All File Changes

v451_base to v452_preview (2023-07-17 to 2023-07-24) v452

• confs/hgwbeta.hg.conf
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    e2b0cd247716941c3fb99cc5b66a9ddb43372242 Sun Jul 23 01:11:22 2023 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cgilib/annoFormatVep.c
  • lines changed 4, context: html, text, full: html, text
    f3d3d03be73576bd1011a6b34e604c9c6566751b Fri Jul 21 20:55:57 2023 -0700
    Move up NULL check of scoreStr before use (doh). refs MLQ #31782
• src/hg/hgTracks/cds.c
  • lines changed 3, context: html, text, full: html, text
    7f8cbd77c72c1f24031395bbbeaf701e60c01fee Fri Jul 21 15:56:07 2023 -0700
    initialize some pointers to NULL and check if they're NULL before using them refs #31729
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    cb9de88c1e416860a1a69047f6e4c9b338a1cfec Tue Jul 18 17:22:47 2023 -0700
    first cut at liftOver on the fly
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    4806dfe43d8059bae36c0eee610ac1f50170c58e Wed Jul 19 17:41:36 2023 -0700
    add CGI version to track log output
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    901f8a2f2f4ed337dc849212025c0b20a5370a9a Thu Jul 20 06:18:30 2023 -0700
    adding timer to make sure that slow performance warning is shown even if page doesnt load, refs #31576
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    1876769e8169968bc53619c1b8a257ec76b2f74f Thu Jul 20 07:25:06 2023 -0700
    evert "adding timer to make sure that slow performance warning is shown even if page doesnt load, refs #31576" This reverts commit 901f8a2f2f4ed337dc849212025c0b20a5370a9a.
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    cb9de88c1e416860a1a69047f6e4c9b338a1cfec Tue Jul 18 17:22:47 2023 -0700
    first cut at liftOver on the fly
• src/hg/hgTracks/instaPortTrack.c
  • lines changed 104, context: html, text, full: html, text
    cb9de88c1e416860a1a69047f6e4c9b338a1cfec Tue Jul 18 17:22:47 2023 -0700
    first cut at liftOver on the fly
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    cb9de88c1e416860a1a69047f6e4c9b338a1cfec Tue Jul 18 17:22:47 2023 -0700
    first cut at liftOver on the fly
• src/hg/hgTracks/simpleTracks.c
  • lines changed 5, context: html, text, full: html, text
    cb9de88c1e416860a1a69047f6e4c9b338a1cfec Tue Jul 18 17:22:47 2023 -0700
    first cut at liftOver on the fly
• src/hg/hgTracks/wigTrack.c
  • lines changed 2, context: html, text, full: html, text
    e7a5e4344d16066dbde3cb8ab400f0b1c6a55028 Wed Jul 19 13:21:28 2023 -0700
    fix a problem with sequence logos where zero height letters were getting drawn incorrectly
• src/hg/lib/chainNetDbLoad.c
  • lines changed 38, context: html, text, full: html, text
    cb9de88c1e416860a1a69047f6e4c9b338a1cfec Tue Jul 18 17:22:47 2023 -0700
    first cut at liftOver on the fly
• src/hg/lib/customFactory.c
  • lines changed 13, context: html, text, full: html, text
    a3230817faa86411b3dd846711efbad97752c270 Tue Jul 18 09:52:08 2023 -0700
    Improved error message for non-bigDataUrl type specified with bigDataUrl=... instead of inline contents. refs #17455
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    cb9de88c1e416860a1a69047f6e4c9b338a1cfec Tue Jul 18 17:22:47 2023 -0700
    first cut at liftOver on the fly
• src/hg/lib/liftOver.c
  • lines changed 1, context: html, text, full: html, text
    cb9de88c1e416860a1a69047f6e4c9b338a1cfec Tue Jul 18 17:22:47 2023 -0700
    first cut at liftOver on the fly
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    cb9de88c1e416860a1a69047f6e4c9b338a1cfec Tue Jul 18 17:22:47 2023 -0700
    first cut at liftOver on the fly
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 8, context: html, text, full: html, text
    2b46d276f54b4c05bd6ac77b3117eec0bfc81277 Tue Jul 18 11:01:19 2023 -0700
    import of GENCODE V44 final release
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 5, context: html, text, full: html, text
    b1b821e937a458752f9073cec46cebddfbb1b58b Wed Jul 19 11:06:58 2023 -0700
    import of gencode VM33 final release
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 4, context: html, text, full: html, text
    2b46d276f54b4c05bd6ac77b3117eec0bfc81277 Tue Jul 18 11:01:19 2023 -0700
    import of GENCODE V44 final release
  • lines changed 2, context: html, text, full: html, text
    b1b821e937a458752f9073cec46cebddfbb1b58b Wed Jul 19 11:06:58 2023 -0700
    import of gencode VM33 final release
• src/hg/makeDb/trackDb/fantom5.html
  • lines changed 0, context: html, text, full: html, text
    b9d7cbe6071fd2b9c479720de9a407f7ccdb4aec Wed Jul 19 18:09:52 2023 -0700
    Converting files to Unix format using dos2unix, refs #21605
• src/hg/makeDb/trackDb/human/hg19/fantom5.html
  • lines changed 0, context: html, text, full: html, text
    b9d7cbe6071fd2b9c479720de9a407f7ccdb4aec Wed Jul 19 18:09:52 2023 -0700
    Converting files to Unix format using dos2unix, refs #21605
• src/hg/makeDb/trackDb/human/hg19/prs.ra
  • lines changed 84, context: html, text, full: html, text
    e4f165ac18936936b9b09e6c0e334230202ccc53 Thu Jul 20 07:50:37 2023 -0700
    adding Emerge polygenic risk scores track, refs #31772
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    e4f165ac18936936b9b09e6c0e334230202ccc53 Thu Jul 20 07:50:37 2023 -0700
    adding Emerge polygenic risk scores track, refs #31772
• src/hg/makeDb/trackDb/human/hg38/fantom5.html
  • lines changed 0, context: html, text, full: html, text
    b9d7cbe6071fd2b9c479720de9a407f7ccdb4aec Wed Jul 19 18:09:52 2023 -0700
    Converting files to Unix format using dos2unix, refs #21605
• src/hg/makeDb/trackDb/human/hg38/fantom5.ra
  • lines changed 1, context: html, text, full: html, text
    485bf5420c5218ba085f2f7c9451179027274789 Fri Jul 14 12:25:12 2023 -0700
    Updating the html line for the TSS_activity_read_counts track for FANTOM5 on hg38, refs #21605
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    2b46d276f54b4c05bd6ac77b3117eec0bfc81277 Tue Jul 18 11:01:19 2023 -0700
    import of GENCODE V44 final release
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV44.html
  • lines changed 1, context: html, text, full: html, text
    2b46d276f54b4c05bd6ac77b3117eec0bfc81277 Tue Jul 18 11:01:19 2023 -0700
    import of GENCODE V44 final release
• src/hg/makeDb/trackDb/human/hs1/instaPortHg38.ra
  • lines changed 32, context: html, text, full: html, text
    cb9de88c1e416860a1a69047f6e4c9b338a1cfec Tue Jul 18 17:22:47 2023 -0700
    first cut at liftOver on the fly
• src/hg/makeDb/trackDb/human/hs1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    cb9de88c1e416860a1a69047f6e4c9b338a1cfec Tue Jul 18 17:22:47 2023 -0700
    first cut at liftOver on the fly
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    b1b821e937a458752f9073cec46cebddfbb1b58b Wed Jul 19 11:06:58 2023 -0700
    import of gencode VM33 final release
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM33.html
  • lines changed 1, context: html, text, full: html, text
    b1b821e937a458752f9073cec46cebddfbb1b58b Wed Jul 19 11:06:58 2023 -0700
    import of gencode VM33 final release
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 5, context: html, text, full: html, text
    cb9de88c1e416860a1a69047f6e4c9b338a1cfec Tue Jul 18 17:22:47 2023 -0700
    first cut at liftOver on the fly
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
  • lines changed 10, context: html, text, full: html, text
    ea200cd254fbe9b6d231ee610ed51ed8c0eef899 Fri Jul 14 10:56:09 2023 -0700
    Added comments about false mutations induced in XBD, XBP, XBR and XBS when placed in BA.5 and later in BA.2.75.
  • lines changed 5, context: html, text, full: html, text
    c1f41351d9731fd77bc1fcdbcd2f41a91ede93a0 Sun Jul 23 15:11:31 2023 -0700
    Mask noisy sites 21994, 21995, 21998 in XBB (starting 2023-07-21 build). Pick a new representative for XBB.1.5 since order of mutations was switched (now T17124C > T23018C).
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 10, context: html, text, full: html, text
    13dc9939f18ed86230d4e9005bd4ef596214c4e2 Fri Jul 14 08:57:09 2023 -0700
    New lineages.
  • lines changed 5, context: html, text, full: html, text
    1c8ebe4c5ceceaeeee66ea1e68c252d51fde9f09 Fri Jul 14 10:06:15 2023 -0700
    Changes to XBD, XBP, XBR, XBS: they were removed and replaced, moving them from BA.5 to BA.2.75 which caused differences in false mutations from branch-specific masking.
  • lines changed 52, context: html, text, full: html, text
    64f081cb594a5afadce471a0c48eb4de92c88141 Sun Jul 23 15:14:57 2023 -0700
    New lineages. Also mask C21998A in several XBB sublineages because 21998 is now masked in XBB in branchSpecificMask.yml.
• src/htslib/README
  • lines changed 10, context: html, text, full: html, text
    e38129ab0cca601427c31317b9ab4eb7c0061edf Thu Jul 20 12:03:53 2023 -0700
    apparently htslib/ is obsolete
• src/htslib/knetfile.c
  • lines changed 2, context: html, text, full: html, text
    06b0009211c47fc85787ac3d9bb8a55652c13556 Thu Jul 20 11:39:39 2023 -0700
    HTTP/1.1 without persistent connections. Addresses complaints that byterange headers should not be used with old HTTP/1.0, or that HTTP/1.0 should no longer be used. fixes #31774
• src/inc/gff3.h
  • lines changed 1, context: html, text, full: html, text
    4fb78c6bbad5852d825f348e8ec13faaa6b46f5c Tue Jul 18 12:37:09 2023 -0700
    allow UTR as a discontinouis feature
• src/inc/https.h
  • lines changed 1, context: html, text, full: html, text
    06b0009211c47fc85787ac3d9bb8a55652c13556 Thu Jul 20 11:39:39 2023 -0700
    HTTP/1.1 without persistent connections. Addresses complaints that byterange headers should not be used with old HTTP/1.0, or that HTTP/1.0 should no longer be used. fixes #31774
• src/lib/gff3.c
  • lines changed 2, context: html, text, full: html, text
    4fb78c6bbad5852d825f348e8ec13faaa6b46f5c Tue Jul 18 12:37:09 2023 -0700
    allow UTR as a discontinouis feature
• src/lib/https.c
  • lines changed 6, context: html, text, full: html, text
    06b0009211c47fc85787ac3d9bb8a55652c13556 Thu Jul 20 11:39:39 2023 -0700
    HTTP/1.1 without persistent connections. Addresses complaints that byterange headers should not be used with old HTTP/1.0, or that HTTP/1.0 should no longer be used. fixes #31774
• src/lib/net.c
  • lines changed 10, context: html, text, full: html, text
    06b0009211c47fc85787ac3d9bb8a55652c13556 Thu Jul 20 11:39:39 2023 -0700
    HTTP/1.1 without persistent connections. Addresses complaints that byterange headers should not be used with old HTTP/1.0, or that HTTP/1.0 should no longer be used. fixes #31774
• src/utils/louisParse/louisParse.c
  • lines changed 138, context: html, text, full: html, text
    9c1ec624e439a173b8210cc0522961c00777b8cc Wed Jul 19 16:17:00 2023 -0700
    add the little program I'm using to generate log file tales for Louis
• src/utils/louisParse/makefile
  • lines changed 3, context: html, text, full: html, text
    9c1ec624e439a173b8210cc0522961c00777b8cc Wed Jul 19 16:17:00 2023 -0700
    add the little program I'm using to generate log file tales for Louis
• src/utils/qa/weeklybld/buildEnv.csh
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    1d5ae1cc249ca2ed0f3ed01b502e2b5fb4267d76 Mon Jul 24 10:46:49 2023 -0700
    v452 preview1

• lines changed: 597
• files changed: 49