All File Changes

v459_base to v460_preview (2021-01-08 to 2024-01-16) v460

• src/hg/hgTracks/bigBedTrack.c
  • lines changed 23, context: html, text, full: html, text
    cd40e92bef563b1581ea25e4842c884bf5b32efd Mon Jan 15 13:18:03 2024 -0800
    limit maxItems to maxItemsPerRow (1,000). Use one million for the number of items to request from a bigBed file
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    ff3b8b2efad6fb2e1eff9a16da239e079d584139 Thu Jan 11 08:37:43 2024 -0800
    tiny change to coverage mode message, refs #29715
  • lines changed 2, context: html, text, full: html, text
    beb30e4b9bc452fd4e0242c24408002958c7ca27 Tue Jan 16 07:42:10 2024 -0800
    not showing filter message if nothing is filtered. FOund by image comparator. email from Lou
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    f63a7870053591e873ee5492217294d82edd88f8 Sun Jan 14 15:13:25 2024 -0800
    when a track overflows and it's a track that can do density coverage we go straight into density coverage mode instead of reducing visibility
• src/hg/hgTracks/simpleTracks.c
  • lines changed 26, context: html, text, full: html, text
    f63a7870053591e873ee5492217294d82edd88f8 Sun Jan 14 15:13:25 2024 -0800
    when a track overflows and it's a track that can do density coverage we go straight into density coverage mode instead of reducing visibility
  • lines changed 6, context: html, text, full: html, text
    cd40e92bef563b1581ea25e4842c884bf5b32efd Mon Jan 15 13:18:03 2024 -0800
    limit maxItems to maxItemsPerRow (1,000). Use one million for the number of items to request from a bigBed file
• src/hg/hgTracks/vcfTrack.c
  • lines changed 16, context: html, text, full: html, text
    0525b1b26752ba51653ce488a3d141ccf3eee4aa Mon Jan 15 03:24:50 2024 -0800
    adding note to VCF track if filtering or wiggling. Had to restructure filterRecords() a little to get rid of the early return, as otherwise labelTrackAsFilteredNumber() would not have been called if there are no filters but the track is in coverage mode. This seemed like the most minimal change, refs #32864
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    87cd07552199ab0b3ced24264d4cd30ba6051b44 Thu Jan 11 08:50:36 2024 -0800
    adding spider trap link to noPage.html, email from Hiram
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 11, context: html, text, full: html, text
    f4a85a56c3e94484c7ef6c87c89694a2813cd533 Wed Jan 10 15:00:49 2024 -0800
    Adding latest NAR publication to pubs page, no RM.
• src/hg/htdocs/staff.html
  • lines changed 5, context: html, text, full: html, text
    2014839a5bb592e948aa1fa604e41f48ca7a39fe Wed Jan 10 15:06:12 2024 -0800
    Moving Rachel down to the project alumni section, we wish her the best
  • lines changed 6, context: html, text, full: html, text
    0e5702738ac76628f9b2446ad9859abf217a9dd1 Wed Jan 10 15:21:03 2024 -0800
    Moving Jim down to alumni, changing Max to PI, and updating Anna's current role in the team.
• src/hg/js/autocomplete.js
  • lines changed 42, context: html, text, full: html, text
    14dbfe57d9b670fa554c64cd4604e37fdefe037d Fri Jan 5 15:33:17 2024 -0800
    Working version of saving last five user entered terms in the search bar, refs #29611
• src/hg/js/autocompleteCat.js
  • lines changed 33, context: html, text, full: html, text
    14dbfe57d9b670fa554c64cd4604e37fdefe037d Fri Jan 5 15:33:17 2024 -0800
    Working version of saving last five user entered terms in the search bar, refs #29611
• src/hg/js/hgGateway.js
  • lines changed 27, context: html, text, full: html, text
    14dbfe57d9b670fa554c64cd4604e37fdefe037d Fri Jan 5 15:33:17 2024 -0800
    Working version of saving last five user entered terms in the search bar, refs #29611
• src/hg/js/hgSearch.js
  • lines changed 83, context: html, text, full: html, text
    14dbfe57d9b670fa554c64cd4604e37fdefe037d Fri Jan 5 15:33:17 2024 -0800
    Working version of saving last five user entered terms in the search bar, refs #29611
• src/hg/js/hgTracks.js
  • lines changed 3, context: html, text, full: html, text
    921fc5c2ede5f5360aa61b3bc2b7d894c46bfff7 Mon Jan 8 15:06:05 2024 -0800
    when checking to see if tracks have changed their visibility, use limitedVis if set since visibility is not always set if limitedVis is set
  • lines changed 5, context: html, text, full: html, text
    6201cd68e13da77d359284cd7a00cec0c7662e43 Thu Jan 11 14:29:02 2024 -0800
    Make the tutorial warning go away if it has been viewed more than 5 times without being explicitly closed, refs Max meeting
  • lines changed 12, context: html, text, full: html, text
    14dbfe57d9b670fa554c64cd4604e37fdefe037d Fri Jan 5 15:33:17 2024 -0800
    Working version of saving last five user entered terms in the search bar, refs #29611
• src/hg/js/utils.js
  • lines changed 65, context: html, text, full: html, text
    14dbfe57d9b670fa554c64cd4604e37fdefe037d Fri Jan 5 15:33:17 2024 -0800
    Working version of saving last five user entered terms in the search bar, refs #29611
• src/hg/lib/cart.c
  • lines changed 16, context: html, text, full: html, text
    0e001cd4379962ce9af6daa4a6ea710c85bc21c6 Mon Jan 15 07:25:19 2024 -0800
    accept verbose=x on any CGI URL so we can see what UDC is doing, email with Brian/Mark
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 4, context: html, text, full: html, text
    8ea4174323f155bf7c9e13c5f9be3ae420c012a6 Tue Jan 9 09:04:08 2024 -0800
    VGP catchup refs #29545
  • lines changed 1, context: html, text, full: html, text
    be78a31ff622d9512bc04d9383ce387590882668 Sat Jan 13 13:44:12 2024 -0800
    VGP catch up GCA_028885525.1_NHGRI_mPonPyg2-v1.1-hic.freeze_alt refs #29545
  • lines changed 1, context: html, text, full: html, text
    73ea4a7f6eb165b33e5e9c2798e7becfc2b27bf3 Mon Jan 15 10:20:51 2024 -0800
    adding one for VGP GCA_028858805.1_NHGRI_mPanTro3-v1.1-hic.freeze_alt refs #29545
• src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
  • lines changed 3, context: html, text, full: html, text
    a92158f4897218611c25b8469aadf0d4b673a27b Wed Jan 10 08:35:56 2024 -0800
    correctly copy to dynamic blat server avoiding the repeatModeler 2bit file refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    adeb22d84890dc801dfc8e7db14036feefb8b814 Mon Jan 8 21:22:57 2024 -0800
    VGP update adding 3 refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    adeb22d84890dc801dfc8e7db14036feefb8b814 Mon Jan 8 21:22:57 2024 -0800
    VGP update adding 3 refs #29545
  • lines changed 3, context: html, text, full: html, text
    8ea4174323f155bf7c9e13c5f9be3ae420c012a6 Tue Jan 9 09:04:08 2024 -0800
    VGP catchup refs #29545
• src/hg/makeDb/doc/hg19.gencode.txt
  • lines changed 40, context: html, text, full: html, text
    1de6d513b0f0fdd55dee82f8f4dd2cd14bfb349f Thu Jan 11 19:13:08 2024 -0800
    import of gencode 45lift37
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 39, context: html, text, full: html, text
    6a6754a685a2f4019603be08ba8b8bda14c449b1 Thu Jan 11 15:53:28 2024 -0800
    import of gencode V45
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 37, context: html, text, full: html, text
    d19ef54d64fd2e113d0636b1633214ddfb837856 Thu Jan 11 17:54:48 2024 -0800
    GENCODE VM34 import
• src/hg/makeDb/doc/mm39/lastzRuns.txt
  • lines changed 80, context: html, text, full: html, text
    82a6cccdf25e3e8298cab9f78e24c9e167e3fa96 Thu Jan 11 09:44:28 2024 -0800
    mm39 to GCF_019923935.1 water buffalo lastz/chain/net complete refs #32804
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    be78a31ff622d9512bc04d9383ce387590882668 Sat Jan 13 13:44:12 2024 -0800
    VGP catch up GCA_028885525.1_NHGRI_mPonPyg2-v1.1-hic.freeze_alt refs #29545
  • lines changed 1, context: html, text, full: html, text
    73ea4a7f6eb165b33e5e9c2798e7becfc2b27bf3 Mon Jan 15 10:20:51 2024 -0800
    adding one for VGP GCA_028858805.1_NHGRI_mPanTro3-v1.1-hic.freeze_alt refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    adeb22d84890dc801dfc8e7db14036feefb8b814 Mon Jan 8 21:22:57 2024 -0800
    VGP update adding 3 refs #29545
  • lines changed 1, context: html, text, full: html, text
    b630b6031fa0a9718e8f6b2e8e9f0cff93f9ec10 Tue Jan 9 22:29:43 2024 -0800
    adding GCA_026652325.1_ASM2665232v1 Iberian ribbed newt (20211129_DDA 2022) after much trauma large genome refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    18ba3d5532d8357b9d568a5f1280e0bf3e25967d Tue Jan 9 10:04:44 2024 -0800
    catching up VGP primary list with GenArk refs #29545
  • lines changed 1, context: html, text, full: html, text
    b0f1f612cdd0054b1061ea69ffcbe18e8fb07fc3 Tue Jan 9 11:41:15 2024 -0800
    fOsmEpe2.1 ready to go refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 9, context: html, text, full: html, text
    18ba3d5532d8357b9d568a5f1280e0bf3e25967d Tue Jan 9 10:04:44 2024 -0800
    catching up VGP primary list with GenArk refs #29545
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 4, context: html, text, full: html, text
    6a6754a685a2f4019603be08ba8b8bda14c449b1 Thu Jan 11 15:53:28 2024 -0800
    import of gencode V45
  • lines changed 2, context: html, text, full: html, text
    d19ef54d64fd2e113d0636b1633214ddfb837856 Thu Jan 11 17:54:48 2024 -0800
    GENCODE VM34 import
  • lines changed 2, context: html, text, full: html, text
    1de6d513b0f0fdd55dee82f8f4dd2cd14bfb349f Thu Jan 11 19:13:08 2024 -0800
    import of gencode 45lift37
• src/hg/makeDb/trackDb/human/clinvar.alpha.ra
  • lines changed 9, context: html, text, full: html, text
    16f9dcdc9a1ed10c08aae7908039627e194488a6 Fri Jan 12 01:00:29 2024 -0800
    trying a new thing: making clinvar ALPHA track appear on hgwdev and also the public release track, at the same time. Also activating version.txt now that the file has made it to the RR through the autopusher change and autopusher update, emails with QA and cluster-admin
• src/hg/makeDb/trackDb/human/clinvar.ra
  • lines changed 1, context: html, text, full: html, text
    16f9dcdc9a1ed10c08aae7908039627e194488a6 Fri Jan 12 01:00:29 2024 -0800
    trying a new thing: making clinvar ALPHA track appear on hgwdev and also the public release track, at the same time. Also activating version.txt now that the file has made it to the RR through the autopusher change and autopusher update, emails with QA and cluster-admin
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV45lift37.html
  • lines changed 1, context: html, text, full: html, text
    1de6d513b0f0fdd55dee82f8f4dd2cd14bfb349f Thu Jan 11 19:13:08 2024 -0800
    import of gencode 45lift37
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 1, context: html, text, full: html, text
    3b3c5e78f213a20555d66f2ecfb8e51d0eb67703 Mon Jan 8 16:16:44 2024 -0800
    CHanging max draw to coverage so the track stays in dense, and reducing it for lag purposes. Refs Max.
  • lines changed 7, context: html, text, full: html, text
    c983960d33d62bd83f2e3a8990186b4f0f013f23 Mon Jan 15 02:59:16 2024 -0800
    working around VCF speed issue and gnomad4 size by using maxWindowToDraw, refs #32862
• src/hg/makeDb/trackDb/human/hg38/hprcVCF.html
  • lines changed 1, context: html, text, full: html, text
    6f1280bc6d660677550ae0d2a0819442ff88de29 Mon Jan 8 15:24:23 2024 -0800
    Changing text from composite container track to superTrack for the html page, refs #32288
  • lines changed 0, context: html, text, full: html, text
    871d4d58af245d43d0025b72e5b34466544cad35 Fri Jan 12 09:57:11 2024 -0800
    Fixing base pairs typo for the description page, refs #32288
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    6d136693b505cffa77f5ec3862efc55023b67707 Mon Jan 8 15:30:04 2024 -0800
    Releasing the HPRC Short Variants track to the RR, refs #32288
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    6a6754a685a2f4019603be08ba8b8bda14c449b1 Thu Jan 11 15:53:28 2024 -0800
    import of gencode V45
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV45.html
  • lines changed 1, context: html, text, full: html, text
    6a6754a685a2f4019603be08ba8b8bda14c449b1 Thu Jan 11 15:53:28 2024 -0800
    import of gencode V45
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    16f9dcdc9a1ed10c08aae7908039627e194488a6 Fri Jan 12 01:00:29 2024 -0800
    trying a new thing: making clinvar ALPHA track appear on hgwdev and also the public release track, at the same time. Also activating version.txt now that the file has made it to the RR through the autopusher change and autopusher update, emails with QA and cluster-admin
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    24488b899abf5b2eb0caa6c960a6c12ab3ba887f Thu Jan 11 19:05:54 2024 -0800
    forgot to update gencode super track release description
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM34.html
  • lines changed 1, context: html, text, full: html, text
    d19ef54d64fd2e113d0636b1633214ddfb837856 Thu Jan 11 17:54:48 2024 -0800
    GENCODE VM34 import
• src/hg/utils/automation/asmHubRmodelJoinAlign.pl
  • lines changed 338, context: html, text, full: html, text
    77a819d426026e8a6ac3d7965af8f44fbb9a0272 Wed Jan 10 12:42:07 2024 -0800
    better manage large genome construction and add in RepeatModeler track refs #29545
• src/hg/utils/automation/asmHubRmskJoinAlign.pl
  • lines changed 17, context: html, text, full: html, text
    77a819d426026e8a6ac3d7965af8f44fbb9a0272 Wed Jan 10 12:42:07 2024 -0800
    better manage large genome construction and add in RepeatModeler track refs #29545
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 79, context: html, text, full: html, text
    77a819d426026e8a6ac3d7965af8f44fbb9a0272 Wed Jan 10 12:42:07 2024 -0800
    better manage large genome construction and add in RepeatModeler track refs #29545
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 25, context: html, text, full: html, text
    77a819d426026e8a6ac3d7965af8f44fbb9a0272 Wed Jan 10 12:42:07 2024 -0800
    better manage large genome construction and add in RepeatModeler track refs #29545
• src/hg/utils/automation/doCpgIslands.pl
  • lines changed 105, context: html, text, full: html, text
    901ed01df267d53d48309161193d3791bbc5d780 Wed Jan 10 12:40:18 2024 -0800
    alternate split procedure for large genomes in CpG Island track construction refs #29545
• src/product/installer/browserSetup.sh
  • lines changed 1, context: html, text, full: html, text
    c1baf8f9ea237f80359fff57e69c15fd1c2e77ab Tue Jan 9 10:05:43 2024 -0800
    if apache is already installed, make sure that chkconfig is installed, email from Jorge
  • lines changed 2, context: html, text, full: html, text
    eabfddf59feb8e088b8d90e1ba9fe34be4b27e49 Tue Jan 9 13:20:24 2024 -0800
    gbic error message docs, email from Jorge
• src/utils/qa/hubPublicMail
  • lines changed 2, context: html, text, full: html, text
    cfa95f7dc97a3aeb09d609892fcf4c3081be0712 Thu Jan 11 09:14:31 2024 -0800
    Changing the address from genome-www to reduce spam and sending it to the browserqa cron ML instead, refs Max.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    181c59d96faeb1125bbc35300b7e0bfd60d0ef68 Tue Jan 16 14:43:44 2024 -0800
    v460 preview1, refs #32805

• lines changed: 1227
• files changed: 63