All File Changes

v475_preview2 to v475_base (2024-12-02 to 2024-12-09) v475

• src/hg/hgGateway/hgGateway.c
  • lines changed 46, context: html, text, full: html, text
    d3853cf1ab1559c73f28a8bf220aac601c16c015 Wed Dec 4 13:55:17 2024 -0800
    when search matches a dbDb name from the genArk table get that result into the dbDb list for selection refs #34862
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 1, context: html, text, full: html, text
    c3bd8f6446649aa7adedbdabb08cddab57a5707f Wed Dec 4 11:16:44 2024 -0800
    Use hgdownload.gi not .soe for hubs, hope it helps with self-signed cert errors and slowness
• src/hg/hgTracks/config.c
  • lines changed 2, context: html, text, full: html, text
    32bd063f86dbc1b1c26ee3449d2644885c83ad20 Tue Dec 3 04:21:32 2024 -0800
    adding the CGI version to the configure page, refs #34852
• src/hg/htdocs/assemblySearch.html
  • lines changed 10, context: html, text, full: html, text
    9ba1f19df30d17211ebd94e05d6feb398ebc56a9 Mon Dec 9 09:33:28 2024 -0800
    updated per comments from QA refs #32596
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    b0a393711fb4a727d4ea8894a617eb12f621824b Mon Dec 9 11:10:55 2024 -0800
    New version number v475
• src/hg/js/assemblySearch.js
  • lines changed 1, context: html, text, full: html, text
    f6bb6e1854621da0de056c064007c12381326d13 Wed Dec 4 08:29:59 2024 -0800
    turn of debug flag for release refs #32596
  • lines changed 17, context: html, text, full: html, text
    9ba1f19df30d17211ebd94e05d6feb398ebc56a9 Mon Dec 9 09:33:28 2024 -0800
    updated per comments from QA refs #32596
• src/hg/js/hgTracks.js
  • lines changed 17, context: html, text, full: html, text
    59481800d466906fc4f5be900b676f6e4b611470 Thu Dec 5 05:02:36 2024 -0800
    small improvements for highlights: when old and new pos strings are mixed, make sure that the default color is used rather than color of the previous element. Also, avoid running getDb() all the time in a loop. One day, highlights will be stored in a custom track... refs #34911
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 5, context: html, text, full: html, text
    daaa29dc6598c41b9943fe3fdca994ef03186a5c Wed Dec 4 14:43:44 2024 -0800
    special rule to make the jsonData for VGP refs #34370
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 38, context: html, text, full: html, text
    d8fa0018fbf6e18abb5e9ba03ef6421fbf5a5693 Mon Dec 2 11:57:34 2024 -0800
    RefSeq update refs #29545
  • lines changed 1, context: html, text, full: html, text
    9c2fdb7758fc65cddfe5db8901ed17295aa6bed1 Tue Dec 3 14:08:47 2024 -0800
    NCBI changing assembly name refs #34370
  • lines changed 9, context: html, text, full: html, text
    34e16a8f5ab2d54f1f49eb488a3bdc4951ba14b5 Thu Dec 5 14:06:59 2024 -0800
    adding a few per user request refs #29545
  • lines changed 3, context: html, text, full: html, text
    65a6374199c998a2303c455630bb45add3dd3147 Fri Dec 6 12:18:15 2024 -0800
    update per BRC request refs #34337
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    65a6374199c998a2303c455630bb45add3dd3147 Fri Dec 6 12:18:15 2024 -0800
    update per BRC request refs #34337
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    d8fa0018fbf6e18abb5e9ba03ef6421fbf5a5693 Mon Dec 2 11:57:34 2024 -0800
    RefSeq update refs #29545
  • lines changed 1, context: html, text, full: html, text
    9c2fdb7758fc65cddfe5db8901ed17295aa6bed1 Tue Dec 3 14:08:47 2024 -0800
    NCBI changing assembly name refs #34370
  • lines changed 89, context: html, text, full: html, text
    a8364911e404223901ff4cfb4e8f3f56a0e8552c Fri Dec 6 11:40:39 2024 -0800
    coordinating common names (really should be a separate unique list) refs #34370
• src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    63b8ad4bd3b2ec680ea619ef7dd803019cafaed7 Fri Dec 6 12:22:40 2024 -0800
    update per BRC request refs #34337
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    d8fa0018fbf6e18abb5e9ba03ef6421fbf5a5693 Mon Dec 2 11:57:34 2024 -0800
    RefSeq update refs #29545
  • lines changed 56, context: html, text, full: html, text
    a8364911e404223901ff4cfb4e8f3f56a0e8552c Fri Dec 6 11:40:39 2024 -0800
    coordinating common names (really should be a separate unique list) refs #34370
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 13, context: html, text, full: html, text
    d8fa0018fbf6e18abb5e9ba03ef6421fbf5a5693 Mon Dec 2 11:57:34 2024 -0800
    RefSeq update refs #29545
  • lines changed 6, context: html, text, full: html, text
    34e16a8f5ab2d54f1f49eb488a3bdc4951ba14b5 Thu Dec 5 14:06:59 2024 -0800
    adding a few per user request refs #29545
• src/hg/makeDb/doc/hg19.txt
  • lines changed 14, context: html, text, full: html, text
    4ef2450efd0812268ae30457f8c5d2494821e5a3 Thu Dec 5 04:56:51 2024 -0800
    HGMD 2024 update, refs #34903
• src/hg/makeDb/doc/hg38/hgmd.txt
  • lines changed 3, context: html, text, full: html, text
    4ef2450efd0812268ae30457f8c5d2494821e5a3 Thu Dec 5 04:56:51 2024 -0800
    HGMD 2024 update, refs #34903
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
  • lines changed 3, context: html, text, full: html, text
    4ef2450efd0812268ae30457f8c5d2494821e5a3 Thu Dec 5 04:56:51 2024 -0800
    HGMD 2024 update, refs #34903
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 8, context: html, text, full: html, text
    d8fa0018fbf6e18abb5e9ba03ef6421fbf5a5693 Mon Dec 2 11:57:34 2024 -0800
    RefSeq update refs #29545
  • lines changed 2, context: html, text, full: html, text
    34e16a8f5ab2d54f1f49eb488a3bdc4951ba14b5 Thu Dec 5 14:06:59 2024 -0800
    adding a few per user request refs #29545
  • lines changed 5, context: html, text, full: html, text
    a8364911e404223901ff4cfb4e8f3f56a0e8552c Fri Dec 6 11:40:39 2024 -0800
    coordinating common names (really should be a separate unique list) refs #34370
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 105, context: html, text, full: html, text
    a8364911e404223901ff4cfb4e8f3f56a0e8552c Fri Dec 6 11:40:39 2024 -0800
    coordinating common names (really should be a separate unique list) refs #34370
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 12, context: html, text, full: html, text
    d8fa0018fbf6e18abb5e9ba03ef6421fbf5a5693 Mon Dec 2 11:57:34 2024 -0800
    RefSeq update refs #29545
  • lines changed 29, context: html, text, full: html, text
    a8364911e404223901ff4cfb4e8f3f56a0e8552c Fri Dec 6 11:40:39 2024 -0800
    coordinating common names (really should be a separate unique list) refs #34370
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    d8fa0018fbf6e18abb5e9ba03ef6421fbf5a5693 Mon Dec 2 11:57:34 2024 -0800
    RefSeq update refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    d8fa0018fbf6e18abb5e9ba03ef6421fbf5a5693 Mon Dec 2 11:57:34 2024 -0800
    RefSeq update refs #29545
  • lines changed 2, context: html, text, full: html, text
    a8364911e404223901ff4cfb4e8f3f56a0e8552c Fri Dec 6 11:40:39 2024 -0800
    coordinating common names (really should be a separate unique list) refs #34370
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    d8fa0018fbf6e18abb5e9ba03ef6421fbf5a5693 Mon Dec 2 11:57:34 2024 -0800
    RefSeq update refs #29545
  • lines changed 2, context: html, text, full: html, text
    34e16a8f5ab2d54f1f49eb488a3bdc4951ba14b5 Thu Dec 5 14:06:59 2024 -0800
    adding a few per user request refs #29545
  • lines changed 29, context: html, text, full: html, text
    a8364911e404223901ff4cfb4e8f3f56a0e8552c Fri Dec 6 11:40:39 2024 -0800
    coordinating common names (really should be a separate unique list) refs #34370
• src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    8b758f1e95366bca0ee3ad1c0b5584c16647b793 Wed Dec 4 14:46:28 2024 -0800
    update to 2024-11-26 version refs #34370
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
  • lines changed 15, context: html, text, full: html, text
    8b758f1e95366bca0ee3ad1c0b5584c16647b793 Wed Dec 4 14:46:28 2024 -0800
    update to 2024-11-26 version refs #34370
  • lines changed 46, context: html, text, full: html, text
    e835cfc40dd1a513deb18042880fa0f6065ae422 Wed Dec 4 15:47:51 2024 -0800
    moving legacy assemblies to correct list refs #34370
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 34, context: html, text, full: html, text
    8b758f1e95366bca0ee3ad1c0b5584c16647b793 Wed Dec 4 14:46:28 2024 -0800
    update to 2024-11-26 version refs #34370
  • lines changed 75, context: html, text, full: html, text
    e835cfc40dd1a513deb18042880fa0f6065ae422 Wed Dec 4 15:47:51 2024 -0800
    moving legacy assemblies to correct list refs #34370
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 18, context: html, text, full: html, text
    8b758f1e95366bca0ee3ad1c0b5584c16647b793 Wed Dec 4 14:46:28 2024 -0800
    update to 2024-11-26 version refs #34370
• src/hg/makeDb/trackDb/chainNet.html
  • lines changed 5, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/makeDb/trackDb/chicken/galGal6/chainNet.html
  • lines changed 12, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/makeDb/trackDb/drosophila/dm6/chainNetInsects.html
  • lines changed 12, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/makeDb/trackDb/human/altSeqComposite.html
  • lines changed 13, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/makeDb/trackDb/human/hg19/hg19ChainNet.html
  • lines changed 12, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/makeDb/trackDb/human/hg38/hg38primateChainNet.html
  • lines changed 12, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/makeDb/trackDb/human/hg38/t2tChain.html
  • lines changed 12, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/makeDb/trackDb/human/homoSapiensChainNet.html
  • lines changed 5, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/makeDb/trackDb/human/hs1/description.html
  • lines changed 7, context: html, text, full: html, text
    4e652692f69528bbe90771b9b8fccceaff11ed23 Wed Dec 4 11:04:28 2024 -0800
    fixing some broken links pointed out by a user, refs #34880
• src/hg/makeDb/trackDb/human/placentalChainNet.html
  • lines changed 12, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/makeDb/trackDb/human/primateChainNet.html
  • lines changed 12, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    95209de0574bbd39f283a85ab03f0942edc62852 Thu Dec 5 04:59:56 2024 -0800
    HGMD 2024 label update, refs #34903
• src/hg/makeDb/trackDb/human/vertebrateChainNet.html
  • lines changed 12, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/makeDb/trackDb/humanChainNet.html
  • lines changed 12, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/makeDb/trackDb/mouse/altSeqComposite.html
  • lines changed 13, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/makeDb/trackDb/mouse/mm10/chainNet.html
  • lines changed 12, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/makeDb/trackDb/mouse/mm10/mm10Strains1.html
  • lines changed 11, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/makeDb/trackDb/mouse/mm10/vertebrateChainNet.html
  • lines changed 12, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/makeDb/trackDb/rat/rn6/ratChainNet.html
  • lines changed 12, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/makeDb/trackDb/worm/ce11/chainNetNematodes.html
  • lines changed 13, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/makeDb/trackDb/zebrafish/danRer7/danRer7multipleChainNet.html
  • lines changed 12, context: html, text, full: html, text
    5fc81fc9aeef72ee718678ce93da39337b2db6fe Tue Dec 3 19:50:33 2024 -0800
    fixed incorrectly saying LASTZ is a rename of BLASTZ, added missing LASTZ references
• src/hg/utils/bedPartition/bedPartition.c
  • lines changed 22, context: html, text, full: html, text
    0d573301aec0beac41da09b0152c5e74fbe7f2f2 Sun Dec 8 10:16:19 2024 -0800
    Add generate name to output partation BEDs. Remove -partSize, which made no sense to just group by number of partations. It is replaced by -partMergeSize, to allow for merging partations within a certain distance
• src/hg/utils/bedPartition/tests/expected/test1.ranges.bed
  • lines changed 6, context: html, text, full: html, text
    0d573301aec0beac41da09b0152c5e74fbe7f2f2 Sun Dec 8 10:16:19 2024 -0800
    Add generate name to output partation BEDs. Remove -partSize, which made no sense to just group by number of partations. It is replaced by -partMergeSize, to allow for merging partations within a certain distance
• src/hg/utils/bedPartition/tests/expected/test2.ranges.bed
  • lines changed 4, context: html, text, full: html, text
    0d573301aec0beac41da09b0152c5e74fbe7f2f2 Sun Dec 8 10:16:19 2024 -0800
    Add generate name to output partation BEDs. Remove -partSize, which made no sense to just group by number of partations. It is replaced by -partMergeSize, to allow for merging partations within a certain distance
• src/hg/utils/bedPartition/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    0d573301aec0beac41da09b0152c5e74fbe7f2f2 Sun Dec 8 10:16:19 2024 -0800
    Add generate name to output partation BEDs. Remove -partSize, which made no sense to just group by number of partations. It is replaced by -partMergeSize, to allow for merging partations within a certain distance
• src/inc/common.mk
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    87a8394cc5287fd9f117ade776bb414160f22e7f Mon Dec 9 07:21:58 2024 -0800
    switching to dynamic linking for openssl, Hiram was right, refs #27931
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    9d542df73260c3684c03577730164274dc602740 Mon Dec 9 09:45:12 2024 -0800
    Revert "switching to dynamic linking for openssl, Hiram was right, refs #27931" This reverts commit 87a8394cc5287fd9f117ade776bb414160f22e7f.
• src/inc/srcVersion.h
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    b0a393711fb4a727d4ea8894a617eb12f621824b Mon Dec 9 11:10:55 2024 -0800
    New version number v475
• src/lib/https.c
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    cb1fdec8bd07cde7453f8b3bc3299938504945a5 Thu Dec 5 02:11:37 2024 -0800
    Apparently openssl3 is not handling setting the socket to non-blocking, but I can do it easily myself. fixes #rm34900
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    742b9a6d0c3106759a3086307cb4184cc4d01a77 Thu Dec 5 03:05:25 2024 -0800
    Minor improvement in efficiency for https.c.
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    68b9f4ff4154fcade7c63ae6f7629a5ef721d5a6 Sat Dec 7 21:25:11 2024 -0800
    putting back the way it was just in case.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 4, context: html, text, full: html, text
    3068f3a12a3f6e3c1eb678b06ebffd08fac74403 Mon Dec 9 11:10:16 2024 -0800
    v475 final build, refs #34871

• lines changed: 1039
• files changed: 75