All File Changes

v474_preview to v474_preview2 (2024-11-04 to 2024-11-11) v474

• confs/asia.hg.conf
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    0fa8828aa3bb752218a7bf64f28801414c12903c Sun Nov 10 01:11:22 2024 -0800
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 1, context: html, text, full: html, text
    0fa8828aa3bb752218a7bf64f28801414c12903c Sun Nov 10 01:11:22 2024 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 1, context: html, text, full: html, text
    0fa8828aa3bb752218a7bf64f28801414c12903c Sun Nov 10 01:11:22 2024 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 1, context: html, text, full: html, text
    0fa8828aa3bb752218a7bf64f28801414c12903c Sun Nov 10 01:11:22 2024 -0800
    Installing updated hg.conf files from UCSC servers
• docs/gb101.md
  • lines changed 202, context: html, text, full: html, text
    9d466707e0a2fff3df7453c54b5131c46ad8cc61 Fri Nov 8 20:56:23 2024 -0800
    Adding initial pass of tutorial text, refs #30335
• src/hg/cgilib/search.c
  • lines changed 2, context: html, text, full: html, text
    9de7f8216d1c43504692879cb61b76d55934a22f Mon Nov 4 14:14:51 2024 -0800
    Make drop down selects have a unique id from their parent, so document selectors work, refs #34759
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    d2855ee8e2d9c2641bc68e0c0ad253644ebf3f9c Tue Nov 5 09:58:32 2024 -0800
    Revert "Make drop down selects have a unique id from their parent, so document selectors work, refs #34759" This reverts commit 9de7f8216d1c43504692879cb61b76d55934a22f.
• src/hg/cirm/cdw/README
  • lines changed 24, context: html, text, full: html, text
    56a991e6955fd5893f29a4e215dd0cb1042a14c4 Mon Nov 4 13:41:40 2024 -0800
    Adding note about SSPsyGene server SetEnvIf Authorization step, requested by Max 11/4/24
  • lines changed 5, context: html, text, full: html, text
    db0adbfc752f5593bf2b2e33b52c0c3551fb65e1 Thu Nov 7 10:15:18 2024 -0800
    Add a CDW file download dependency on Apache mod_xsendfile, requested by Max 11/7/24
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 31, context: html, text, full: html, text
    0dab88f8198e8e8d35bbb65673186ad8df1a7f64 Thu Nov 7 06:49:40 2024 -0800
    adding API key section to hgHubConnect, for the "hubtools up" command, refs #34405
  • lines changed 1, context: html, text, full: html, text
    eff7c95a6e562d68bf0e04d1abbf8e20fdc728be Thu Nov 7 06:58:29 2024 -0800
    forgot that hg.conf does not have apostrophes, refs #34405
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 8, context: html, text, full: html, text
    d060b70a11099fb693b769c781796b6b577715fb Fri Nov 1 12:47:25 2024 -0700
    If sessionDataDir is in hg.conf, make a new UI option to request that the Auspice JSON output files don't expire after two days, using sessionDataDir/hgPhyloPlace/ for storage.
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 21, context: html, text, full: html, text
    d060b70a11099fb693b769c781796b6b577715fb Fri Nov 1 12:47:25 2024 -0700
    If sessionDataDir is in hg.conf, make a new UI option to request that the Auspice JSON output files don't expire after two days, using sessionDataDir/hgPhyloPlace/ for storage.
  • lines changed 13, context: html, text, full: html, text
    2a8b200a7ce182a27d6f090fe0729e089d3cf9b0 Mon Nov 4 11:31:48 2024 -0800
    Store Auspice JSON files gzip-compressed (.json --> .json.gz). Nextstrain display requires an Apache config change to serve .json with 'Content-Encoding: gzip' header instead of .json.gz.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 23, context: html, text, full: html, text
    2a8b200a7ce182a27d6f090fe0729e089d3cf9b0 Mon Nov 4 11:31:48 2024 -0800
    Store Auspice JSON files gzip-compressed (.json --> .json.gz). Nextstrain display requires an Apache config change to serve .json with 'Content-Encoding: gzip' header instead of .json.gz.
• src/hg/hgSession/hgSession.c
  • lines changed 3, context: html, text, full: html, text
    9bc8d3c62d5b420e0ecbd9afe87c9a52c4103739 Fri Oct 25 10:56:05 2024 -0700
    Move sessionData.c up from hgSession/ to lib/ so that hgPhyloPlace can use sessionDataSaveTrashFile.
• src/hg/hgSession/hgSession.h
  • lines changed 5, context: html, text, full: html, text
    9bc8d3c62d5b420e0ecbd9afe87c9a52c4103739 Fri Oct 25 10:56:05 2024 -0700
    Move sessionData.c up from hgSession/ to lib/ so that hgPhyloPlace can use sessionDataSaveTrashFile.
• src/hg/hgSession/makefile
  • lines changed 1, context: html, text, full: html, text
    9bc8d3c62d5b420e0ecbd9afe87c9a52c4103739 Fri Oct 25 10:56:05 2024 -0700
    Move sessionData.c up from hgSession/ to lib/ so that hgPhyloPlace can use sessionDataSaveTrashFile.
• src/hg/hgSession/sessionData.c
  • lines changed 513, context: html, text, full: html, text
    9bc8d3c62d5b420e0ecbd9afe87c9a52c4103739 Fri Oct 25 10:56:05 2024 -0700
    Move sessionData.c up from hgSession/ to lib/ so that hgPhyloPlace can use sessionDataSaveTrashFile.
• src/hg/hgTracks/config.c
  • lines changed 8, context: html, text, full: html, text
    57fc6dd48cdec755ddaf91ed6194d2b8c0f3116c Fri Nov 8 19:52:11 2024 -0800
    Adds missing hgTracks object setting. Fixes the user complaint Can't exit Multi-Region mode. fixes #34776.
• src/hg/hgTracks/hgTracks.c
  • lines changed 5, context: html, text, full: html, text
    5d977ca7c6fef8eaa84f3289bffa3405bf4e0209 Wed Nov 6 07:29:21 2024 -0800
    forgot closing parentheses in previous commit
  • lines changed 5, context: html, text, full: html, text
    a582c17ed7b4049895cdfa148458173dae6f6cdc Wed Nov 6 07:31:59 2024 -0800
    Revert "forgot closing parentheses in previous commit" This reverts commit 5d977ca7c6fef8eaa84f3289bffa3405bf4e0209.
  • lines changed 2, context: html, text, full: html, text
    cb245d0c42739a9904c6239e59817e5dec052f49 Wed Nov 6 07:40:02 2024 -0800
    hide legend if all gnomad pli tracks are hidden, refs #26169
• src/hg/hgTracks/simpleTracks.c
  • lines changed 5, context: html, text, full: html, text
    5d977ca7c6fef8eaa84f3289bffa3405bf4e0209 Wed Nov 6 07:29:21 2024 -0800
    forgot closing parentheses in previous commit
  • lines changed 5, context: html, text, full: html, text
    a582c17ed7b4049895cdfa148458173dae6f6cdc Wed Nov 6 07:31:59 2024 -0800
    Revert "forgot closing parentheses in previous commit" This reverts commit 5d977ca7c6fef8eaa84f3289bffa3405bf4e0209.
  • lines changed 1, context: html, text, full: html, text
    cb245d0c42739a9904c6239e59817e5dec052f49 Wed Nov 6 07:40:02 2024 -0800
    hide legend if all gnomad pli tracks are hidden, refs #26169
• src/hg/hgTracks/wigTrack.c
  • lines changed 9, context: html, text, full: html, text
    c089010fe023fc7c73b6eb93aabacccfe52a1aaa Tue Nov 5 17:00:18 2024 -0800
    fix a problem that happened when we were at the last element of the color array
  • lines changed 2, context: html, text, full: html, text
    56ea4a038024442a203bb806c0779635c02925b8 Wed Nov 6 10:01:43 2024 -0800
    oops... was stepping one beyond the array end
• src/hg/hgc/gencodeClick.c
  • lines changed 6, context: html, text, full: html, text
    66635461c471e0fa874ab79b300ce66b55370ace Sun Nov 10 07:21:58 2024 -0800
    Add in GENCODE hgc gene and transcript name display in table, as check for HGCN is missing miRNAs not in HGNC but in mirBASE.
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 4, context: html, text, full: html, text
    b73f216db33fc474f4ec57ec8638fef390d69cef Tue Nov 5 13:16:41 2024 -0800
    Making changes from the code review, refs #34767
• src/hg/htdocs/goldenPath/help/assemblyHubGuidelines.html
  • lines changed 289, context: html, text, full: html, text
    f4c970b7a77aab27b11515a03c719731ff2b693e Wed Nov 6 10:49:33 2024 -0800
    initial commit of the assembly hub guidelines. Copy of the public hubs guidelines with no edits, refs #34740
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 74, context: html, text, full: html, text
    ba4275b1d91899277e26b44b226cc1ee29309fb3 Wed Nov 6 16:58:24 2024 -0800
    Adding highlight stripe examples to the trackDb definitions page, refs #33692
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    122804d031b83d8c67abba1b5beba1d2db61abf9 Wed Nov 6 17:04:38 2024 -0800
    Fixing a spacing issue, refs #33692
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 25, context: html, text, full: html, text
    3a506cd303b10c3c81e3196e990d4487f8757e2e Tue Nov 5 11:07:01 2024 -0800
    Announcing the release of the difficult regions from GIAB tracks, refs #32715
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    d9ed0bc0c700980005dd57943ac7e176bf8470b0 Tue Nov 5 11:15:07 2024 -0800
    Updating the hs1 track link for difficult regions from GIAB tracks, refs #32715
  • lines changed 39, context: html, text, full: html, text
    c5ce282587dbf8ec6a7b28470e0449ca6af9e250 Fri Nov 8 15:24:16 2024 -0800
    Announcing the release of All GENCODE for hg38, hg19 (V47), and mm39 (VM36). refs #34215 #34214 #34217
• src/hg/htdocs/inc/recTrackSets.hg19.tab
  • lines changed 1, context: html, text, full: html, text
    3a11a2cb7b1bc56c0ee32ae18fe900683d9e2120 Wed Nov 6 16:57:19 2024 -0800
    Adding a new RTS for the ENIGMA VCEP. No RM.
• src/hg/htdocs/inc/recTrackSets.hg38.tab
  • lines changed 1, context: html, text, full: html, text
    3a11a2cb7b1bc56c0ee32ae18fe900683d9e2120 Wed Nov 6 16:57:19 2024 -0800
    Adding a new RTS for the ENIGMA VCEP. No RM.
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    e689771885dfe692d6814feed144b5d0c5c1ad42 Wed Nov 6 17:01:36 2024 -0800
    My tabs turned to spaces when I copied, oops.
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    3a506cd303b10c3c81e3196e990d4487f8757e2e Tue Nov 5 11:07:01 2024 -0800
    Announcing the release of the difficult regions from GIAB tracks, refs #32715
  • lines changed 13, context: html, text, full: html, text
    c5ce282587dbf8ec6a7b28470e0449ca6af9e250 Fri Nov 8 15:24:16 2024 -0800
    Announcing the release of All GENCODE for hg38, hg19 (V47), and mm39 (VM36). refs #34215 #34214 #34217
• src/hg/inc/sessionData.h
  • lines changed 21, context: html, text, full: html, text
    9bc8d3c62d5b420e0ecbd9afe87c9a52c4103739 Fri Oct 25 10:56:05 2024 -0700
    Move sessionData.c up from hgSession/ to lib/ so that hgPhyloPlace can use sessionDataSaveTrashFile.
• src/hg/inc/wikiLink.h
  • lines changed 7, context: html, text, full: html, text
    0dab88f8198e8e8d35bbb65673186ad8df1a7f64 Thu Nov 7 06:49:40 2024 -0800
    adding API key section to hgHubConnect, for the "hubtools up" command, refs #34405
• src/hg/js/ddcl.js
  • lines changed 1, context: html, text, full: html, text
    0c4f83cacbb6b3489d039e3207f39d1b54fb4591 Mon Nov 4 13:52:20 2024 -0800
    Fix hgTracks track search tabs, the 'select' method has been deprecated so we weren't setting up dropdownchecklists when switching tabs, refs #34759
• src/hg/js/hgHubConnect.js
  • lines changed 6, context: html, text, full: html, text
    0dab88f8198e8e8d35bbb65673186ad8df1a7f64 Thu Nov 7 06:49:40 2024 -0800
    adding API key section to hgHubConnect, for the "hubtools up" command, refs #34405
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    0c4f83cacbb6b3489d039e3207f39d1b54fb4591 Mon Nov 4 13:52:20 2024 -0800
    Fix hgTracks track search tabs, the 'select' method has been deprecated so we weren't setting up dropdownchecklists when switching tabs, refs #34759
  • lines changed 2, context: html, text, full: html, text
    83f2164bda909e69ada0e67e8a3e791304ea4702 Tue Nov 5 10:07:38 2024 -0800
    When switching tabs on hgTracks track search, explicitly set the hidden form input for what tab we are on, because jquery-ui tabs does not do that for us anymore, refs #34771
  • lines changed 3, context: html, text, full: html, text
    dc83328fa5ea74ae26e5feb35d1a38e9a8724814 Wed Nov 6 07:00:00 2024 -0800
    another fix for hideOthers, make sure that tracks that are on by default are really hidden, refs #27890
  • lines changed 13, context: html, text, full: html, text
    cb245d0c42739a9904c6239e59817e5dec052f49 Wed Nov 6 07:40:02 2024 -0800
    hide legend if all gnomad pli tracks are hidden, refs #26169
• src/hg/js/utils.js
  • lines changed 5, context: html, text, full: html, text
    0c4f83cacbb6b3489d039e3207f39d1b54fb4591 Mon Nov 4 13:52:20 2024 -0800
    Fix hgTracks track search tabs, the 'select' method has been deprecated so we weren't setting up dropdownchecklists when switching tabs, refs #34759
  • lines changed 3, context: html, text, full: html, text
    83f2164bda909e69ada0e67e8a3e791304ea4702 Tue Nov 5 10:07:38 2024 -0800
    When switching tabs on hgTracks track search, explicitly set the hidden form input for what tab we are on, because jquery-ui tabs does not do that for us anymore, refs #34771
• src/hg/lib/hdb.c
  • lines changed 3, context: html, text, full: html, text
    6abbabb8e05b4f9bc098732786d715aee612ed3b Thu Nov 7 15:19:50 2024 -0800
    deal with hubId not found in hubStatus
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    9bc8d3c62d5b420e0ecbd9afe87c9a52c4103739 Fri Oct 25 10:56:05 2024 -0700
    Move sessionData.c up from hgSession/ to lib/ so that hgPhyloPlace can use sessionDataSaveTrashFile.
• src/hg/lib/sessionData.c
  • lines changed 514, context: html, text, full: html, text
    9bc8d3c62d5b420e0ecbd9afe87c9a52c4103739 Fri Oct 25 10:56:05 2024 -0700
    Move sessionData.c up from hgSession/ to lib/ so that hgPhyloPlace can use sessionDataSaveTrashFile.
• src/hg/lib/straw/straw.cpp
  • lines changed 8, context: html, text, full: html, text
    ff67e7b0b5e3338d066afedf2464f8056bb2e0cc Tue Nov 5 19:29:36 2024 -0800
    Replacing a stderr warning about absent hic normalization with a thrown exception that can be caught, refs #34394
• src/hg/lib/wikiLink.c
  • lines changed 18, context: html, text, full: html, text
    0dab88f8198e8e8d35bbb65673186ad8df1a7f64 Thu Nov 7 06:49:40 2024 -0800
    adding API key section to hgHubConnect, for the "hubtools up" command, refs #34405
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    3a104cf1e3c51b2d1bfe61395765a8ca753533bf Mon Nov 11 00:28:57 2024 -0800
    remove name changed assembly refs #34370
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    be493d28f90207835c1dc59a816f5b25bc05a322 Mon Nov 11 02:44:30 2024 -0800
    VGP update refs #34370
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    1b9f37e450e37425d9ebaf7c152d88cb8843e884 Mon Nov 11 02:43:49 2024 -0800
    asmHubs/master.run.list
• src/hg/makeDb/doc/hg38/decipher.txt
  • lines changed 102, context: html, text, full: html, text
    ea3708197af0c9d0a081a656bf9a88b8aaa68f15 Tue Nov 5 10:55:10 2024 -0800
    Adding the makedoc for the DDG2P track, refs #34097
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    5fcddbe40be61db85506092f6d7fb206f4fa90b1 Tue Nov 5 15:29:13 2024 -0800
    Adding steps to create symlinks, refs #34097
• src/hg/makeDb/doc/hg38/problematic.txt
  • lines changed 51, context: html, text, full: html, text
    687239fe5e1d9407369eb985448dc1f844b261b0 Tue Nov 5 11:24:23 2024 -0800
    Moving the programaticGIAB.txt text to the problematic.txt makedoc, refs #32715
• src/hg/makeDb/doc/hg38/problematicGIAB.txt
  • lines changed 49, context: html, text, full: html, text
    687239fe5e1d9407369eb985448dc1f844b261b0 Tue Nov 5 11:24:23 2024 -0800
    Moving the programaticGIAB.txt text to the problematic.txt makedoc, refs #32715
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    1b9f37e450e37425d9ebaf7c152d88cb8843e884 Mon Nov 11 02:43:49 2024 -0800
    asmHubs/master.run.list
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    1b9f37e450e37425d9ebaf7c152d88cb8843e884 Mon Nov 11 02:43:49 2024 -0800
    asmHubs/master.run.list
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    1b9f37e450e37425d9ebaf7c152d88cb8843e884 Mon Nov 11 02:43:49 2024 -0800
    asmHubs/master.run.list
• src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv
  • lines changed 32, context: html, text, full: html, text
    6bb32f2687b57a34df9189d8126975f2dca12ee2 Fri Nov 8 03:35:30 2024 -0800
    updating VGP with 87 new assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 56, context: html, text, full: html, text
    6bb32f2687b57a34df9189d8126975f2dca12ee2 Fri Nov 8 03:35:30 2024 -0800
    updating VGP with 87 new assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 87, context: html, text, full: html, text
    6bb32f2687b57a34df9189d8126975f2dca12ee2 Fri Nov 8 03:35:30 2024 -0800
    updating VGP with 87 new assemblies refs #29545
• src/hg/makeDb/scripts/enigma/BRCAmla.py
  • lines changed 4, context: html, text, full: html, text
    89e9ea11b4ddd52983382a8731503dbb82421ca6 Thu Nov 7 17:56:00 2024 -0800
    Changing the track to have 5 decimals, feedback from Melissa.
• src/hg/makeDb/trackDb/human/dbSnp155Composite.html
  • lines changed 2, context: html, text, full: html, text
    b73f216db33fc474f4ec57ec8638fef390d69cef Tue Nov 5 13:16:41 2024 -0800
    Making changes from the code review, refs #34767
• src/hg/makeDb/trackDb/human/decipher.alpha.ra
  • lines changed 19, context: html, text, full: html, text
    bc2575203fb033d240ca8301ccb393f76ce15a1c Tue Nov 5 16:48:36 2024 -0800
    Adding the DECIPHER DDG2P track for hg38 and hg19 on hgwdev, refs #34097
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    5d12e4662634fcfea421ec57f86a9ef660c96c07 Wed Nov 6 16:00:20 2024 -0800
    Removing the score filter since all fields are Zero. Adding a filter for the CNV type and sample_size, refs #34097
• src/hg/makeDb/trackDb/human/decipherContainer.html
  • lines changed 52, context: html, text, full: html, text
    bc2575203fb033d240ca8301ccb393f76ce15a1c Tue Nov 5 16:48:36 2024 -0800
    Adding the DECIPHER DDG2P track for hg38 and hg19 on hgwdev, refs #34097
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
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    2e2a7ae5365a981764f16c1797062fbd87f39b87 Thu Nov 7 15:39:08 2024 -0800
    Staging 3 All GENCODE tracks, refs #34215 #34214 #34217
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    c5ce282587dbf8ec6a7b28470e0449ca6af9e250 Fri Nov 8 15:24:16 2024 -0800
    Announcing the release of All GENCODE for hg38, hg19 (V47), and mm39 (VM36). refs #34215 #34214 #34217
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV46lift37.ra
  • lines changed 1, context: html, text, full: html, text
    2e2a7ae5365a981764f16c1797062fbd87f39b87 Thu Nov 7 15:39:08 2024 -0800
    Staging 3 All GENCODE tracks, refs #34215 #34214 #34217
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV47lift37.ra
  • lines changed 1, context: html, text, full: html, text
    2e2a7ae5365a981764f16c1797062fbd87f39b87 Thu Nov 7 15:39:08 2024 -0800
    Staging 3 All GENCODE tracks, refs #34215 #34214 #34217
  • lines changed 1, context: html, text, full: html, text
    c5ce282587dbf8ec6a7b28470e0449ca6af9e250 Fri Nov 8 15:24:16 2024 -0800
    Announcing the release of All GENCODE for hg38, hg19 (V47), and mm39 (VM36). refs #34215 #34214 #34217
• src/hg/makeDb/trackDb/human/hg38/problematic.html
  • lines changed 11, context: html, text, full: html, text
    fd2ffa40617f21bcddc57634e25ca4eb5c63d8b1 Mon Nov 4 12:04:08 2024 -0800
    Updating the track description page and adding pennant icons to the difficult regions from GIAB tracks, refs #32715
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    05c63fe738c053ec8ef8de5b13bf2159ae64772b Tue Nov 5 09:52:08 2024 -0800
    Adding new paper to the difficult regions from GIAB references per user request, refs #32715
• src/hg/makeDb/trackDb/human/hg38/problematic.ra
  • lines changed 2, context: html, text, full: html, text
    fd2ffa40617f21bcddc57634e25ca4eb5c63d8b1 Mon Nov 4 12:04:08 2024 -0800
    Updating the track description page and adding pennant icons to the difficult regions from GIAB tracks, refs #32715
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
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    2e2a7ae5365a981764f16c1797062fbd87f39b87 Thu Nov 7 15:39:08 2024 -0800
    Staging 3 All GENCODE tracks, refs #34215 #34214 #34217
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    c5ce282587dbf8ec6a7b28470e0449ca6af9e250 Fri Nov 8 15:24:16 2024 -0800
    Announcing the release of All GENCODE for hg38, hg19 (V47), and mm39 (VM36). refs #34215 #34214 #34217
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV46.ra
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    2e2a7ae5365a981764f16c1797062fbd87f39b87 Thu Nov 7 15:39:08 2024 -0800
    Staging 3 All GENCODE tracks, refs #34215 #34214 #34217
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV47.ra
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    2e2a7ae5365a981764f16c1797062fbd87f39b87 Thu Nov 7 15:39:08 2024 -0800
    Staging 3 All GENCODE tracks, refs #34215 #34214 #34217
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    c5ce282587dbf8ec6a7b28470e0449ca6af9e250 Fri Nov 8 15:24:16 2024 -0800
    Announcing the release of All GENCODE for hg38, hg19 (V47), and mm39 (VM36). refs #34215 #34214 #34217
• src/hg/makeDb/trackDb/human/hs1/problematic.html
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    fd2ffa40617f21bcddc57634e25ca4eb5c63d8b1 Mon Nov 4 12:04:08 2024 -0800
    Updating the track description page and adding pennant icons to the difficult regions from GIAB tracks, refs #32715
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    05c63fe738c053ec8ef8de5b13bf2159ae64772b Tue Nov 5 09:52:08 2024 -0800
    Adding new paper to the difficult regions from GIAB references per user request, refs #32715
• src/hg/makeDb/trackDb/human/hs1/problematic.ra
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    fd2ffa40617f21bcddc57634e25ca4eb5c63d8b1 Mon Nov 4 12:04:08 2024 -0800
    Updating the track description page and adding pennant icons to the difficult regions from GIAB tracks, refs #32715
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
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    2e2a7ae5365a981764f16c1797062fbd87f39b87 Thu Nov 7 15:39:08 2024 -0800
    Staging 3 All GENCODE tracks, refs #34215 #34214 #34217
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    c5ce282587dbf8ec6a7b28470e0449ca6af9e250 Fri Nov 8 15:24:16 2024 -0800
    Announcing the release of All GENCODE for hg38, hg19 (V47), and mm39 (VM36). refs #34215 #34214 #34217
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM35.ra
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    2e2a7ae5365a981764f16c1797062fbd87f39b87 Thu Nov 7 15:39:08 2024 -0800
    Staging 3 All GENCODE tracks, refs #34215 #34214 #34217
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM36.ra
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    2e2a7ae5365a981764f16c1797062fbd87f39b87 Thu Nov 7 15:39:08 2024 -0800
    Staging 3 All GENCODE tracks, refs #34215 #34214 #34217
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    c5ce282587dbf8ec6a7b28470e0449ca6af9e250 Fri Nov 8 15:24:16 2024 -0800
    Announcing the release of All GENCODE for hg38, hg19 (V47), and mm39 (VM36). refs #34215 #34214 #34217
• src/hg/utils/otto/mane/doMane.py
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    6b8b18fac6940d56a6317b23f1aedf107079a277 Fri Nov 8 17:12:59 2024 -0800
    Adding archiving to the mane otto, refs #34761
• src/hg/utils/otto/otto.crontab
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    aaf8bdaf91a9b7d6de89cc705ea9e183fd5636fe Mon Nov 11 12:08:50 2024 -0800
    Updating the otto sandbox first thing every day so that the git comparison cron doesn't complain that there is a difference, when it just hasn't pulled in the git changes yet. No RM.
• src/lib/freeType.c
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    64fac50ece48848fe46f959064b49eec36e33e72 Fri Nov 8 10:54:49 2024 -0800
    fix problem with iconv that was barfing on the translation of control codes even if translit was specified. refs #34782
• src/lib/psGfx.c
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    64fac50ece48848fe46f959064b49eec36e33e72 Fri Nov 8 10:54:49 2024 -0800
    fix problem with iconv that was barfing on the translation of control codes even if translit was specified. refs #34782
• src/lib/reEncodeFont.c
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    4d3e786558c13c7d262af79473f6fb6e8c965a8e Fri Nov 8 11:26:56 2024 -0800
    add reEncodeFont.c to the GIT archive
• src/utils/hubtools/hubtools
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    afcc702b2a413d9ee8ee3455f0730a5237026e57 Thu Nov 7 07:00:36 2024 -0800
    allow upload to hubspace using an apiKey, skip files that were already uploaded, refs #34405
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    8e26ba52245b12b2cc7e5d2f569ba346bfa59625 Thu Nov 7 09:38:53 2024 -0800
    fixing hubtools error, chmalee zoom
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    26e71c08d975868515ff8ea4c584dc6eeb7368d6 Fri Nov 8 03:56:54 2024 -0800
    adding fields requested by chris, refs #34405
• src/utils/qa/weeklybld/buildEnv.csh
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    febb548b22bbb246e4092729a9daf55a112d73e0 Mon Nov 11 22:19:12 2024 -0800
    v474 preview2, refs #34758

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