All File Changes

v453_base to v454_preview (2023-08-28 to 2023-09-04) v454

• build/kent-core/makeKentCore
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    a8a18af13151e5dabad2bcc1156e3533ff5d9028 Mon Aug 28 03:55:14 2023 -0700
    replacing a LICENSE file that I forgot before, no redmine
• src/hg/cgilib/pcrResult.c
  • lines changed 30, context: html, text, full: html, text
    1484bda490e2b8be6af6889f09b258b4e63a7618 Wed Aug 30 15:01:22 2023 -0700
    Restore revoked commit that fixes hgc for old pcr result clicks, refs #32026
• src/hg/hgTracks/hgTracks.c
  • lines changed 6, context: html, text, full: html, text
    e3bf2345348955e44ee5d7d5be325162f0b4475f Tue Aug 29 09:24:13 2023 -0700
    Fix notification box setup for udcTimeout messages, refs #32045
  • lines changed 5, context: html, text, full: html, text
    ff29e6faa49df5473ddd5ef2bec9b4c33cfa588c Tue Aug 29 15:35:31 2023 -0700
    Fix new mouseover code to account for track description heights, refs #31365
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    909bdb6bed63032ec35e20e6e3e60ca3f541f2bb Thu Aug 31 09:54:01 2023 -0700
    Make some style changes to mouseovers as suggested by Max, mostly getting the background color to match the web browser default and adding a box-shadow, refs #31365
• src/hg/hgc/hgc.c
  • lines changed 5, context: html, text, full: html, text
    1484bda490e2b8be6af6889f09b258b4e63a7618 Wed Aug 30 15:01:22 2023 -0700
    Restore revoked commit that fixes hgc for old pcr result clicks, refs #32026
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 1, context: html, text, full: html, text
    29244376c9a56ed7ffcf50fa8012b47799156844 Tue Aug 29 11:04:34 2023 -0700
    Removed the table part and included an example for the baseColorUseCds setting, refs #20424
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 1, context: html, text, full: html, text
    29244376c9a56ed7ffcf50fa8012b47799156844 Tue Aug 29 11:04:34 2023 -0700
    Removed the table part and included an example for the baseColorUseCds setting, refs #20424
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 4, context: html, text, full: html, text
    29244376c9a56ed7ffcf50fa8012b47799156844 Tue Aug 29 11:04:34 2023 -0700
    Removed the table part and included an example for the baseColorUseCds setting, refs #20424
• src/hg/htdocs/style/HGStyle.css
  • lines changed 6, context: html, text, full: html, text
    909bdb6bed63032ec35e20e6e3e60ca3f541f2bb Thu Aug 31 09:54:01 2023 -0700
    Make some style changes to mouseovers as suggested by Max, mostly getting the background color to match the web browser default and adding a box-shadow, refs #31365
  • lines changed 1, context: html, text, full: html, text
    d4fd4a86c5c2270cd29a729b889962ef47b5bccd Thu Aug 31 09:56:27 2023 -0700
    Woops forgot one more style change, refs #31365
• src/hg/js/utils.js
  • lines changed 25, context: html, text, full: html, text
    e3bf2345348955e44ee5d7d5be325162f0b4475f Tue Aug 29 09:24:13 2023 -0700
    Fix notification box setup for udcTimeout messages, refs #32045
  • lines changed 14, context: html, text, full: html, text
    ff29e6faa49df5473ddd5ef2bec9b4c33cfa588c Tue Aug 29 15:35:31 2023 -0700
    Fix new mouseover code to account for track description heights, refs #31365
  • lines changed 1, context: html, text, full: html, text
    909bdb6bed63032ec35e20e6e3e60ca3f541f2bb Thu Aug 31 09:54:01 2023 -0700
    Make some style changes to mouseovers as suggested by Max, mostly getting the background color to match the web browser default and adding a box-shadow, refs #31365
• src/hg/lib/jksql.c
  • lines changed 4, context: html, text, full: html, text
    b5ffaecde00b0e38291f3833f1ecfdc271d7ab8a Mon Aug 28 03:58:05 2023 -0700
    hardening of jksql against sc==NULL. A crash happened at some point when running a tool from the command line. no redmine
• src/hg/lib/web.c
  • lines changed 11, context: html, text, full: html, text
    377ada15ebf2514739f715bcbff18c72f84ecb33 Fri Sep 1 09:48:17 2023 -0700
    Put the database into the web page title on hgc pages, refs #19985
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 10, context: html, text, full: html, text
    fc8bc86160e4f3e2afb2cd7ef272871b059e75fb Fri Sep 1 15:14:13 2023 -0700
    update with new mammal assemblies refs #29545
• src/hg/makeDb/doc/hg38/cactus447.txt
  • lines changed 714, context: html, text, full: html, text
    33401c5cafc069c3f78bcecc3c0d6f2d0b77aeda Wed Aug 30 14:36:08 2023 -0700
    phyloP done for both all and primates subset refs #31528
• src/hg/makeDb/doc/hg38/gnomadPLI.txt
  • lines changed 135, context: html, text, full: html, text
    a15237248f41fbaef682becb3ff2e083a40c2ead Thu Aug 31 15:44:23 2023 -0700
    Re-mapping gnomAD constraint items to hg38 to get more mappings after user wrote in about popular genes missing annotations, refs #31989
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 43, context: html, text, full: html, text
    4c3e9c5bca8c085e7cb5c7caece08a6ea93222be Tue Aug 29 12:54:45 2023 -0700
    adding new hprc row to grp table refs #31561
  • lines changed 12, context: html, text, full: html, text
    a24f5436f9ba6dde0c17e14939f40cc88b1292ec Fri Sep 1 13:14:53 2023 -0700
    Fixing the cosmic track which had items with same start+end, also updated the .as file. Refs #29625
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    fc8bc86160e4f3e2afb2cd7ef272871b059e75fb Fri Sep 1 15:14:13 2023 -0700
    update with new mammal assemblies refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 12, context: html, text, full: html, text
    fc8bc86160e4f3e2afb2cd7ef272871b059e75fb Fri Sep 1 15:14:13 2023 -0700
    update with new mammal assemblies refs #29545
• src/hg/makeDb/trackDb/chainNetGCA_009914755.4.trackDb.ra
  • lines changed 98, context: html, text, full: html, text
    5d9b2264aab7759c0f58dfaa3ec1523d295eb759 Wed Aug 30 10:42:32 2023 -0700
    fixup release tag issues with include statement to make the tdbQuery -check -release=public -strict "select count(*) from *" >/dev/null be silent no redmine
• src/hg/makeDb/trackDb/human/chainNetHuman.ra
  • lines changed 1, context: html, text, full: html, text
    d034e9b946b16c86295130008ec33d457ca45335 Tue Aug 29 13:08:03 2023 -0700
    collecting all the HPRC track experiments into the "hprc" track group refs #31561
• src/hg/makeDb/trackDb/human/hg38/chainNetHumanExperiment.ra
  • lines changed 1, context: html, text, full: html, text
    d034e9b946b16c86295130008ec33d457ca45335 Tue Aug 29 13:08:03 2023 -0700
    collecting all the HPRC track experiments into the "hprc" track group refs #31561
• src/hg/makeDb/trackDb/human/hg38/chainsHprc.ra
  • lines changed 1, context: html, text, full: html, text
    d034e9b946b16c86295130008ec33d457ca45335 Tue Aug 29 13:08:03 2023 -0700
    collecting all the HPRC track experiments into the "hprc" track group refs #31561
• src/hg/makeDb/trackDb/human/hg38/chainsReHprc.ra
  • lines changed 1, context: html, text, full: html, text
    d034e9b946b16c86295130008ec33d457ca45335 Tue Aug 29 13:08:03 2023 -0700
    collecting all the HPRC track experiments into the "hprc" track group refs #31561
• src/hg/makeDb/trackDb/human/hg38/gnomadPLI.html
  • lines changed 13, context: html, text, full: html, text
    a15237248f41fbaef682becb3ff2e083a40c2ead Thu Aug 31 15:44:23 2023 -0700
    Re-mapping gnomAD constraint items to hg38 to get more mappings after user wrote in about popular genes missing annotations, refs #31989
• src/hg/makeDb/trackDb/human/hg38/hprc.ra
  • lines changed 1, context: html, text, full: html, text
    d034e9b946b16c86295130008ec33d457ca45335 Tue Aug 29 13:08:03 2023 -0700
    collecting all the HPRC track experiments into the "hprc" track group refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcArr.ra
  • lines changed 7, context: html, text, full: html, text
    d034e9b946b16c86295130008ec33d457ca45335 Tue Aug 29 13:08:03 2023 -0700
    collecting all the HPRC track experiments into the "hprc" track group refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcChain.ra
  • lines changed 1, context: html, text, full: html, text
    d034e9b946b16c86295130008ec33d457ca45335 Tue Aug 29 13:08:03 2023 -0700
    collecting all the HPRC track experiments into the "hprc" track group refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcCoverage.ra
  • lines changed 1, context: html, text, full: html, text
    d034e9b946b16c86295130008ec33d457ca45335 Tue Aug 29 13:08:03 2023 -0700
    collecting all the HPRC track experiments into the "hprc" track group refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcCoverage97.ra
  • lines changed 1, context: html, text, full: html, text
    d034e9b946b16c86295130008ec33d457ca45335 Tue Aug 29 13:08:03 2023 -0700
    collecting all the HPRC track experiments into the "hprc" track group refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcVCF.ra
  • lines changed 12, context: html, text, full: html, text
    ac37789fa393ebd3f10312e9cb69965dc756841e Tue Aug 29 14:16:07 2023 -0700
    adding HPRC VCF track refs #31561
• src/hg/makeDb/trackDb/human/hg38/knownGene.v44.alpha.ra
  • lines changed 44, context: html, text, full: html, text
    5ed68f4dd6c6350f40db82794a334287e13d97fe Tue Aug 29 08:47:09 2023 -0700
    TrackDb updates for GENCODE V44 knownGene on hg38, refs #30840
• src/hg/makeDb/trackDb/human/hg38/knownGeneV44.html
  • lines changed 178, context: html, text, full: html, text
    5ed68f4dd6c6350f40db82794a334287e13d97fe Tue Aug 29 08:47:09 2023 -0700
    TrackDb updates for GENCODE V44 knownGene on hg38, refs #30840
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    a477fbe023c1cfdb0c00eb3381efdeb690bd75e9 Fri Sep 1 15:54:51 2023 -0700
    Staging new GENCODE Known Gene tracks for hg38 and mm39, refs #30840 #30841
• src/hg/makeDb/trackDb/human/hg38/netsReHprc.ra
  • lines changed 1, context: html, text, full: html, text
    d034e9b946b16c86295130008ec33d457ca45335 Tue Aug 29 13:08:03 2023 -0700
    collecting all the HPRC track experiments into the "hprc" track group refs #31561
• src/hg/makeDb/trackDb/human/hg38/trackDb.447way.ra
  • lines changed 39, context: html, text, full: html, text
    5917d23457a98ec2a907c4538dd64122ba05ccb0 Wed Aug 30 15:07:29 2023 -0700
    now with Primates subset calculation for phyloP refs #31528
• src/hg/makeDb/trackDb/human/hg38/trackDb.hprc90way.ra
  • lines changed 4, context: html, text, full: html, text
    d034e9b946b16c86295130008ec33d457ca45335 Tue Aug 29 13:08:03 2023 -0700
    collecting all the HPRC track experiments into the "hprc" track group refs #31561
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    5ed68f4dd6c6350f40db82794a334287e13d97fe Tue Aug 29 08:47:09 2023 -0700
    TrackDb updates for GENCODE V44 knownGene on hg38, refs #30840
  • lines changed 20, context: html, text, full: html, text
    d034e9b946b16c86295130008ec33d457ca45335 Tue Aug 29 13:08:03 2023 -0700
    collecting all the HPRC track experiments into the "hprc" track group refs #31561
  • lines changed 1, context: html, text, full: html, text
    ac37789fa393ebd3f10312e9cb69965dc756841e Tue Aug 29 14:16:07 2023 -0700
    adding HPRC VCF track refs #31561
  • lines changed 2, context: html, text, full: html, text
    a477fbe023c1cfdb0c00eb3381efdeb690bd75e9 Fri Sep 1 15:54:51 2023 -0700
    Staging new GENCODE Known Gene tracks for hg38 and mm39, refs #30840 #30841
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    3facd6d2cfe2e571d7c05c4e547ba3f9ed7b5a8e Tue Aug 29 07:42:37 2023 -0700
    changing hgmd labels refs #32001
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    a477fbe023c1cfdb0c00eb3381efdeb690bd75e9 Fri Sep 1 15:54:51 2023 -0700
    Staging new GENCODE Known Gene tracks for hg38 and mm39, refs #30840 #30841
• src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
  • lines changed 1, context: html, text, full: html, text
    a524fbce830be71b5889237f3e68766d33aea9ab Tue Aug 29 12:23:58 2023 -0700
    the CHM13 T2T Chain/Net track should be alpha only no redmine
  • lines changed 94, context: html, text, full: html, text
    5d9b2264aab7759c0f58dfaa3ec1523d295eb759 Wed Aug 30 10:42:32 2023 -0700
    fixup release tag issues with include statement to make the tdbQuery -check -release=public -strict "select count(*) from *" >/dev/null be silent no redmine
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    ea4fde5d4da8107799d542f3a1d7d95797de5097 Tue Aug 29 22:46:16 2023 -0700
    set release alpha for the crisprKmers experiment refs #32048
  • lines changed 2, context: html, text, full: html, text
    5d9b2264aab7759c0f58dfaa3ec1523d295eb759 Wed Aug 30 10:42:32 2023 -0700
    fixup release tag issues with include statement to make the tdbQuery -check -release=public -strict "select count(*) from *" >/dev/null be silent no redmine
• src/hg/utils/otto/knownGene/buildCore.sh
  • lines changed 10, context: html, text, full: html, text
    a3e12468afaf6ebf85e84e22f87123826b3d0289 Tue Aug 29 11:43:04 2023 -0700
    Make sure future knownGene builds update the search snippet indexes
• src/hg/utils/otto/knownGene/buildTo.sh
  • lines changed 6, context: html, text, full: html, text
    030eb76bec5c124428fd35626ea30609df945cbc Wed Aug 23 15:44:06 2023 -0700
    Slight name change to improve readability, no ticket
• src/utils/qa/hubCheckDraftEmails.py
  • lines changed 3, context: html, text, full: html, text
    5a72e57b4580dca3eb0e33214dceea71f8cb9eb7 Wed Aug 30 23:27:06 2023 -0700
    Correcting the file to be filtered_output.txt to get the errors and draft messages, refs #29319
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    57320fc37cb3b2e14b332f6687efd9b92fd59863 Mon Sep 4 10:05:13 2023 -0700
    v454 preview1

• lines changed: 1610
• files changed: 55