All File Changes

v442_base to v443_preview (2023-01-09 to 2023-01-17) v443

• confs/hgwdev.hg.conf
  • lines changed 5, context: html, text, full: html, text
    b73b6a7de54200d2ffb2ee2cbee28b448f88544d Sun Jan 15 01:11:24 2023 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/gar/garTable.pl
  • lines changed 5, context: html, text, full: html, text
    452b689cab327a20bb7ac506eaf89a3f69d23feb Tue Jan 17 08:23:41 2023 -0800
    invertebrates has become invertebrate and master.run.list has changed columns no redmine
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    44a49f19a31a807dc1f7e956c99d16e6e0101da8 Tue Jan 17 08:32:37 2023 -0800
    invertebrates really is invertebrate must be this way for the selection menus to function no redmine
• src/hg/gar/garTable.sh
  • lines changed 2, context: html, text, full: html, text
    452b689cab327a20bb7ac506eaf89a3f69d23feb Tue Jan 17 08:23:41 2023 -0800
    invertebrates has become invertebrate and master.run.list has changed columns no redmine
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 3, context: html, text, full: html, text
    b02d20dede590203b6ecca10be473e7e22179a51 Thu Jan 12 13:12:53 2023 -0800
    deal with some weird edge cases in hub that Hiram's hub illicit. Don't read a single trackDb.txt file more than once even if it's referenced from mulitple hubs. Also, only the first time a genome is defined does it get to populate its own groups. Subsequent examples get put into their own group, just like a normal track hub does.
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 4, context: html, text, full: html, text
    00ae0ed0644312e30a2227d71a92e6b1ca9efc8c Mon Jan 9 10:49:20 2023 -0800
    Add support for RSV-A and RSV-B viruses.
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 3, context: html, text, full: html, text
    00ae0ed0644312e30a2227d71a92e6b1ca9efc8c Mon Jan 9 10:49:20 2023 -0800
    Add support for RSV-A and RSV-B viruses.
• src/hg/hgTracks/searchTracks.c
  • lines changed 3, context: html, text, full: html, text
    b02d20dede590203b6ecca10be473e7e22179a51 Thu Jan 12 13:12:53 2023 -0800
    deal with some weird edge cases in hub that Hiram's hub illicit. Don't read a single trackDb.txt file more than once even if it's referenced from mulitple hubs. Also, only the first time a genome is defined does it get to populate its own groups. Subsequent examples get put into their own group, just like a normal track hub does.
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 5, context: html, text, full: html, text
    2c124828cadde4d299fb5ac5e401498a57d9e923 Fri Jan 13 16:58:33 2023 -0800
    Noting the new hgSearch page to be clear that search terms of other kinds are accepted, no just positional queries. Refs Max and ChrisL
• src/hg/htdocs/goldenPath/help/trix.html
  • lines changed 5, context: html, text, full: html, text
    35ad0a3238e9a98b1b2872e0de88e87b0f519e3a Fri Jan 13 17:05:29 2023 -0800
    Clarifying that the trix searching is note case sensitive, and fixing an example that is misleading. Refs #30451
• src/hg/htdocs/style/jquery.qtip.min.css
  • lines changed 1, context: html, text, full: html, text
    2648e954eb83fa169fa9164622d9baff598e2d1d Tue Jan 10 05:10:53 2023 -0800
    fixing selection in hgTracks to respect left-right bounds, refs #30458
• src/hg/htdocs/style/theme-classic.css
  • lines changed 3, context: html, text, full: html, text
    5e7abdfb0830d2f20bc45a577bef3024852cad28 Wed Jan 11 06:16:04 2023 -0800
    adding tiny CSS themes as demonstrations, got back to ticket after 10 years, thanks lou!, refs #7867
• src/hg/htdocs/style/theme-dark.css
  • lines changed 12, context: html, text, full: html, text
    5e7abdfb0830d2f20bc45a577bef3024852cad28 Wed Jan 11 06:16:04 2023 -0800
    adding tiny CSS themes as demonstrations, got back to ticket after 10 years, thanks lou!, refs #7867
• src/hg/htdocs/style/theme-default.css
  • lines changed 0, context: html, text, full: html, text
    5e7abdfb0830d2f20bc45a577bef3024852cad28 Wed Jan 11 06:16:04 2023 -0800
    adding tiny CSS themes as demonstrations, got back to ticket after 10 years, thanks lou!, refs #7867
• src/hg/hubApi/apiUtils.c
  • lines changed 2, context: html, text, full: html, text
    12c80e276f91d0920d4c39e76870745a69e19b4d Mon Jan 9 16:47:40 2023 -0800
    add support for curated hubs to hubApi
  • lines changed 2, context: html, text, full: html, text
    b02d20dede590203b6ecca10be473e7e22179a51 Thu Jan 12 13:12:53 2023 -0800
    deal with some weird edge cases in hub that Hiram's hub illicit. Don't read a single trackDb.txt file more than once even if it's referenced from mulitple hubs. Also, only the first time a genome is defined does it get to populate its own groups. Subsequent examples get put into their own group, just like a normal track hub does.
• src/hg/hubApi/hubApi.c
  • lines changed 14, context: html, text, full: html, text
    12c80e276f91d0920d4c39e76870745a69e19b4d Mon Jan 9 16:47:40 2023 -0800
    add support for curated hubs to hubApi
• src/hg/inc/hubConnect.h
  • lines changed 3, context: html, text, full: html, text
    427fef992306654becd9988cbd95cc8e98d34156 Mon Jan 9 16:50:30 2023 -0800
    oops, forgot an include file
  • lines changed 4, context: html, text, full: html, text
    b02d20dede590203b6ecca10be473e7e22179a51 Thu Jan 12 13:12:53 2023 -0800
    deal with some weird edge cases in hub that Hiram's hub illicit. Don't read a single trackDb.txt file more than once even if it's referenced from mulitple hubs. Also, only the first time a genome is defined does it get to populate its own groups. Subsequent examples get put into their own group, just like a normal track hub does.
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    bebcb6453c54164564b24899c6f407310b551a93 Thu Jan 5 06:37:34 2023 -0800
    first go at s3:// support, refs #30445 adding cache file to UDC protocol support, refs #30445 handling expired presigned URLs in udc protocol, refs #30445
• src/hg/inc/trackHub.h
  • lines changed 3, context: html, text, full: html, text
    b02d20dede590203b6ecca10be473e7e22179a51 Thu Jan 12 13:12:53 2023 -0800
    deal with some weird edge cases in hub that Hiram's hub illicit. Don't read a single trackDb.txt file more than once even if it's referenced from mulitple hubs. Also, only the first time a genome is defined does it get to populate its own groups. Subsequent examples get put into their own group, just like a normal track hub does.
• src/hg/js/hgTracks.js
  • lines changed 24, context: html, text, full: html, text
    2648e954eb83fa169fa9164622d9baff598e2d1d Tue Jan 10 05:10:53 2023 -0800
    fixing selection in hgTracks to respect left-right bounds, refs #30458
• src/hg/lib/asmAlias.c
  • lines changed 3, context: html, text, full: html, text
    0f2021c604acf2101f3481e94e768940aa0358f6 Tue Jan 10 16:07:00 2023 -0800
    make sure connection to hgCentral is closed even if the asmAlias table doesn't exist
• src/hg/lib/cart.c
  • lines changed 6, context: html, text, full: html, text
    bebcb6453c54164564b24899c6f407310b551a93 Thu Jan 5 06:37:34 2023 -0800
    first go at s3:// support, refs #30445 adding cache file to UDC protocol support, refs #30445 handling expired presigned URLs in udc protocol, refs #30445
• src/hg/lib/customFactory.c
  • lines changed 12, context: html, text, full: html, text
    bebcb6453c54164564b24899c6f407310b551a93 Thu Jan 5 06:37:34 2023 -0800
    first go at s3:// support, refs #30445 adding cache file to UDC protocol support, refs #30445 handling expired presigned URLs in udc protocol, refs #30445
• src/hg/lib/gencodeBGP.as
  • lines changed 1, context: html, text, full: html, text
    72a519115340ddb42712b0e0b8d29f093be28400 Thu Jan 12 13:33:54 2023 -0800
    add transcript rank to knownGene format GENCODE
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    b02d20dede590203b6ecca10be473e7e22179a51 Thu Jan 12 13:12:53 2023 -0800
    deal with some weird edge cases in hub that Hiram's hub illicit. Don't read a single trackDb.txt file more than once even if it's referenced from mulitple hubs. Also, only the first time a genome is defined does it get to populate its own groups. Subsequent examples get put into their own group, just like a normal track hub does.
• src/hg/lib/hubConnect.c
  • lines changed 33, context: html, text, full: html, text
    12c80e276f91d0920d4c39e76870745a69e19b4d Mon Jan 9 16:47:40 2023 -0800
    add support for curated hubs to hubApi
  • lines changed 17, context: html, text, full: html, text
    b02d20dede590203b6ecca10be473e7e22179a51 Thu Jan 12 13:12:53 2023 -0800
    deal with some weird edge cases in hub that Hiram's hub illicit. Don't read a single trackDb.txt file more than once even if it's referenced from mulitple hubs. Also, only the first time a genome is defined does it get to populate its own groups. Subsequent examples get put into their own group, just like a normal track hub does.
• src/hg/lib/hui.c
  • lines changed 12, context: html, text, full: html, text
    bebcb6453c54164564b24899c6f407310b551a93 Thu Jan 5 06:37:34 2023 -0800
    first go at s3:// support, refs #30445 adding cache file to UDC protocol support, refs #30445 handling expired presigned URLs in udc protocol, refs #30445
• src/hg/lib/knownAttrs.sql
  • lines changed 1, context: html, text, full: html, text
    72a519115340ddb42712b0e0b8d29f093be28400 Thu Jan 12 13:33:54 2023 -0800
    add transcript rank to knownGene format GENCODE
• src/hg/lib/trackHub.c
  • lines changed 6, context: html, text, full: html, text
    b02d20dede590203b6ecca10be473e7e22179a51 Thu Jan 12 13:12:53 2023 -0800
    deal with some weird edge cases in hub that Hiram's hub illicit. Don't read a single trackDb.txt file more than once even if it's referenced from mulitple hubs. Also, only the first time a genome is defined does it get to populate its own groups. Subsequent examples get put into their own group, just like a normal track hub does.
• src/hg/lib/web.c
  • lines changed 6, context: html, text, full: html, text
    088c1ae0aed4212f6939ac991cb6fe7d1393acda Tue Jan 10 10:18:49 2023 -0800
    revert a change I made to recognize bad db's instead of defaulting to the cart or hg38, but this broke undecorated specification of "genome", which is handled through the cart. Oops.
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    6f145a3419b4c4e6a82ac99f8280eaf55f5cec9b Thu Jan 12 11:09:59 2023 -0800
    adding some E. coli sequences per user request refs #29545
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    2e2143f8df217ab78f1226b76f3d1ecbe72fc258 Thu Jan 12 11:24:24 2023 -0800
    adding GCF_019356215.1_ASM1935621v1 Acinetobacter baumannii (17978UN 2021) per user request refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    c9997b8280ac1a0982d6aa2bbc93721942040c44 Fri Jan 13 11:09:05 2023 -0800
    an E.coli assembly has aged out refs #29545
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    044a512bb8f36d27f51c5afe2607641e3a2a7ede Fri Jan 13 11:16:08 2023 -0800
    adding an older Arabidopsis thaliana per user request for a liftOver refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    0f32b15f7f6a73cce994c1ca3805eca7f7a6c0ac Fri Jan 13 11:15:16 2023 -0800
    improve common name for thale cress since there is now another in legacy refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    456312ae0b3c23231ee6fe31e3afbe31f28348d6 Mon Jan 9 13:58:27 2023 -0800
    now with GCF_000001405.40_GRCh38.p14 no redmine
  • lines changed 8, context: html, text, full: html, text
    5ec6ec1ee09993c90f13dc8a98204dc6b3617933 Tue Jan 17 09:02:55 2023 -0800
    move the extra human assemblies to legacy to avoid confusion with hg38 no redmine
• src/hg/utils/automation/doRepeatModeler.pl
  • lines changed 1, context: html, text, full: html, text
    2fac81d9c77176cc08e09a602904f116d493828a Mon Jan 9 13:05:00 2023 -0800
    record modelerVersion.txt no redmine
  • lines changed 2, context: html, text, full: html, text
    3dbc2036473e40fda245db7df8fa725ef6e8d5de Mon Jan 9 13:54:49 2023 -0800
    and adding in a families.fa.gz download file no redmine
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 2, context: html, text, full: html, text
    b02d20dede590203b6ecca10be473e7e22179a51 Thu Jan 12 13:12:53 2023 -0800
    deal with some weird edge cases in hub that Hiram's hub illicit. Don't read a single trackDb.txt file more than once even if it's referenced from mulitple hubs. Also, only the first time a genome is defined does it get to populate its own groups. Subsequent examples get put into their own group, just like a normal track hub does.
• src/hg/utils/hubCrawl/hubCrawl.c
  • lines changed 2, context: html, text, full: html, text
    b7e9664a721ac8e117840473859dcd25ae412842 Fri Jan 13 13:42:04 2023 -0800
    oops, missed a place
• src/hg/utils/otto/knownGene/buildCore.sh
  • lines changed 4, context: html, text, full: html, text
    72a519115340ddb42712b0e0b8d29f093be28400 Thu Jan 12 13:33:54 2023 -0800
    add transcript rank to knownGene format GENCODE
• src/hg/utils/otto/knownGene/genIspcrMail.sh
  • lines changed 2, context: html, text, full: html, text
    1f99db8cf7ec62a0a6e8a4418ce2ad8441a4c1f8 Sat Dec 31 14:25:56 2022 -0800
    the script actually sends the mail now.
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
  • lines changed 18, context: html, text, full: html, text
    23036e8b97ae73f56eeee54d68a7668d4881e77b Mon Jan 9 18:00:29 2023 -0800
    Don't make old taxodium/v1 protobuf anymore, everyone has moved on to taxonium/v2. Make names file for big tree so hgPhyloPlace doesn't have to read in protobuf to get names for matching uploaded names/IDs.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 2, context: html, text, full: html, text
    e174398ee58fcdd6fb59b393ac7af1c59645ab53 Mon Jan 9 18:01:23 2023 -0800
    Save failed .zip files for reporting to NCBI.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
  • lines changed 15, context: html, text, full: html, text
    7c9ef333258146c91b2abba00508a7d76b44b080 Mon Jan 9 18:00:56 2023 -0800
    Adding some recently proposed recombinants
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 82, context: html, text, full: html, text
    c71577525f5e69232510269be6dd6e20ef9dfd79 Mon Jan 9 17:56:49 2023 -0800
    Many new lineages -- pango-designation release v1.18
• src/hg/utils/otto/sarscov2phylo/runPangolin.sh
  • lines changed 1, context: html, text, full: html, text
    edc4389658f330657da35d00e56837afdc95c4a7 Mon Jan 9 18:02:05 2023 -0800
    Use as many threads as possible on the ku nodes, with current memory requirements.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 21, context: html, text, full: html, text
    23036e8b97ae73f56eeee54d68a7668d4881e77b Mon Jan 9 18:00:29 2023 -0800
    Don't make old taxodium/v1 protobuf anymore, everyone has moved on to taxonium/v2. Make names file for big tree so hgPhyloPlace doesn't have to read in protobuf to get names for matching uploaded names/IDs.
• src/hg/utils/vcfToBed/vcfToBed.c
  • lines changed 10, context: html, text, full: html, text
    eb35a6e5f41ce7a3a21f72c7f5b19390c6566d47 Fri Jan 13 12:08:13 2023 -0800
    Add fixChromName option to vcfToBed so it doesn't automatically create UCSC style names, refs Lou email
• src/inc/obscure.h
  • lines changed 2, context: html, text, full: html, text
    bebcb6453c54164564b24899c6f407310b551a93 Thu Jan 5 06:37:34 2023 -0800
    first go at s3:// support, refs #30445 adding cache file to UDC protocol support, refs #30445 handling expired presigned URLs in udc protocol, refs #30445
• src/inc/udc.h
  • lines changed 9, context: html, text, full: html, text
    bebcb6453c54164564b24899c6f407310b551a93 Thu Jan 5 06:37:34 2023 -0800
    first go at s3:// support, refs #30445 adding cache file to UDC protocol support, refs #30445 handling expired presigned URLs in udc protocol, refs #30445
• src/inc/verbose.h
  • lines changed 3, context: html, text, full: html, text
    bebcb6453c54164564b24899c6f407310b551a93 Thu Jan 5 06:37:34 2023 -0800
    first go at s3:// support, refs #30445 adding cache file to UDC protocol support, refs #30445 handling expired presigned URLs in udc protocol, refs #30445
• src/lib/obscure.c
  • lines changed 17, context: html, text, full: html, text
    bebcb6453c54164564b24899c6f407310b551a93 Thu Jan 5 06:37:34 2023 -0800
    first go at s3:// support, refs #30445 adding cache file to UDC protocol support, refs #30445 handling expired presigned URLs in udc protocol, refs #30445
• src/lib/udc.c
  • lines changed 168, context: html, text, full: html, text
    bebcb6453c54164564b24899c6f407310b551a93 Thu Jan 5 06:37:34 2023 -0800
    first go at s3:// support, refs #30445 adding cache file to UDC protocol support, refs #30445 handling expired presigned URLs in udc protocol, refs #30445
• src/lib/verbose.c
  • lines changed 24, context: html, text, full: html, text
    bebcb6453c54164564b24899c6f407310b551a93 Thu Jan 5 06:37:34 2023 -0800
    first go at s3:// support, refs #30445 adding cache file to UDC protocol support, refs #30445 handling expired presigned URLs in udc protocol, refs #30445
• src/utils/qa/searchedTermsCron.py
  • lines changed 2, context: html, text, full: html, text
    3480a5c52ee775f2e58e0e15fbfd63877117b6f6 Tue Jan 10 14:36:57 2023 -0800
    Code review change for the try/except block to create a directory, refs #30461
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    c13a2de7b58184577b474d387281784ad7c62afc Tue Jan 17 10:03:55 2023 -0800
    v443 preview1, refs #TICKETNUM

• lines changed: 614
• files changed: 61