All File Changes

v426_base to v427_preview (2022-01-31 to 2022-02-07) v427

• src/hg/cgilib/cartRewrite.c
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    418ddc85df90579c88010c122604ced2163c60bf Tue Feb 1 13:05:55 2022 -0800
    make cart rewrites on by default. Can still be turned off in hg.conf with "cartVersion=off" Refs #28831
• src/hg/hgCustom/hgCustom.c
  • lines changed 2, context: html, text, full: html, text
    3e2b4ddc034a23bb6c0e53849570b1dee5e281b5 Tue Feb 1 04:41:49 2022 -0800
    adding vcf.gz as a special case to hgCustom binary upload error popup, refs #8155
• src/hg/hgGene/hgGeneData/Human/hg38/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    ffd744dea4416cfde3244bcc8520bc83693e9b4d Mon Feb 7 10:03:40 2022 -0800
    hg38 knownGene uses danRer11 for the zebrafish orthlogs
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    d6b685f5964b94f86db82ae4e02df4db410c32ec Fri Feb 4 02:12:29 2022 -0800
    taking back accidental font size change, refs #28788
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 43, context: html, text, full: html, text
    83f882f60dd6bdfa9279fdc5e28eac471842383f Tue Feb 1 13:32:33 2022 -0800
    Doing some wordsmithing on new HTTPS help section for hubs, refs #28792
• src/hg/lib/hic.c
  • lines changed 2, context: html, text, full: html, text
    1a5ce25f9d4654448acab051b4bac615c319d13e Wed Feb 2 15:42:24 2022 -0800
    hic shouldn't free a hahs it didn't allocate
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    fffd6cb4e8449911d9a162db6d2993f6a7559ca9 Wed Feb 2 10:42:06 2022 -0800
    adding fungi per user request refs #28821
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    07616f16475ee63c918409477d379535d6f7cc04 Fri Feb 4 00:56:57 2022 -0800
    adding invertebrate per user request, refs #28824
• src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
  • lines changed 9, context: html, text, full: html, text
    bedc0fc4c072a0a530a9556a9d00fdd1d43286ed Tue Feb 1 20:04:30 2022 -0800
    verify there are gfidx files to go before trying that no redmine
• src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
  • lines changed 8, context: html, text, full: html, text
    582387938e39d0805578075549b3675d66e825f9 Thu Feb 3 11:48:17 2022 -0800
    please show error message when a build has too few tracks no redmine
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    cf38c2e4f4be48ec2e9ee1d3fca6944f751fbbb2 Wed Feb 2 10:49:12 2022 -0800
    adding yeast K.pastoris per user request refs #28821
• src/hg/makeDb/doc/hg19.txt
  • lines changed 11, context: html, text, full: html, text
    c64fb92069b7de689f74f37765554ec8c3b31d54 Tue Feb 1 05:47:43 2022 -0800
    updating Twist exome 2.0 again, email with Brian lee and Tina Han from Twist, refs #28655
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    27b34f3b3cbd349fd33413703dfb1c6d80d9d797 Fri Feb 4 01:36:07 2022 -0800
    adding Leishmania braziliensis MHOM/BR/75/M2903 per user request, refs #28824
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    61d9ab6df55b1487edc33c3f5e96d053704cdb72 Wed Feb 2 15:53:16 2022 -0800
    Adding v39 lift to .ra file, refs #28771
• src/hg/makeDb/trackDb/human/hg38/omimGene2.html
  • lines changed 1, context: html, text, full: html, text
    aea4ca828248cfa33a3f2c4765a7842180c1c08a Thu Feb 3 17:18:32 2022 -0800
    made quotes match others on page. refs #28856
• src/hg/makeDb/trackDb/human/hg38/tabulaSapiens.html
  • lines changed 96, context: html, text, full: html, text
    6b54c387ad6f077c67129347701bb1db91ee4ec3 Tue Feb 1 11:18:33 2022 -0800
    Pushing file so that Rachel can have updated changes to html page for Tabula Sapiens.
• src/hg/makeDb/trackDb/human/omimGene2.html
  • lines changed 1, context: html, text, full: html, text
    aea4ca828248cfa33a3f2c4765a7842180c1c08a Thu Feb 3 17:18:32 2022 -0800
    made quotes match others on page. refs #28856
• src/hg/utils/automation/asmHubNcbiGene.pl
  • lines changed 81, context: html, text, full: html, text
    97c0cf7b73c8ffe9d37ac58bc899b82009c2c76b Thu Feb 3 11:25:37 2022 -0800
    check in missing file no redmine
• src/hg/utils/genePredToBigGenePred/genePredToBigGenePred.c
  • lines changed 10, context: html, text, full: html, text
    f6b440a99776b79f399a2646442a5e079723cb0e Sun Feb 6 13:49:28 2022 -0800
    don't crash if geneName or color not found for a genePred
• src/lib/bbiRead.c
  • lines changed 1, context: html, text, full: html, text
    b88bd07c19e4224a3e1dc86356bd056f570c592f Tue Feb 1 14:07:19 2022 -0800
    fix a bug that resulted in erroneous bigBed entries being reported
  • lines changed 1, context: html, text, full: html, text
    ffb14ca7ea496e76f5dc2052d8c02f4f59fd75b4 Tue Feb 1 17:28:37 2022 -0800
    Revert "fix a bug that resulted in erroneous bigBed entries being reported" This reverts commit b88bd07c19e4224a3e1dc86356bd056f570c592f.
  • lines changed 5, context: html, text, full: html, text
    1ff13b05ec6129e0fad8708bee411fab56443b14 Tue Feb 1 17:41:59 2022 -0800
    deal properly with chroms with no items on any chroms, including aliases
• src/lib/common.c
  • lines changed 22, context: html, text, full: html, text
    f87aaedc9bcdbda819ff0e01e942b5e74c477829 Thu Feb 3 02:12:18 2022 -0800
    Fixing multi-threading issues by removing setenv usage in https.c and common.c. refs #28844
  • lines changed 7, context: html, text, full: html, text
    0e8b1724da5c8472e3527f10619d3978025e169d Thu Feb 3 20:20:51 2022 -0800
    Since MacOS and BSDs have the Linux-originated function timegm now, we are free to use it. Even though I loved the other function and could prove its correctness, this is simple and reliable.
• src/lib/https.c
  • lines changed 35, context: html, text, full: html, text
    f87aaedc9bcdbda819ff0e01e942b5e74c477829 Thu Feb 3 02:12:18 2022 -0800
    Fixing multi-threading issues by removing setenv usage in https.c and common.c. refs #28844
  • lines changed 16, context: html, text, full: html, text
    5128fb83640188e13bbd88c4ae876b32b03dff52 Fri Feb 4 01:55:05 2022 -0800
    Further moving getenv together and cloning values for better safer getenv use.
  • lines changed 20, context: html, text, full: html, text
    8320051a3223d39076c23531af15640b8012f4a9 Fri Feb 4 17:39:50 2022 -0800
    making https.c more consistent across all the settings.
  • lines changed 10, context: html, text, full: html, text
    86f01ce419ca228c5857eac751e5ffb747699df9 Sat Feb 5 00:31:34 2022 -0800
    adding 10 domains to https whitelist
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    8fcdf7f1183704eded9c3d313968409236d3394e Mon Feb 7 10:16:28 2022 -0800
    v427 preview1, refs #28762

• lines changed: 391
• files changed: 29