All File Changes

v452_base to v453_preview (2023-08-07 to 2023-08-13) v453

• src/hg/hgPcr/hgPcr.c
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    c26640b68ba8ad219e7d79c3f8251ea20f9f57e0 Fri Aug 11 16:48:41 2023 -0700
    Fix dead url to primer3. refs #31950.
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 27, context: html, text, full: html, text
    13b584581e6d7b1860e0cab97adc3594b1899308 Mon Aug 7 12:05:10 2023 -0700
    add instaPort to bigBed support
• src/hg/hgTracks/simpleTracks.c
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    13b584581e6d7b1860e0cab97adc3594b1899308 Mon Aug 7 12:05:10 2023 -0700
    add instaPort to bigBed support
• src/hg/hgc/bigBedClick.c
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    13b584581e6d7b1860e0cab97adc3594b1899308 Mon Aug 7 12:05:10 2023 -0700
    add instaPort to bigBed support
• src/hg/htdocs/images/phylo/hg38_477way.png
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    a4ef39a41aa0b1ca27fca9bcc4fd10c89e188640 Mon Aug 7 15:59:57 2023 -0700
    adding phylo tree sample for Cactus 477-way track refs #31528
• src/hg/inc/bed.h
  • lines changed 3, context: html, text, full: html, text
    13b584581e6d7b1860e0cab97adc3594b1899308 Mon Aug 7 12:05:10 2023 -0700
    add instaPort to bigBed support
• src/hg/inc/genePred.h
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    13b584581e6d7b1860e0cab97adc3594b1899308 Mon Aug 7 12:05:10 2023 -0700
    add instaPort to bigBed support
• src/hg/inc/instaPort.h
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    08b22891ddc65ed6275151a0ff4b07ac4a8cb1b0 Wed Aug 9 09:25:02 2023 -0700
    oops. need instaPort.h !
• src/hg/inc/liftOver.h
  • lines changed 12, context: html, text, full: html, text
    13b584581e6d7b1860e0cab97adc3594b1899308 Mon Aug 7 12:05:10 2023 -0700
    add instaPort to bigBed support
• src/hg/lib/bed.c
  • lines changed 8, context: html, text, full: html, text
    13b584581e6d7b1860e0cab97adc3594b1899308 Mon Aug 7 12:05:10 2023 -0700
    add instaPort to bigBed support
• src/hg/lib/chainArrange.as
  • lines changed 14, context: html, text, full: html, text
    3e39804e374b48ecc82eec8ae77b9de1a0846173 Sat Aug 12 16:16:44 2023 -0700
    second cut at HPRC rearrangement summary tracks
• src/hg/lib/genePred.c
  • lines changed 25, context: html, text, full: html, text
    13b584581e6d7b1860e0cab97adc3594b1899308 Mon Aug 7 12:05:10 2023 -0700
    add instaPort to bigBed support
• src/hg/lib/instaPort.c
  • lines changed 111, context: html, text, full: html, text
    13b584581e6d7b1860e0cab97adc3594b1899308 Mon Aug 7 12:05:10 2023 -0700
    add instaPort to bigBed support
• src/hg/lib/liftOver.c
  • lines changed 48, context: html, text, full: html, text
    13b584581e6d7b1860e0cab97adc3594b1899308 Mon Aug 7 12:05:10 2023 -0700
    add instaPort to bigBed support
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    13b584581e6d7b1860e0cab97adc3594b1899308 Mon Aug 7 12:05:10 2023 -0700
    add instaPort to bigBed support
• src/hg/lib/trackDbCustom.c
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    13b584581e6d7b1860e0cab97adc3594b1899308 Mon Aug 7 12:05:10 2023 -0700
    add instaPort to bigBed support
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    13b584581e6d7b1860e0cab97adc3594b1899308 Mon Aug 7 12:05:10 2023 -0700
    add instaPort to bigBed support
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
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    8135abf0dbdcbdc1c0e0c3a5bf1c3a1a166b93aa Sat Aug 12 13:47:36 2023 -0700
    fission yeast GCF_000002945.1 vs. bakers yeast GCF_000146045.2, lastz/chain/net run for user, refs #31596
• src/hg/makeDb/doc/dm6/lastzRuns.txt
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    b85993b9ee03fc6b36fc752de2051f2eb06f7e83 Sat Aug 12 13:36:04 2023 -0700
    dm6 vs. GCF_016746395.2/GCF_004382195.2/GCF_018902025.1/GCF_009870125.1/GCF_017639315.1/GCF_016746365.2, lastz/chain/net run for user, refs #31548
• src/hg/makeDb/doc/hg19.gencode.txt
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    ec1552835f9e75357243ac6e1bd315d45413cd23 Tue Aug 8 09:18:29 2023 -0700
    import of gencode v44lift37
• src/hg/makeDb/doc/hg38/cactus447.txt
  • lines changed 445, context: html, text, full: html, text
    5b1483d60866e637703c920a8ff02516b52d53a8 Mon Aug 7 13:25:52 2023 -0700
    add the frames procedure refs #31528
• src/hg/makeDb/doc/hg38/hprcRearrange.txt
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    3a91631b10c28b2f0f4d0f51ce2db8cbd9dee0a7 Sat Aug 12 16:13:11 2023 -0700
    instructions for hprc arrangement tracks
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
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    ec1552835f9e75357243ac6e1bd315d45413cd23 Tue Aug 8 09:18:29 2023 -0700
    import of gencode v44lift37
• src/hg/makeDb/schema/all.joiner
  • lines changed 89, context: html, text, full: html, text
    ec1552835f9e75357243ac6e1bd315d45413cd23 Tue Aug 8 09:18:29 2023 -0700
    import of gencode v44lift37
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    758646fd053b6538ffa00fd9ec15030fb28232ab Thu Aug 10 16:04:42 2023 -0700
    fixing weird type extra character on line 5501
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    ec1552835f9e75357243ac6e1bd315d45413cd23 Tue Aug 8 09:18:29 2023 -0700
    import of gencode v44lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    ec1552835f9e75357243ac6e1bd315d45413cd23 Tue Aug 8 09:18:29 2023 -0700
    import of gencode v44lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV44lift37.html
  • lines changed 32, context: html, text, full: html, text
    ec1552835f9e75357243ac6e1bd315d45413cd23 Tue Aug 8 09:18:29 2023 -0700
    import of gencode v44lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV44lift37.ra
  • lines changed 210, context: html, text, full: html, text
    ec1552835f9e75357243ac6e1bd315d45413cd23 Tue Aug 8 09:18:29 2023 -0700
    import of gencode v44lift37
• src/hg/makeDb/trackDb/human/hg38/cactus447way.html
  • lines changed 124, context: html, text, full: html, text
    53265648ce108661220f0d0108e17772ef4f68fc Mon Aug 7 12:57:06 2023 -0700
    adding a description of the phylo tree construction and the gene annotation accounting listings refs #31528
• src/hg/makeDb/trackDb/human/hg38/trackDb.447way.ra
  • lines changed 1, context: html, text, full: html, text
    f86605565fe791a40e6d46d631e7b34edcc3be19 Mon Aug 7 16:00:13 2023 -0700
    adding phylo tree sample for Cactus 477-way track refs #31528
• src/hg/pyLib/hgLib.py
  • lines changed 33, context: html, text, full: html, text
    4e87977d27175e20f01bb740de6a5c54b0e0bbd6 Thu Aug 10 23:00:36 2023 -0700
    Updating the CSP policy in python hgLib and hgLib3. refs #31954
• src/hg/pyLib/hgLib3.py
  • lines changed 37, context: html, text, full: html, text
    4e87977d27175e20f01bb740de6a5c54b0e0bbd6 Thu Aug 10 23:00:36 2023 -0700
    Updating the CSP policy in python hgLib and hgLib3. refs #31954
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 1, context: html, text, full: html, text
    682135a7366fcde9b3314ee6c5093cec2a71052a Fri Aug 11 21:56:17 2023 -0700
    correctly use bigClusterHub for doIdKeys no redmine
• src/hg/utils/bigChainArrange/bigChainArrange.c
  • lines changed 135, context: html, text, full: html, text
    3e39804e374b48ecc82eec8ae77b9de1a0846173 Sat Aug 12 16:16:44 2023 -0700
    second cut at HPRC rearrangement summary tracks
• src/hg/utils/bigChainArrange/makefile
  • lines changed 3, context: html, text, full: html, text
    3e39804e374b48ecc82eec8ae77b9de1a0846173 Sat Aug 12 16:16:44 2023 -0700
    second cut at HPRC rearrangement summary tracks
• src/hg/utils/bigChainToChain/bigChainToChain.c
  • lines changed 50, context: html, text, full: html, text
    fd85559cf680f17b7c31e6d0028149afecc49bb7 Fri Aug 11 10:50:47 2023 -0700
    add bigChainToChain command
• src/hg/utils/bigChainToChain/makefile
  • lines changed 3, context: html, text, full: html, text
    fd85559cf680f17b7c31e6d0028149afecc49bb7 Fri Aug 11 10:50:47 2023 -0700
    add bigChainToChain command
• src/hg/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    fd85559cf680f17b7c31e6d0028149afecc49bb7 Fri Aug 11 10:50:47 2023 -0700
    add bigChainToChain command
• src/htslib/knetfile.c
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    93b69d0872dab89b3ab88455a0d51c2c6500a13b Tue Aug 8 11:46:46 2023 -0700
    Roll-back using HTTP/1.1 to HTTP/1.0 in knetfile.c. refs #31859
• src/lib/gff3.c
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    fed8da255b8c4f2e63f0218992e87bf40d74b127 Fri Aug 11 12:20:17 2023 -0700
    allow gff3 minor versions in headers
• src/lib/htmshell.c
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    cebb22e349ef7292cb4deea3d9addf6c2c88c95f Thu Aug 10 20:32:28 2023 -0700
    Fixing a devilish way hackers have found to exploit bugs in javascript libraries at public sites. By including multiple bugs from multiple libraries that they insert into your page, this allows them to loads anything from those sites. We have to change the policy to only list specific files actuallly needed and not be lazy and just whitelist the entire domain. This was a lot of work to though every line of the policy, do grep searches, combine the results and double check it all. refs #31954, #31855
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    4e87977d27175e20f01bb740de6a5c54b0e0bbd6 Thu Aug 10 23:00:36 2023 -0700
    Updating the CSP policy in python hgLib and hgLib3. refs #31954
  • lines changed 1, context: html, text, full: html, text
    ae259436702e0ac87bb3390ec43864e027f36aaf Fri Aug 11 13:14:28 2023 -0700
    increasing size of temp string by 4 so it does not overflow.
• src/lib/net.c
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    0a62db350135eb565d33aa1e8da130d56b41f9a2 Tue Aug 8 10:08:00 2023 -0700
    Roll-back using HTTP/1.1 to HTTP/1.0 in net.c. refs #31859
• src/utils/bedCollect/bedCollect.c
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    3e39804e374b48ecc82eec8ae77b9de1a0846173 Sat Aug 12 16:16:44 2023 -0700
    second cut at HPRC rearrangement summary tracks
• src/utils/bedCollect/makefile
  • lines changed 3, context: html, text, full: html, text
    3e39804e374b48ecc82eec8ae77b9de1a0846173 Sat Aug 12 16:16:44 2023 -0700
    second cut at HPRC rearrangement summary tracks
• src/utils/qa/weeklybld/buildEnv.csh
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    024e21b89b414c27a8d30ed519fe72606bea940f Sun Aug 13 10:12:32 2023 -0700
    v453 preview1

• lines changed: 2300
• files changed: 48