs #36001
• src/hg/makeDb/trackDb/human/exomeProbesets.html
  • lines changed 4, context: html, text, full: html, text
    18bdb7e650b738210115316787b9691f4d4c6969 Fri Jul 4 05:21:50 2025 -0700
    adding bionano tracks to hg19 and hg38, refs #36033
  • lines changed 8, context: html, text, full: html, text
    a38a591af4c79bd4853bf4e55fbb52887ad3a03e Fri Jul 4 05:24:40 2025 -0700
    fixing typo in previous commit, refs #36033
• src/hg/makeDb/trackDb/human/hg19/denovoDb.ra
  • lines changed 1, context: html, text, full: html, text
    553f892edf37a754bcf2ae6975be07e8cf8e608d Tue Jul 1 16:28:15 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg19/exomeProbesets.ra
  • lines changed 8, context: html, text, full: html, text
    18bdb7e650b738210115316787b9691f4d4c6969 Fri Jul 4 05:21:50 2025 -0700
    adding bionano tracks to hg19 and hg38, refs #36033
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    553f892edf37a754bcf2ae6975be07e8cf8e608d Tue Jul 1 16:28:15 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV48lift37.ra
  • lines changed 1, context: html, text, full: html, text
    5e03648c60553bf87f9399b4dd070e5ef79a8074 Tue Jul 1 12:38:28 2025 -0700
    Code review edits, refs #36009
• src/hg/makeDb/trackDb/human/hg38/exomeProbesets.ra
  • lines changed 8, context: html, text, full: html, text
    18bdb7e650b738210115316787b9691f4d4c6969 Fri Jul 4 05:21:50 2025 -0700
    adding bionano tracks to hg19 and hg38, refs #36033
• src/hg/makeDb/trackDb/human/hg38/pseudogenes.ra
  • lines changed 1, context: html, text, full: html, text
    553f892edf37a754bcf2ae6975be07e8cf8e608d Tue Jul 1 16:28:15 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/psuVsUcscChains.ra
  • lines changed 15, context: html, text, full: html, text
    f29fbfb4ce5b6e3e9097fa17e891044965a35577 Wed Jul 2 05:48:47 2025 -0700
    adding galaxy versus UCSC chain files comparison track to hgwdev, no ticket
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    553f892edf37a754bcf2ae6975be07e8cf8e608d Tue Jul 1 16:28:15 2025 -0700
    Squashing old pennantIcons.
  • lines changed 1, context: html, text, full: html, text
    f29fbfb4ce5b6e3e9097fa17e891044965a35577 Wed Jul 2 05:48:47 2025 -0700
    adding galaxy versus UCSC chain files comparison track to hgwdev, no ticket
  • lines changed 1, context: html, text, full: html, text
    a4569e4234f602107730a8ef6e0b7326d15a8102 Thu Jul 3 11:45:13 2025 -0700
    Staging the unusual conservation track on beta, refs #35703
  • lines changed 1, context: html, text, full: html, text
    8a064607cb194e5b9926a009aed93914b495a3b5 Thu Jul 3 12:21:22 2025 -0700
    Releasing the Unusual conservation for hg38, refs #35703
• src/hg/makeDb/trackDb/human/hg38/unusualcons.ra
  • lines changed 1, context: html, text, full: html, text
    1d3c0bc29b0b44eb037b007f09339975b5b3f085 Thu Jul 3 12:39:43 2025 -0700
    Adding pennantIcon for the Unusual conservation track, refs #35703
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV48.ra
  • lines changed 1, context: html, text, full: html, text
    5e03648c60553bf87f9399b4dd070e5ef79a8074 Tue Jul 1 12:38:28 2025 -0700
    Code review edits, refs #36009
• src/hg/makeDb/trackDb/human/mcap.ra
  • lines changed 1, context: html, text, full: html, text
    5238bc2c6663f5fdc03e6237c605f7ab6f77e814 Thu Jul 3 17:24:08 2025 -0700
    TrackDb tweaks for release of two new tracks, and clarifying the interpretation of mutscore, refs #35806 #35922
• src/hg/makeDb/trackDb/human/mutscore.ra
  • lines changed 2, context: html, text, full: html, text
    5238bc2c6663f5fdc03e6237c605f7ab6f77e814 Thu Jul 3 17:24:08 2025 -0700
    TrackDb tweaks for release of two new tracks, and clarifying the interpretation of mutscore, refs #35806 #35922
• src/hg/makeDb/trackDb/human/predictionScoresSuper.html
  • lines changed 6, context: html, text, full: html, text
    5238bc2c6663f5fdc03e6237c605f7ab6f77e814 Thu Jul 3 17:24:08 2025 -0700
    TrackDb tweaks for release of two new tracks, and clarifying the interpretation of mutscore, refs #35806 #35922
  • lines changed 5, context: html, text, full: html, text
    b3e1b430e5439ca135d95fb540c1d3393a126e2e Thu Jul 3 17:52:58 2025 -0700
    Adding the M-CAP guidelines, refs #35806 #35922
• src/hg/makeDb/trackDb/human/spliceImpactSuper.ra
  • lines changed 1, context: html, text, full: html, text
    553f892edf37a754bcf2ae6975be07e8cf8e608d Tue Jul 1 16:28:15 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/splicevardb.ra
  • lines changed 1, context: html, text, full: html, text
    553f892edf37a754bcf2ae6975be07e8cf8e608d Tue Jul 1 16:28:15 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    553f892edf37a754bcf2ae6975be07e8cf8e608d Tue Jul 1 16:28:15 2025 -0700
    Squashing old pennantIcons.
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM37.ra
  • lines changed 1, context: html, text, full: html, text
    5e03648c60553bf87f9399b4dd070e5ef79a8074 Tue Jul 1 12:38:28 2025 -0700
    Code review edits, refs #36009
• src/hg/makeDb/trackDb/rhesus/rheMac10/mgap.html
  • lines changed 39, context: html, text, full: html, text
    fb1f5e7813084d80c19ff0e394457b5ff1b59386 Fri Jul 4 03:36:19 2025 -0700
    adding mgap track, refs #36032
• src/hg/makeDb/trackDb/rhesus/rheMac10/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    fb1f5e7813084d80c19ff0e394457b5ff1b59386 Fri Jul 4 03:36:19 2025 -0700
    adding mgap track, refs #36032
• src/hg/utils/otto/otto.crontab
  • lines changed 1, context: html, text, full: html, text
    d2ba607d9473e0ab7983cd09fe44652db733ffee Thu Jul 3 02:04:42 2025 -0700
    Changed otto crontab to use doUpdate for pubtatorDbSnp instead of BUILD refs #36011
• src/hg/utils/otto/pubtatorDbSnp/.gitignore
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    6f6777bc15f21a8bbb6b2f402eb328a1ecb21652 Thu Jul 3 01:58:56 2025 -0700
    Refactored a bit
• src/hg/utils/otto/pubtatorDbSnp/dbs_combiner.py
  • lines changed 28, context: html, text, full: html, text
    6f6777bc15f21a8bbb6b2f402eb328a1ecb21652 Thu Jul 3 01:58:56 2025 -0700
    Refactored a bit
• src/hg/utils/otto/pubtatorDbSnp/doUpdate.sh
  • lines changed 5, context: html, text, full: html, text
    6f6777bc15f21a8bbb6b2f402eb328a1ecb21652 Thu Jul 3 01:58:56 2025 -0700
    Refactored a bit
• src/hg/utils/otto/varChat/varChatOtto.sh
  • lines changed 2, context: html, text, full: html, text
    0201b0880739fab2da294d38254ab0deb1752899 Wed Jul 2 16:45:52 2025 -0700
    Commiting changes that were active on hive but not in the source tree, no Redmine
• src/inc/common.mk
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    3b55640299a9fb73fb2169247e95dad63c1fd8fd Wed Jul 2 11:58:43 2025 -0700
    adding back lowerlab make section, email from Patricia
• src/utils/bigBedInfo/bigBedInfo.c
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    8dac953a863d1e7ca35327c3b326d50e776ffcac Wed Jul 2 08:00:48 2025 -0700
    making bigBedInfo field indices 1-based, not 0-based as they used to be. No redmine, email with Brian
• src/utils/qa/weeklybld/buildEnv.csh
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    be6b8f8749f470a686ee437035aa6c2ec5ea04ae Mon Jul 7 11:25:36 2025 -0700
    v485 preview1, refs #TICKETNUM

• lines changed: 1594
• files changed: 78