All File Changes

v444_preview2 to v444_base (2023-02-13 to 2023-02-20) v444

• confs/hgwdev.hg.conf
  • lines changed 4, context: html, text, full: html, text
    36785d9bdc44b7593c2af05787abfced2815e424 Sun Feb 19 01:11:25 2023 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/cgilib/cartTrackDb.c
  • lines changed 44, context: html, text, full: html, text
    2770a53d1e8e0e5773020965d19c2499439481ca Tue Feb 7 13:33:08 2023 -0800
    Make hubApi return data from multiple tracks at once. Get trackDb tableBrowser setting working correctly in the api
• src/hg/hgTracks/chainTrack.c
  • lines changed 7, context: html, text, full: html, text
    047c85400af7d7ce10d040bd0dfce223d0054129 Thu Feb 16 14:52:37 2023 -0800
    fixup bigChain support to load the links at load time instead of draw time
• src/hg/hgTracks/extTools.c
  • lines changed 6, context: html, text, full: html, text
    98874f1656202cd5781466a5d9b25f47da1f104d Mon Feb 13 16:03:53 2023 -0800
    a bit closer to correct NCBI links, not perfect, but better than it was no redmine
• src/hg/hgTracks/hgTracks.c
  • lines changed 13, context: html, text, full: html, text
    9a1f31b4284285d135ddc7ccbf02e11e90983305 Tue Feb 14 13:41:44 2023 -0800
    make hgCustom do the same checks as hgTracks does for suitability for parallel loading.
  • lines changed 1, context: html, text, full: html, text
    cb2201abad0f29ab6eea3274738f71bcf70b7c22 Wed Feb 15 11:30:30 2023 -0800
    Only click one of the refresh buttons instead of all of them on 'r f' keyboard shortcut, refs #30589
  • lines changed 4, context: html, text, full: html, text
    b508259e8ce75a2aa1f919b8152befea99a2e1df Fri Jan 27 10:31:59 2023 -0800
    Prototype download track data button. An hg.conf controlled button that allows users to download all of the track data in the current window without leaving hgTracks, refs #30024
  • lines changed 10, context: html, text, full: html, text
    1d0753f141a617d2ce2b8167cee89bb8e3f2d5eb Fri Feb 17 10:28:14 2023 -0800
    fix problem with duplicating wig tracks
• src/hg/hgTracks/menu.c
  • lines changed 14, context: html, text, full: html, text
    98874f1656202cd5781466a5d9b25f47da1f104d Mon Feb 13 16:03:53 2023 -0800
    a bit closer to correct NCBI links, not perfect, but better than it was no redmine
• src/hg/hgTracks/wigTrack.c
  • lines changed 3, context: html, text, full: html, text
    dd1d497191bd730a2accfa06ec62b3fc0d276722 Tue Feb 14 13:59:23 2023 -0800
    sequence logo tracks should pay attention to change of viewing strand
• src/hg/hgc/hgc.c
  • lines changed 6, context: html, text, full: html, text
    fde4ec4b4860e59c9cc451241b1e584bc1e7cb85 Mon Feb 13 16:03:21 2023 -0800
    fix crash if bigPsl doesn't have sequence or "otherTwoBitUrl" in the track stanza
  • lines changed 1, context: html, text, full: html, text
    a9fde73d32daf74780765442de44324061b01d66 Sun Jan 22 22:13:52 2023 -0800
    Add URL resolver plugin functionality to allow an external program to convert cloud URLs (s3:, gs: drs:, or really any non-HTTP RUL) to http/https URLs. This can include signed URLs. The cloud URL is used to index the UDC cache rather than the resolved URL. This allows for re-resolving signed URLs if they time out. Joint work by Max and Markd
• src/hg/hgc/togaClick.c
  • lines changed 13, context: html, text, full: html, text
    34dc2bb14c176fb8f788df267fdb3fd4c8f461b4 Fri Feb 17 07:00:46 2023 -0800
    fix some encoding issues and an errant printf on the TOGO hgc page.
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 38, context: html, text, full: html, text
    a9fde73d32daf74780765442de44324061b01d66 Sun Jan 22 22:13:52 2023 -0800
    Add URL resolver plugin functionality to allow an external program to convert cloud URLs (s3:, gs: drs:, or really any non-HTTP RUL) to http/https URLs. This can include signed URLs. The cloud URL is used to index the UDC cache rather than the resolved URL. This allows for re-resolving signed URLs if they time out. Joint work by Max and Markd
• src/hg/hubApi/apiUtils.c
  • lines changed 39, context: html, text, full: html, text
    2770a53d1e8e0e5773020965d19c2499439481ca Tue Feb 7 13:33:08 2023 -0800
    Make hubApi return data from multiple tracks at once. Get trackDb tableBrowser setting working correctly in the api
• src/hg/hubApi/dataApi.h
  • lines changed 2, context: html, text, full: html, text
    2770a53d1e8e0e5773020965d19c2499439481ca Tue Feb 7 13:33:08 2023 -0800
    Make hubApi return data from multiple tracks at once. Get trackDb tableBrowser setting working correctly in the api
• src/hg/hubApi/getData.c
  • lines changed 21, context: html, text, full: html, text
    2770a53d1e8e0e5773020965d19c2499439481ca Tue Feb 7 13:33:08 2023 -0800
    Make hubApi return data from multiple tracks at once. Get trackDb tableBrowser setting working correctly in the api
  • lines changed 20, context: html, text, full: html, text
    b508259e8ce75a2aa1f919b8152befea99a2e1df Fri Jan 27 10:31:59 2023 -0800
    Prototype download track data button. An hg.conf controlled button that allows users to download all of the track data in the current window without leaving hgTracks, refs #30024
• src/hg/hubApi/hubApi.c
  • lines changed 14, context: html, text, full: html, text
    2770a53d1e8e0e5773020965d19c2499439481ca Tue Feb 7 13:33:08 2023 -0800
    Make hubApi return data from multiple tracks at once. Get trackDb tableBrowser setting working correctly in the api
• src/hg/hubApi/list.c
  • lines changed 9, context: html, text, full: html, text
    2770a53d1e8e0e5773020965d19c2499439481ca Tue Feb 7 13:33:08 2023 -0800
    Make hubApi return data from multiple tracks at once. Get trackDb tableBrowser setting working correctly in the api
• src/hg/inc/asmEquivalent.h
  • lines changed 3, context: html, text, full: html, text
    98874f1656202cd5781466a5d9b25f47da1f104d Mon Feb 13 16:03:53 2023 -0800
    a bit closer to correct NCBI links, not perfect, but better than it was no redmine
• src/hg/inc/cartTrackDb.h
  • lines changed 4, context: html, text, full: html, text
    2770a53d1e8e0e5773020965d19c2499439481ca Tue Feb 7 13:33:08 2023 -0800
    Make hubApi return data from multiple tracks at once. Get trackDb tableBrowser setting working correctly in the api
• src/hg/inc/chromAlias.h
  • lines changed 6, context: html, text, full: html, text
    98874f1656202cd5781466a5d9b25f47da1f104d Mon Feb 13 16:03:53 2023 -0800
    a bit closer to correct NCBI links, not perfect, but better than it was no redmine
• src/hg/inc/customFactory.h
  • lines changed 3, context: html, text, full: html, text
    9a1f31b4284285d135ddc7ccbf02e11e90983305 Tue Feb 14 13:41:44 2023 -0800
    make hgCustom do the same checks as hgTracks does for suitability for parallel loading.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    2d8ef74e61f892042592a21712bbebaf19edd385 Mon Feb 20 10:22:26 2023 -0800
    New version number v444
• src/hg/js/hgTracks.js
  • lines changed 218, context: html, text, full: html, text
    b508259e8ce75a2aa1f919b8152befea99a2e1df Fri Jan 27 10:31:59 2023 -0800
    Prototype download track data button. An hg.conf controlled button that allows users to download all of the track data in the current window without leaving hgTracks, refs #30024
  • lines changed 3, context: html, text, full: html, text
    077cbfb1d51137375853a1f850ed191f780e5c30 Thu Feb 16 16:20:49 2023 -0800
    Strip hub_id when making api requests for hub tracks/genomes, refs #30024
  • lines changed 54, context: html, text, full: html, text
    6973440613177762ca6434fa91d3d276b4190c01 Fri Feb 17 13:38:00 2023 -0800
    Woops need to build the list of downloadable tracks each time the button is clicked, not just the first time. Also ignore tracks with vis 0, refs #30024
• src/hg/js/utils.js
  • lines changed 1, context: html, text, full: html, text
    a9fde73d32daf74780765442de44324061b01d66 Sun Jan 22 22:13:52 2023 -0800
    Add URL resolver plugin functionality to allow an external program to convert cloud URLs (s3:, gs: drs:, or really any non-HTTP RUL) to http/https URLs. This can include signed URLs. The cloud URL is used to index the UDC cache rather than the resolved URL. This allows for re-resolving signed URLs if they time out. Joint work by Max and Markd
  • lines changed 20, context: html, text, full: html, text
    077cbfb1d51137375853a1f850ed191f780e5c30 Thu Feb 16 16:20:49 2023 -0800
    Strip hub_id when making api requests for hub tracks/genomes, refs #30024
• src/hg/lib/asmEquivalent.c
  • lines changed 10, context: html, text, full: html, text
    98874f1656202cd5781466a5d9b25f47da1f104d Mon Feb 13 16:03:53 2023 -0800
    a bit closer to correct NCBI links, not perfect, but better than it was no redmine
• src/hg/lib/chromAlias.c
  • lines changed 53, context: html, text, full: html, text
    98874f1656202cd5781466a5d9b25f47da1f104d Mon Feb 13 16:03:53 2023 -0800
    a bit closer to correct NCBI links, not perfect, but better than it was no redmine
• src/hg/lib/customFactory.c
  • lines changed 18, context: html, text, full: html, text
    9a1f31b4284285d135ddc7ccbf02e11e90983305 Tue Feb 14 13:41:44 2023 -0800
    make hgCustom do the same checks as hgTracks does for suitability for parallel loading.
  • lines changed 3, context: html, text, full: html, text
    9945a7e7ff9e10eaf995ac84bdbf68e5e3799476 Thu Feb 16 07:37:38 2023 -0800
    will I ever learn to check for NULL
• src/hg/lib/hdb.c
  • lines changed 3, context: html, text, full: html, text
    98874f1656202cd5781466a5d9b25f47da1f104d Mon Feb 13 16:03:53 2023 -0800
    a bit closer to correct NCBI links, not perfect, but better than it was no redmine
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    a9fde73d32daf74780765442de44324061b01d66 Sun Jan 22 22:13:52 2023 -0800
    Add URL resolver plugin functionality to allow an external program to convert cloud URLs (s3:, gs: drs:, or really any non-HTTP RUL) to http/https URLs. This can include signed URLs. The cloud URL is used to index the UDC cache rather than the resolved URL. This allows for re-resolving signed URLs if they time out. Joint work by Max and Markd
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 4, context: html, text, full: html, text
    404562a0949bf43b853017fa20a6fc70d22d4ccc Thu Feb 16 11:43:56 2023 -0800
    update to GenArk hubs per user requests refs #29545
• src/hg/makeDb/doc/asmHubs/commonNames.pl
  • lines changed 14, context: html, text, full: html, text
    404562a0949bf43b853017fa20a6fc70d22d4ccc Thu Feb 16 11:43:56 2023 -0800
    update to GenArk hubs per user requests refs #29545
  • lines changed 21, context: html, text, full: html, text
    1a2aa31bfa14f809ee4093cea7b436e331b86ff4 Thu Feb 16 14:56:34 2023 -0800
    improved common names for fungi and bacteria an lower limits for valid number of tracks in bacteria and plants refs #29545
  • lines changed 23, context: html, text, full: html, text
    06b372f6628c2c35eebb105d5f5d6262b23e6d5c Sun Feb 19 15:36:21 2023 -0800
    some improvements after running through every single RefSeq assembly no redmine
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 197, context: html, text, full: html, text
    bfb9aa1b3a8a17c3100f6e7570bb55dd4b00d46c Tue Feb 14 08:18:45 2023 -0800
    checking in crispor update no redmine
  • lines changed 85, context: html, text, full: html, text
    8568eb14b474e031f19a108acf516646fa05ba0d Wed Feb 15 10:10:52 2023 -0800
    eliminate a bunch of duplicates that were mistakenly checked in no redmine
  • lines changed 11, context: html, text, full: html, text
    3cdd218974321e097486b7ac68e147e9785612b2 Wed Feb 15 10:16:38 2023 -0800
    something broke down with the clade classification system fixed bogus duplicate entries no redmine
  • lines changed 1, context: html, text, full: html, text
    a9e5c878cb63422a19c9ad6564d1588c5df10c9f Wed Feb 15 16:56:29 2023 -0800
    adding a nematode per user request refs #29545
• src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
  • lines changed 11, context: html, text, full: html, text
    404562a0949bf43b853017fa20a6fc70d22d4ccc Thu Feb 16 11:43:56 2023 -0800
    update to GenArk hubs per user requests refs #29545
• src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
  • lines changed 2, context: html, text, full: html, text
    1a2aa31bfa14f809ee4093cea7b436e331b86ff4 Thu Feb 16 14:56:34 2023 -0800
    improved common names for fungi and bacteria an lower limits for valid number of tracks in bacteria and plants refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 31, context: html, text, full: html, text
    58839314d83dd1b8a70c0d41969e9e9eb67dc53b Thu Feb 16 14:54:38 2023 -0800
    adding bacteria sequences per user request refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    8a972a814894c3c825fd8d7c4019d288dda40d32 Fri Feb 17 12:13:44 2023 -0800
    catching up to CCGP list of genomes no redmine
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 40, context: html, text, full: html, text
    404562a0949bf43b853017fa20a6fc70d22d4ccc Thu Feb 16 11:43:56 2023 -0800
    update to GenArk hubs per user requests refs #29545
• src/hg/makeDb/doc/hg19.gencode.txt
  • lines changed 33, context: html, text, full: html, text
    f3e62b71a2cc47befbcd5308b6e1989d4df60f34 Wed Feb 15 10:38:59 2023 -0800
    import of GENCODE V43lift38
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 4, context: html, text, full: html, text
    745fa18179254a7298615ae2b6e1a30a596cbe5f Mon Feb 13 14:22:48 2023 -0800
    import of GENCODE Versions V43 release
  • lines changed 5, context: html, text, full: html, text
    3c73a97372107c7ad967e3f446673bf1cf5ebe42 Mon Feb 13 18:05:17 2023 -0800
    update release notes on GENCODE V43 and remove alpha tag
• src/hg/makeDb/doc/hg38/tabulaSapiens.txt
  • lines changed 42, context: html, text, full: html, text
    b1c4de4679118861216d329d842b6ed33bcccd78 Fri Feb 17 16:20:15 2023 -0800
    started tabula-sapiens intron called, but stuck on help from CZI
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    23d4ca1bff614e40ff402f54fca6771bddcfc351 Wed Feb 15 17:00:47 2023 -0800
    adding a nematode O.tipulae CEW1 2020 per user request refs #29545
  • lines changed 23, context: html, text, full: html, text
    404562a0949bf43b853017fa20a6fc70d22d4ccc Thu Feb 16 11:43:56 2023 -0800
    update to GenArk hubs per user requests refs #29545
  • lines changed 3, context: html, text, full: html, text
    2e620bc3f85609612abd64cf5ef4cb8edd3e3dbf Fri Feb 17 12:13:28 2023 -0800
    catching up to CCGP list of genomes no redmine
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 15, context: html, text, full: html, text
    404562a0949bf43b853017fa20a6fc70d22d4ccc Thu Feb 16 11:43:56 2023 -0800
    update to GenArk hubs per user requests refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 16, context: html, text, full: html, text
    404562a0949bf43b853017fa20a6fc70d22d4ccc Thu Feb 16 11:43:56 2023 -0800
    update to GenArk hubs per user requests refs #29545
  • lines changed 1, context: html, text, full: html, text
    4865125e312f383396ea8d7080dbd1fefdcf6f9e Fri Feb 17 13:00:56 2023 -0800
    catch up an older version of the porpoise which is in CCGP no redmine
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    404562a0949bf43b853017fa20a6fc70d22d4ccc Thu Feb 16 11:43:56 2023 -0800
    update to GenArk hubs per user requests refs #29545
  • lines changed 2, context: html, text, full: html, text
    e710ecdfe8a38cd878fbb93b4b53df847c0d168b Fri Feb 17 12:11:44 2023 -0800
    catching up to CCGP list of genomes no redmine
  • lines changed 1, context: html, text, full: html, text
    c7d20855bc1689ff0d6f85d113c2e735d4f5329c Fri Feb 17 13:00:13 2023 -0800
    clarify versions of the Yangtze porpoise no redmine
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 6, context: html, text, full: html, text
    831e4469f7332b20ec3f6aa30fa6d5884bb5ff89 Mon Feb 13 19:03:31 2023 -0800
    import of GENCODE VM32
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 35, context: html, text, full: html, text
    404562a0949bf43b853017fa20a6fc70d22d4ccc Thu Feb 16 11:43:56 2023 -0800
    update to GenArk hubs per user requests refs #29545
  • lines changed 2, context: html, text, full: html, text
    403c5b11948650301cfd70fbaa521c08c3723169 Fri Feb 17 11:48:49 2023 -0800
    catch up to CCGP assemblies no redmine
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    830d7ce0370d22ff771e703d3ea2d2c4680b20cd Tue Feb 14 08:30:28 2023 -0800
    adding Asian tiger no redmine
  • lines changed 1, context: html, text, full: html, text
    85ea918488f0ea187d32633718810982b91ece09 Tue Feb 14 09:08:58 2023 -0800
    mosquito is not a primate no redmine
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    aff749c5723ebbde6bb1fa33546c06fae1dec455 Fri Feb 17 12:19:20 2023 -0800
    catching up to CCGP list of genomes no redmine
• src/hg/makeDb/doc/vicPac2.txt
  • lines changed 111, context: html, text, full: html, text
    9ea6efeaf7d92fa6d49865aa8f2bcfa3e72272a9 Mon Feb 13 10:57:42 2023 -0800
    document the chromAlias construction for both chromAlias table and download files no redmine
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    b7dd2ec4d968aa3adb8dc2abf8e50e1b4d1e5b32 Wed Feb 15 14:28:25 2023 -0800
    updating to add 3 viral sequences refs #29545
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 4, context: html, text, full: html, text
    745fa18179254a7298615ae2b6e1a30a596cbe5f Mon Feb 13 14:22:48 2023 -0800
    import of GENCODE Versions V43 release
  • lines changed 2, context: html, text, full: html, text
    831e4469f7332b20ec3f6aa30fa6d5884bb5ff89 Mon Feb 13 19:03:31 2023 -0800
    import of GENCODE VM32
  • lines changed 2, context: html, text, full: html, text
    f3e62b71a2cc47befbcd5308b6e1989d4df60f34 Wed Feb 15 10:38:59 2023 -0800
    import of GENCODE V43lift38
• src/hg/makeDb/schema/all.joiner
  • lines changed 89, context: html, text, full: html, text
    f3e62b71a2cc47befbcd5308b6e1989d4df60f34 Wed Feb 15 10:38:59 2023 -0800
    import of GENCODE V43lift38
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    f3e62b71a2cc47befbcd5308b6e1989d4df60f34 Wed Feb 15 10:38:59 2023 -0800
    import of GENCODE V43lift38
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    f3e62b71a2cc47befbcd5308b6e1989d4df60f34 Wed Feb 15 10:38:59 2023 -0800
    import of GENCODE V43lift38
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV43lift37.html
  • lines changed 32, context: html, text, full: html, text
    f3e62b71a2cc47befbcd5308b6e1989d4df60f34 Wed Feb 15 10:38:59 2023 -0800
    import of GENCODE V43lift38
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV43lift37.ra
  • lines changed 210, context: html, text, full: html, text
    f3e62b71a2cc47befbcd5308b6e1989d4df60f34 Wed Feb 15 10:38:59 2023 -0800
    import of GENCODE V43lift38
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    3c73a97372107c7ad967e3f446673bf1cf5ebe42 Mon Feb 13 18:05:17 2023 -0800
    update release notes on GENCODE V43 and remove alpha tag
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    3c73a97372107c7ad967e3f446673bf1cf5ebe42 Mon Feb 13 18:05:17 2023 -0800
    update release notes on GENCODE V43 and remove alpha tag
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV43.html
  • lines changed 1, context: html, text, full: html, text
    745fa18179254a7298615ae2b6e1a30a596cbe5f Mon Feb 13 14:22:48 2023 -0800
    import of GENCODE Versions V43 release
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    2770a53d1e8e0e5773020965d19c2499439481ca Tue Feb 7 13:33:08 2023 -0800
    Make hubApi return data from multiple tracks at once. Get trackDb tableBrowser setting working correctly in the api
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    831e4469f7332b20ec3f6aa30fa6d5884bb5ff89 Mon Feb 13 19:03:31 2023 -0800
    import of GENCODE VM32
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    831e4469f7332b20ec3f6aa30fa6d5884bb5ff89 Mon Feb 13 19:03:31 2023 -0800
    import of GENCODE VM32
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM32.html
  • lines changed 1, context: html, text, full: html, text
    831e4469f7332b20ec3f6aa30fa6d5884bb5ff89 Mon Feb 13 19:03:31 2023 -0800
    import of GENCODE VM32
• src/hg/utils/automation/aliasTabToText.pl
  • lines changed 69, context: html, text, full: html, text
    b7d1b1b10c2fa9a037b3104bb2540e02da60e3ec Mon Feb 13 10:39:47 2023 -0800
    replace the obsolete chromAliasToTxt.pl with the aliasTabToText.pl equivalent no redmine
• src/hg/utils/automation/chromAliasToTxt.pl
  • lines changed 5, context: html, text, full: html, text
    b7d1b1b10c2fa9a037b3104bb2540e02da60e3ec Mon Feb 13 10:39:47 2023 -0800
    replace the obsolete chromAliasToTxt.pl with the aliasTabToText.pl equivalent no redmine
• src/hg/utils/hubCrawl/hubCrawl.c
  • lines changed 2, context: html, text, full: html, text
    a9fde73d32daf74780765442de44324061b01d66 Sun Jan 22 22:13:52 2023 -0800
    Add URL resolver plugin functionality to allow an external program to convert cloud URLs (s3:, gs: drs:, or really any non-HTTP RUL) to http/https URLs. This can include signed URLs. The cloud URL is used to index the UDC cache rather than the resolved URL. This allows for re-resolving signed URLs if they time out. Joint work by Max and Markd
• src/hg/utils/otto/otto.crontab
  • lines changed 1, context: html, text, full: html, text
    ec301d2ed3e444a70ac83f03586daf2db375288d Wed Feb 15 10:07:50 2023 -0800
    change grcIncident to 6 AM instead of 9 AM to avoid mysterious interference no redmine
• src/htslib/hfile_net.c
  • lines changed 1, context: html, text, full: html, text
    a9fde73d32daf74780765442de44324061b01d66 Sun Jan 22 22:13:52 2023 -0800
    Add URL resolver plugin functionality to allow an external program to convert cloud URLs (s3:, gs: drs:, or really any non-HTTP RUL) to http/https URLs. This can include signed URLs. The cloud URL is used to index the UDC cache rather than the resolved URL. This allows for re-resolving signed URLs if they time out. Joint work by Max and Markd
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    2d8ef74e61f892042592a21712bbebaf19edd385 Mon Feb 20 10:22:26 2023 -0800
    New version number v444
• src/inc/udc.h
  • lines changed 12, context: html, text, full: html, text
    a9fde73d32daf74780765442de44324061b01d66 Sun Jan 22 22:13:52 2023 -0800
    Add URL resolver plugin functionality to allow an external program to convert cloud URLs (s3:, gs: drs:, or really any non-HTTP RUL) to http/https URLs. This can include signed URLs. The cloud URL is used to index the UDC cache rather than the resolved URL. This allows for re-resolving signed URLs if they time out. Joint work by Max and Markd
• src/lib/udc.c
  • lines changed 101, context: html, text, full: html, text
    a9fde73d32daf74780765442de44324061b01d66 Sun Jan 22 22:13:52 2023 -0800
    Add URL resolver plugin functionality to allow an external program to convert cloud URLs (s3:, gs: drs:, or really any non-HTTP RUL) to http/https URLs. This can include signed URLs. The cloud URL is used to index the UDC cache rather than the resolved URL. This allows for re-resolving signed URLs if they time out. Joint work by Max and Markd
• src/product/ex.hg.conf
  • lines changed 3, context: html, text, full: html, text
    a9fde73d32daf74780765442de44324061b01d66 Sun Jan 22 22:13:52 2023 -0800
    Add URL resolver plugin functionality to allow an external program to convert cloud URLs (s3:, gs: drs:, or really any non-HTTP RUL) to http/https URLs. This can include signed URLs. The cloud URL is used to index the UDC cache rather than the resolved URL. This allows for re-resolving signed URLs if they time out. Joint work by Max and Markd
• src/product/mirrorManual.txt
  • lines changed 26, context: html, text, full: html, text
    a9fde73d32daf74780765442de44324061b01d66 Sun Jan 22 22:13:52 2023 -0800
    Add URL resolver plugin functionality to allow an external program to convert cloud URLs (s3:, gs: drs:, or really any non-HTTP RUL) to http/https URLs. This can include signed URLs. The cloud URL is used to index the UDC cache rather than the resolved URL. This allows for re-resolving signed URLs if they time out. Joint work by Max and Markd
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    0a3ac3842b54279287876612b0a623ebd3963702 Mon Feb 20 10:19:57 2023 -0800
    v444 final build, refs #30618

• lines changed: 2002
• files changed: 96