All File Changes

v460_base to v461_preview (2024-01-29 to 2024-02-06) v461

• src/README
  • lines changed 14, context: html, text, full: html, text
    40c4d8dae2dcdb5ce1793bcfa999fd753b1c861e Tue Feb 6 07:05:20 2024 -0800
    documenting the online/offline and dev options in GBIC, no ticket
• src/hg/hgBeacon/makefile
  • lines changed 1, context: html, text, full: html, text
    84b6a4eed4c7e32abe9e33c246ad54c0b450a7c0 Tue Feb 6 05:47:32 2024 -0800
    removing testBeacon on cgi build, not needed in bin directory, no redmine
• src/hg/hgGeneGraph/hgGeneGraph
  • lines changed 4, context: html, text, full: html, text
    f76022a8ee809aa35882a2808b67a45756dd0d1f Wed Jan 31 08:25:28 2024 -0800
    trying to get rid of a warning message that appears only on the RR due to some fontconfig issue, refs #32691
• src/hg/hgTracks/hgTracks.c
  • lines changed 9, context: html, text, full: html, text
    b3fa58bc96f662c6b997ee8003e2cb15a16b68ab Wed Jan 31 08:05:52 2024 -0800
    reload hgTracksif the pix variable is not set, refs #32925
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    cecfab8cb58f595bc4de9062292c5f0b6ec38666 Tue Jan 30 02:03:50 2024 -0800
    changing url of spider trap, email with Hiram/Lou
• src/hg/htdocs/goldenPath/noPageHere.html
  • lines changed 15, context: html, text, full: html, text
    cecfab8cb58f595bc4de9062292c5f0b6ec38666 Tue Jan 30 02:03:50 2024 -0800
    changing url of spider trap, email with Hiram/Lou
• src/hg/htdocs/indexMeetings.html
  • lines changed 8, context: html, text, full: html, text
    d0f3ab33b9001beb392bbec8182c395d2b2cf03f Tue Jan 30 13:50:39 2024 -0800
    Updating a new meeting from b0b.
  • lines changed 8, context: html, text, full: html, text
    dc862e2e8defa738d502f692d04224ca74df8729 Fri Feb 2 15:08:07 2024 -0800
    Updating a new meeting from b0b, and temporarily removing the EHG conference, No Redmine
• src/hg/htdocs/noPage.html
  • lines changed 15, context: html, text, full: html, text
    eebe3d904194d8e4fbf7575fd518d91ec4c314cd Mon Jan 29 11:38:05 2024 -0800
    committing empty page to trap web robots, no redmine, suggestion at team meeting by Hiram and others
  • lines changed 15, context: html, text, full: html, text
    cecfab8cb58f595bc4de9062292c5f0b6ec38666 Tue Jan 30 02:03:50 2024 -0800
    changing url of spider trap, email with Hiram/Lou
• src/hg/hubApi/dataApi.h
  • lines changed 8, context: html, text, full: html, text
    be00edb2a6ef8c715b715cf0261572feead28c21 Sat Feb 3 13:11:41 2024 -0800
    beginning to run FULLTEXT search on asmSummary table refs #23589
  • lines changed 2, context: html, text, full: html, text
    6b90bc1b27dafa410579a6cbb479cd4ab44403c8 Sun Feb 4 20:54:17 2024 -0800
    add stats output function and timing measure refs #32897
• src/hg/hubApi/findGenome.c
  • lines changed 199, context: html, text, full: html, text
    be00edb2a6ef8c715b715cf0261572feead28c21 Sat Feb 3 13:11:41 2024 -0800
    beginning to run FULLTEXT search on asmSummary table refs #23589
  • lines changed 305, context: html, text, full: html, text
    fec4e5d98ee6a52aac4506f02dc28980f52c738f Sat Feb 3 16:29:45 2024 -0800
    beginning to combine the outputs from asmSummary and genark tables refs #23589
  • lines changed 102, context: html, text, full: html, text
    6b90bc1b27dafa410579a6cbb479cd4ab44403c8 Sun Feb 4 20:54:17 2024 -0800
    add stats output function and timing measure refs #32897
  • lines changed 65, context: html, text, full: html, text
    454f6d047a6d35baa30335cbe939c41b6df3865f Mon Feb 5 12:24:56 2024 -0800
    now honoring allowAll in single word searches refs #32897
  • lines changed 93, context: html, text, full: html, text
    8d9253332f172e52c7ecb7fbc6ecde2bad30561f Mon Feb 5 15:36:52 2024 -0800
    with browserUrl and finding equivalent asmSummary for UCSC dbDb browser refs #32897
• src/hg/hubApi/hubApi.c
  • lines changed 2, context: html, text, full: html, text
    be00edb2a6ef8c715b715cf0261572feead28c21 Sat Feb 3 13:11:41 2024 -0800
    beginning to run FULLTEXT search on asmSummary table refs #23589
  • lines changed 1, context: html, text, full: html, text
    6b90bc1b27dafa410579a6cbb479cd4ab44403c8 Sun Feb 4 20:54:17 2024 -0800
    add stats output function and timing measure refs #32897
• src/hg/hubApi/makefile
  • lines changed 1, context: html, text, full: html, text
    623507d68d435e62ba460a992f6cb7b44280bb5c Sat Feb 3 13:16:03 2024 -0800
    beginning to run FULLTEXT search on asmSummary table refs #23589
• src/hg/inc/asmSummary.h
  • lines changed 117, context: html, text, full: html, text
    0bc6be88baf4061ca10c6f207331ec04e36c17f1 Fri Feb 2 11:34:37 2024 -0800
    better name for this table refs #23589
  • lines changed 7, context: html, text, full: html, text
    2d5c21f0d3a8b67dd86f1f9f999f2aa384f67275 Sat Feb 3 13:17:19 2024 -0800
    beginning to run FULLTEXT search on asmSummary table refs #23589
  • lines changed 9, context: html, text, full: html, text
    c88b8a093cac2bc72ca4b4e3ff1fc2d1aea17f55 Sat Feb 3 13:59:52 2024 -0800
    the NULL specification confused autoSql for numbers that should be zero refs #23589
• src/hg/inc/genomeData.h
  • lines changed 117, context: html, text, full: html, text
    4ba0a7d92cc93673915bb6f24ae81435ea179ce3 Wed Jan 31 17:02:58 2024 -0800
    beginning to add a searchable table of genome meta data refs #23589;
  • lines changed 117, context: html, text, full: html, text
    c8f3ff3c555def2c55f0c498fe0eb24df8c29b6c Fri Feb 2 11:35:26 2024 -0800
    name changed to asmSummary refs #23589
• src/hg/js/utils.js
  • lines changed 14, context: html, text, full: html, text
    b3fa58bc96f662c6b997ee8003e2cb15a16b68ab Wed Jan 31 08:05:52 2024 -0800
    reload hgTracksif the pix variable is not set, refs #32925
  • lines changed 1, context: html, text, full: html, text
    171c52177527ae126d3186ff4c1e225dfcd7526d Mon Feb 5 07:52:29 2024 -0800
    fixing dumb bug in previous commit, refs #32925
• src/hg/lib/asmSummary.as
  • lines changed 41, context: html, text, full: html, text
    0bc6be88baf4061ca10c6f207331ec04e36c17f1 Fri Feb 2 11:34:37 2024 -0800
    better name for this table refs #23589
• src/hg/lib/asmSummary.c
  • lines changed 844, context: html, text, full: html, text
    0bc6be88baf4061ca10c6f207331ec04e36c17f1 Fri Feb 2 11:34:37 2024 -0800
    better name for this table refs #23589
  • lines changed 14, context: html, text, full: html, text
    be00edb2a6ef8c715b715cf0261572feead28c21 Sat Feb 3 13:11:41 2024 -0800
    beginning to run FULLTEXT search on asmSummary table refs #23589
  • lines changed 155, context: html, text, full: html, text
    c88b8a093cac2bc72ca4b4e3ff1fc2d1aea17f55 Sat Feb 3 13:59:52 2024 -0800
    the NULL specification confused autoSql for numbers that should be zero refs #23589
• src/hg/lib/asmSummary.sql
  • lines changed 47, context: html, text, full: html, text
    0bc6be88baf4061ca10c6f207331ec04e36c17f1 Fri Feb 2 11:34:37 2024 -0800
    better name for this table refs #23589
• src/hg/lib/genomeData.as
  • lines changed 41, context: html, text, full: html, text
    4ba0a7d92cc93673915bb6f24ae81435ea179ce3 Wed Jan 31 17:02:58 2024 -0800
    beginning to add a searchable table of genome meta data refs #23589;
  • lines changed 41, context: html, text, full: html, text
    c8f3ff3c555def2c55f0c498fe0eb24df8c29b6c Fri Feb 2 11:35:26 2024 -0800
    name changed to asmSummary refs #23589
• src/hg/lib/genomeData.c
  • lines changed 856, context: html, text, full: html, text
    4ba0a7d92cc93673915bb6f24ae81435ea179ce3 Wed Jan 31 17:02:58 2024 -0800
    beginning to add a searchable table of genome meta data refs #23589;
  • lines changed 856, context: html, text, full: html, text
    c8f3ff3c555def2c55f0c498fe0eb24df8c29b6c Fri Feb 2 11:35:26 2024 -0800
    name changed to asmSummary refs #23589
• src/hg/lib/genomeData.sql
  • lines changed 47, context: html, text, full: html, text
    4ba0a7d92cc93673915bb6f24ae81435ea179ce3 Wed Jan 31 17:02:58 2024 -0800
    beginning to add a searchable table of genome meta data refs #23589;
  • lines changed 47, context: html, text, full: html, text
    c8f3ff3c555def2c55f0c498fe0eb24df8c29b6c Fri Feb 2 11:35:26 2024 -0800
    name changed to asmSummary refs #23589
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    814c4588a63f364744576bebd4e98cdff4ae860c Sat Feb 3 13:18:10 2024 -0800
    adding asmSummary functions refs #23589
• src/hg/makeDb/doc/hs1/crispr.txt
  • lines changed 43, context: html, text, full: html, text
    bcbf2dfc5f3cfe6c33b1cf8b630bfb11806e4dc3 Mon Jan 29 16:47:04 2024 -0800
    crispr track build refs #32827
• src/hg/makeDb/trackDb/TOGAannotation.html
  • lines changed 8, context: html, text, full: html, text
    6d7150d4b11cf16b7b58d4c1eae3dbf6d240dffd Wed Jan 31 09:25:51 2024 -0800
    fixing track refs, email from M Hiller
• src/hg/makeDb/trackDb/human/hg38/gnomad.html
  • lines changed 12, context: html, text, full: html, text
    b1f12063e33feb9427afa17f0f50b18a0b2eb143 Tue Jan 30 04:45:08 2024 -0800
    the gnomad paper came out, no redmine
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 3, context: html, text, full: html, text
    b1f12063e33feb9427afa17f0f50b18a0b2eb143 Tue Jan 30 04:45:08 2024 -0800
    the gnomad paper came out, no redmine
• src/hg/makeDb/trackDb/human/hg38/gnomadV4.html
  • lines changed 18, context: html, text, full: html, text
    b44200085524ad29f244699a5ce06fcda4e9af16 Tue Jan 30 05:01:28 2024 -0800
    realized too late that gnomad.html is not actually shown anywhere, strange, no redmine
• src/hg/makeDb/trackDb/human/hg38/trackDb.hprc90way.ra
  • lines changed 1, context: html, text, full: html, text
    2ce9ffc88a8e2d89aaa23c7618196b1a0563e224 Fri Feb 2 10:51:44 2024 -0800
    Added mafDot on, which will display bases identical to reference as dots by default, refs #32285
  • lines changed 2, context: html, text, full: html, text
    a05dca985b13971e783106aff6a61ffd09de8da7 Fri Feb 2 11:09:05 2024 -0800
    Moving the mafDot on setting to the subTrack due to the setting not allowed for bed type, refs #32285
• src/hg/utils/automation/asmHubTOGA.pl
  • lines changed 6, context: html, text, full: html, text
    830e8a9193ae7906770c396cee7e58b2b14dfdda Wed Jan 31 13:43:17 2024 -0800
    update to publication reference no redmine
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 9, context: html, text, full: html, text
    6361ad1b494f51fe3d761b1cefacc1f8c12be1c9 Wed Jan 31 07:09:14 2024 -0800
    adding linebreaks to clinvar mouseover and review status, #32915
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
  • lines changed 3, context: html, text, full: html, text
    28e901dcf7f05026044feb8f4cc0fe9a267df7be Sun Feb 4 09:21:18 2024 -0800
    Mask the range 21610-21624 due to Ns/run-of-muts. sars-cov-2-variants/lineage-proposals#1347
• src/hg/utils/otto/sarscov2phylo/combineMetadata.sh
  • lines changed 2, context: html, text, full: html, text
    a087918aa0bbba12853825bd8a588ab26b0b70bd Sun Feb 4 09:24:02 2024 -0800
    Update to nextclade v3 output column indices.
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
  • lines changed 2, context: html, text, full: html, text
    7f46acdf8f879de28c3ba40534e58a881941e168 Sun Feb 4 09:24:53 2024 -0800
    CNCB is updated daily so make version.txt more concise.
• src/hg/utils/otto/sarscov2phylo/findDropoutContam.pl
  • lines changed 22, context: html, text, full: html, text
    a087918aa0bbba12853825bd8a588ab26b0b70bd Sun Feb 4 09:24:02 2024 -0800
    Update to nextclade v3 output column indices.
• src/hg/utils/otto/sarscov2phylo/getCncb.sh
  • lines changed 1, context: html, text, full: html, text
    71a5bf4d42948792ba96729c01bec373eed86918 Sun Feb 4 09:16:38 2024 -0800
    Use nextclade v3 output column indices.
• src/hg/utils/otto/sarscov2phylo/getCogUk.sh
  • lines changed 1, context: html, text, full: html, text
    71a5bf4d42948792ba96729c01bec373eed86918 Sun Feb 4 09:16:38 2024 -0800
    Use nextclade v3 output column indices.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 2, context: html, text, full: html, text
    71a5bf4d42948792ba96729c01bec373eed86918 Sun Feb 4 09:16:38 2024 -0800
    Use nextclade v3 output column indices.
• src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
  • lines changed 4, context: html, text, full: html, text
    a087918aa0bbba12853825bd8a588ab26b0b70bd Sun Feb 4 09:24:02 2024 -0800
    Update to nextclade v3 output column indices.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 28, context: html, text, full: html, text
    d6e1c182b3f78991221452f89d940a6bea7d4b5f Sun Feb 4 09:13:25 2024 -0800
    New lineages and correction to C.37 (Lambda)
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 4, context: html, text, full: html, text
    7f46acdf8f879de28c3ba40534e58a881941e168 Sun Feb 4 09:24:53 2024 -0800
    CNCB is updated daily so make version.txt more concise.
• src/hg/utils/vcfToBed/vcfToBed.c
  • lines changed 26, context: html, text, full: html, text
    6ba8692a29a9cdd90cf4a133a4d8a3ee488dc899 Thu Feb 1 17:22:40 2024 -0800
    Add a flag -fieldsIsFile to vcfToBed to read the -fields argument from a file rather than the command line
• src/inc/common.mk
  • lines changed 208, context: html, text, full: html, text
    c4e215c27ac760c75d100338703a99009e33125c Tue Feb 6 05:28:53 2024 -0800
    We got various reports that the source tree is not building on Ubuntu anymore. Also, we got reports that there are strange issues with binaries built on Rocky8. To get the tree to build again on Ubuntu, and to narrow down problems on Rocky8, I'm removing a lot of the library auto-detection code in common.mk. The code was looking for hardcoded paths to .a files, which caused the strange linking errors on Ubuntu: even when the correct mysql lib version was installed, the makefile picked up an unrelated .a file and whatever was done to the mysql config, the dynamic libs were not picked up. This change removes most of these special cases. Most of the removals affect only the build on very old macports versions. I left untouched the IS_HGWDEV parts. SSL support is not optional anymore with this change, which hopefully affects not even builds on smartwatches and thermostats. Most users who want to use special library versions need to set their PATHs such that mysql_config and similar x_config programs return the right directories. Macports users probably need to do something like this (HT to Markd): export CFLAGS=-I/opt/local/include export LDFLAGs=-L/opt/local/lib
• src/inc/vcf.h
  • lines changed 1, context: html, text, full: html, text
    3f6e034cd0844d8e99a69e56af72e8c4cce98a9c Tue Jan 30 15:55:18 2024 -0800
    Hash INFO keys during header parsing for faster lookups later when loading records
• src/lib/vcf.c
  • lines changed 17, context: html, text, full: html, text
    3f6e034cd0844d8e99a69e56af72e8c4cce98a9c Tue Jan 30 15:55:18 2024 -0800
    Hash INFO keys during header parsing for faster lookups later when loading records
• src/product/installer/browserSetup.sh
  • lines changed 2, context: html, text, full: html, text
    8229e76fc318e703dda4fbd5557b22112ee627af Mon Feb 5 06:52:54 2024 -0800
    fixing typo in browserSetup.sh that lead to corrupted script
  • lines changed 36, context: html, text, full: html, text
    54195fff8bba3952c7fe45c9a228cbe7ab4855cc Mon Feb 5 08:05:54 2024 -0800
    adding development mode to GBIC script, refs #32762
  • lines changed 7, context: html, text, full: html, text
    74bbf1d81bdc64b42d6397eb8fb95d8403ed7ad5 Tue Feb 6 02:44:24 2024 -0800
    fix for GBIC for Ubuntu 21 and later, email from Glenn
  • lines changed 3, context: html, text, full: html, text
    a50fb85605c0248d9236aac95af75cfc2a31653a Tue Feb 6 06:11:19 2024 -0800
    making gbic dev mode work on debian distros
  • lines changed 16, context: html, text, full: html, text
    40c4d8dae2dcdb5ce1793bcfa999fd753b1c861e Tue Feb 6 07:05:20 2024 -0800
    documenting the online/offline and dev options in GBIC, no ticket
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    e01be94b2df0b6b467170df7e304ed87493317bd Tue Feb 6 09:53:30 2024 -0800
    v461 preview1, refs #32867

• lines changed: 4729
• files changed: 68