All File Changes

v448_preview to v448_preview2 (2023-05-01 to 2023-05-08) v448

• confs/asia.hg.conf
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    759a03dbb28ca4d6a73e0e5c1c250d9473e0f13f Sun May 7 01:11:21 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 6, context: html, text, full: html, text
    759a03dbb28ca4d6a73e0e5c1c250d9473e0f13f Sun May 7 01:11:21 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 3, context: html, text, full: html, text
    759a03dbb28ca4d6a73e0e5c1c250d9473e0f13f Sun May 7 01:11:21 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 2, context: html, text, full: html, text
    759a03dbb28ca4d6a73e0e5c1c250d9473e0f13f Sun May 7 01:11:21 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 6, context: html, text, full: html, text
    759a03dbb28ca4d6a73e0e5c1c250d9473e0f13f Sun May 7 01:11:21 2023 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 15, context: html, text, full: html, text
    4de18188ae5bb1336c3f49ad155358ee8f94db00 Wed May 3 10:20:58 2023 -0700
    adding new endpoint /list/files definitions and examples refs #23589
• src/hg/hubApi/list.c
  • lines changed 12, context: html, text, full: html, text
    c11b5a4152074f716254867f3de4fd020e602c26 Mon May 1 13:06:03 2023 -0700
    handling errors from failed rsync command refs #23589
  • lines changed 1, context: html, text, full: html, text
    dd5c3865981aea2bd1e395a18c38d75a6585b790 Wed May 3 10:15:26 2023 -0700
    eliminate extraneous trailing slash on the genArkUrl refs #23589
• src/hg/hubApi/tests/expected/err51.gz
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    d3e5b46dce2bbb50ec754d4c5ae8c20978fba191 Mon May 1 13:04:57 2023 -0700
    error tests for the /list/files/ function refs #23589
• src/hg/hubApi/tests/expected/err52.gz
  • lines changed 0, context: html, text, full: html, text
    d3e5b46dce2bbb50ec754d4c5ae8c20978fba191 Mon May 1 13:04:57 2023 -0700
    error tests for the /list/files/ function refs #23589
• src/hg/hubApi/tests/expected/err53.gz
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    d3e5b46dce2bbb50ec754d4c5ae8c20978fba191 Mon May 1 13:04:57 2023 -0700
    error tests for the /list/files/ function refs #23589
• src/hg/hubApi/tests/expected/list22.gz
  • lines changed 0, context: html, text, full: html, text
    156d4c6ffb3166b462f0780475c8d84dbf049213 Mon May 1 10:36:32 2023 -0700
    can not use dateTime in list files comparison that may change refs #23589
• src/hg/hubApi/tests/expected/list23.gz
  • lines changed 0, context: html, text, full: html, text
    156d4c6ffb3166b462f0780475c8d84dbf049213 Mon May 1 10:36:32 2023 -0700
    can not use dateTime in list files comparison that may change refs #23589
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    b46d0bfeffb4be0931fac5e5cfc4e4a5ac9253ad Wed May 3 10:19:59 2023 -0700
    eliminate extraneous trailing slash on the genArkUrl refs #23589
• src/hg/hubApi/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    156d4c6ffb3166b462f0780475c8d84dbf049213 Mon May 1 10:36:32 2023 -0700
    can not use dateTime in list files comparison that may change refs #23589
  • lines changed 23, context: html, text, full: html, text
    d3e5b46dce2bbb50ec754d4c5ae8c20978fba191 Mon May 1 13:04:57 2023 -0700
    error tests for the /list/files/ function refs #23589
• src/hg/js/hgGateway.js
  • lines changed 1, context: html, text, full: html, text
    6c35d93066d3052cc44a4bdda331b177d5536d55 Wed May 3 10:00:59 2023 -0700
    Missing one call to setTaxId() when explicitly adding 'org' to the species name lookup, refs #31230
• src/hg/js/hgSearch.js
  • lines changed 1, context: html, text, full: html, text
    c7e4ddd05cd273158892d2a778246910adb2bed2 Wed May 3 08:08:15 2023 -0700
    Fix unencoded user search strings being shown when a search term doesn't match anything, refs Galt email
• src/hg/lib/bigBedFind.c
  • lines changed 2, context: html, text, full: html, text
    8e9aacb756ee3723ad7210a3b078e1d15ffbb446 Tue May 2 15:15:56 2023 -0700
    Fix for hub tracks not being searchable for some assembly hubs, refs #31109
• src/hg/makeDb/doc/asmHubs/chromAuthority.pl
  • lines changed 2, context: html, text, full: html, text
    c06a002b9717812e29ce9d073643413e71f3fcf1 Wed May 3 23:10:40 2023 -0700
    correct buildDir and chromAlias locations refs #29545
• src/hg/makeDb/doc/asmHubs/commonHtml.pm
  • lines changed 8, context: html, text, full: html, text
    8ccd7b6237d9d6d6113a0c97087471874ccb0d8f Fri Apr 28 15:08:23 2023 -0700
    add the CCGP to the index listing table refs #30508
  • lines changed 15, context: html, text, full: html, text
    d80214c2c09b31f36020e9fd54e9c598c9496e4f Thu May 4 11:16:54 2023 -0700
    separate section in the bottom page index table to indicate subsets refs #29545
• src/hg/makeDb/doc/asmHubs/commonNames.pl
  • lines changed 36, context: html, text, full: html, text
    e2308c5c79c89d179d3b983f1413d52c4771f06c Wed May 3 23:11:44 2023 -0700
    improvements in haplotype detection nad some more generic categories recognized refs #29545
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    f3db002db8f34a63096bb10de1abd5486f0d1d3b Mon May 1 23:08:35 2023 -0700
    adding GCA_024217435.4_RoL_Ssco_1.2 per user request refs #29545
  • lines changed 57, context: html, text, full: html, text
    8477e5cb58b2aa75f71ab903f97638b7f9e5130e Wed May 3 12:41:20 2023 -0700
    adding 58 for an update refs #29545
  • lines changed 1, context: html, text, full: html, text
    9b03e9371988b026313c2b9eb5751dbf606b2a25 Thu May 4 10:41:54 2023 -0700
    one more for RefSeq update refs #29545
• src/hg/makeDb/doc/asmHubs/trackData.pl
  • lines changed 15, context: html, text, full: html, text
    13eb4b7b261fe9065ec6b1ff0f893148bd8ddb6b Wed May 3 23:09:36 2023 -0700
    allow ebiGene to become ensGene for HPRC assemblies refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    2f3415eee771eb334b13c7220fe7d23571e40b22 Wed May 3 17:08:08 2023 -0700
    catching up RefSeq assemblies refs #29545
  • lines changed 1, context: html, text, full: html, text
    da680e5e58b713188d24447cab8fad600f29ad12 Thu May 4 10:56:00 2023 -0700
    one more RefSeq for update refs #29545
• src/hg/makeDb/doc/ccgpAsmHub/ccgp.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    eaf1629823204ee851feaef01c34e14b8cc6b821 Thu May 4 13:40:40 2023 -0700
    coordinating common names refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    f3db002db8f34a63096bb10de1abd5486f0d1d3b Mon May 1 23:08:35 2023 -0700
    adding GCA_024217435.4_RoL_Ssco_1.2 per user request refs #29545
  • lines changed 17, context: html, text, full: html, text
    2f3415eee771eb334b13c7220fe7d23571e40b22 Wed May 3 17:08:08 2023 -0700
    catching up RefSeq assemblies refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 14, context: html, text, full: html, text
    2f3415eee771eb334b13c7220fe7d23571e40b22 Wed May 3 17:08:08 2023 -0700
    catching up RefSeq assemblies refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 20, context: html, text, full: html, text
    4ca55974c606b06a6126be29700027715435ae8d Wed May 3 23:07:36 2023 -0700
    update RefSeq assemblies moved some to legacy refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 23, context: html, text, full: html, text
    2f3415eee771eb334b13c7220fe7d23571e40b22 Wed May 3 17:08:08 2023 -0700
    catching up RefSeq assemblies refs #29545
  • lines changed 4, context: html, text, full: html, text
    eaf1629823204ee851feaef01c34e14b8cc6b821 Thu May 4 13:40:40 2023 -0700
    coordinating common names refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 19, context: html, text, full: html, text
    2f3415eee771eb334b13c7220fe7d23571e40b22 Wed May 3 17:08:08 2023 -0700
    catching up RefSeq assemblies refs #29545
  • lines changed 42, context: html, text, full: html, text
    eaf1629823204ee851feaef01c34e14b8cc6b821 Thu May 4 13:40:40 2023 -0700
    coordinating common names refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 8, context: html, text, full: html, text
    2f3415eee771eb334b13c7220fe7d23571e40b22 Wed May 3 17:08:08 2023 -0700
    catching up RefSeq assemblies refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 9, context: html, text, full: html, text
    2f3415eee771eb334b13c7220fe7d23571e40b22 Wed May 3 17:08:08 2023 -0700
    catching up RefSeq assemblies refs #29545
  • lines changed 6, context: html, text, full: html, text
    eaf1629823204ee851feaef01c34e14b8cc6b821 Thu May 4 13:40:40 2023 -0700
    coordinating common names refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    2f3415eee771eb334b13c7220fe7d23571e40b22 Wed May 3 17:08:08 2023 -0700
    catching up RefSeq assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    eaf1629823204ee851feaef01c34e14b8cc6b821 Thu May 4 13:40:40 2023 -0700
    coordinating common names refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
  • lines changed 22, context: html, text, full: html, text
    eaf1629823204ee851feaef01c34e14b8cc6b821 Thu May 4 13:40:40 2023 -0700
    coordinating common names refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    64bc32d8e4784ec95010301065cf0a6d8392b5e6 Thu May 4 12:23:03 2023 -0700
    catching up 11 assemblies for VGP refs #29545
  • lines changed 21, context: html, text, full: html, text
    eaf1629823204ee851feaef01c34e14b8cc6b821 Thu May 4 13:40:40 2023 -0700
    coordinating common names refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 10, context: html, text, full: html, text
    64bc32d8e4784ec95010301065cf0a6d8392b5e6 Thu May 4 12:23:03 2023 -0700
    catching up 11 assemblies for VGP refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.trio.orderList.tsv
  • lines changed 11, context: html, text, full: html, text
    eaf1629823204ee851feaef01c34e14b8cc6b821 Thu May 4 13:40:40 2023 -0700
    coordinating common names refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.userTracks.tsv
  • lines changed 1, context: html, text, full: html, text
    eaf1629823204ee851feaef01c34e14b8cc6b821 Thu May 4 13:40:40 2023 -0700
    coordinating common names refs #29545
• src/hg/makeDb/doc/zoonomiaAsmHub/zoonomia.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    eaf1629823204ee851feaef01c34e14b8cc6b821 Thu May 4 13:40:40 2023 -0700
    coordinating common names refs #29545
• src/hg/makeDb/trackDb/human/hg38/trackDb.100way.alpha.ra
  • lines changed 114, context: html, text, full: html, text
    c5637214da64886872d03842995a4434e4800e30 Wed May 3 17:18:05 2023 -0700
    Releasing first example of the logoMaf dynseq display, refs #31060
• src/hg/makeDb/trackDb/human/hg38/trackDb.100way.ra
  • lines changed 1, context: html, text, full: html, text
    c5637214da64886872d03842995a4434e4800e30 Wed May 3 17:18:05 2023 -0700
    Releasing first example of the logoMaf dynseq display, refs #31060
• src/hg/makeDb/trackDb/human/hg38/trackDb.470way.ra
  • lines changed 1, context: html, text, full: html, text
    24e301ca256e48991ebeddc95cedbb9a091ee45a Fri May 5 16:21:09 2023 -0700
    add logoMaf to 470 way
  • lines changed 1, context: html, text, full: html, text
    da3eef6dc271f7ac612636a897a88877625ad7cc Sat May 6 07:15:40 2023 -0700
    take out logoMaf from 470 way because it's not supported on bigMaf yet
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    4644723d445d0a43da37f68c2ca8e16408205567 Thu May 4 09:23:12 2023 -0700
    Releasing first example of the logoMaf dynseq display, refs #31060
• src/hg/makeDb/trackDb/refSeqComposite.html
  • lines changed 27, context: html, text, full: html, text
    9f975b6fc35649e71cfbf7c63bb8cd06c2244598 Tue May 2 02:59:23 2023 -0700
    adding more details to refseq docs page, and preparing the removal of the hg19-specific refseq docs page, refs #31118
• src/hg/makeDb/trackDb/relatedTracks.ra
  • lines changed 3, context: html, text, full: html, text
    9f975b6fc35649e71cfbf7c63bb8cd06c2244598 Tue May 2 02:59:23 2023 -0700
    adding more details to refseq docs page, and preparing the removal of the hg19-specific refseq docs page, refs #31118
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    fab43de5f919eb32e6a7e77bd41c257ff1a2fa0e Fri May 5 16:18:54 2023 -0700
    added bigWig to types for logoMaf
• src/hg/utils/automation/asmHubEbiGene.pl
  • lines changed 138, context: html, text, full: html, text
    f713fa48a499ca9d09a7b59e36e3c438b29216ed Tue May 2 13:32:07 2023 -0700
    update ebiGene for HPRC assemblies and now with html description page refs #30508
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 19, context: html, text, full: html, text
    f713fa48a499ca9d09a7b59e36e3c438b29216ed Tue May 2 13:32:07 2023 -0700
    update ebiGene for HPRC assemblies and now with html description page refs #30508
• src/hg/utils/overlapSelect/usage.txt
  • lines changed 1, context: html, text, full: html, text
    208487f343486678f30923d5cfea34b4ec34c366 Sun May 7 20:34:31 2023 -0700
    fixed typo in help message
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    a469da340198fe8022005d49330a35b7fe570c93 Mon May 8 10:04:58 2023 -0700
    v448 preview2, refs #31125

• lines changed: 800
• files changed: 62