All File Changes

v374_preview2 to v374_base (2018-11-05 to 2018-11-12) v374

• python/lib/ucscGb/qa/qaUtils.py
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    b4a83c38d23276e9ece4f3bd038b7ba49a4e11cf Thu Nov 8 13:37:45 2018 -0800
    qaGbTracks now reports stderr when a command fails, and call to bedIntersect fixed, refs #21010 '
• python/lib/ucscGb/qa/tables/checkGapOverlap.py
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    b4a83c38d23276e9ece4f3bd038b7ba49a4e11cf Thu Nov 8 13:37:45 2018 -0800
    qaGbTracks now reports stderr when a command fails, and call to bedIntersect fixed, refs #21010 '
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    7c96305a8cc177ad7792386ab9978f66fc82e0a2 Thu Nov 8 14:26:53 2018 -0800
    make filterBy and labels be smarter about being configured at the view level
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    5dea522615a407b872263372cc02e848f1ce03a3 Thu Nov 8 14:34:28 2018 -0800
    oops... some functions needed modifying from label change
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    7c96305a8cc177ad7792386ab9978f66fc82e0a2 Thu Nov 8 14:26:53 2018 -0800
    make filterBy and labels be smarter about being configured at the view level
• src/hg/hgc/barChartClick.c
  • lines changed 1, context: html, text, full: html, text
    19161f281baa640afdecdd0593b7025a7bab2f1f Wed Nov 7 11:16:26 2018 -0800
    Quoting barChartUnits string substition in order to allow multi word units in trackDb, refs #22064
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    197873a2610df8024481f5233470e13c6b140d45 Wed Nov 7 15:34:41 2018 -0800
    feedback after code review, refs #22414
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 21, context: html, text, full: html, text
    daff686dad039ad297c503f4913072b901ae3eb7 Thu Nov 8 11:40:06 2018 -0800
    adding chr_alt section to FAQdownloads.html, refs #14284
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 28, context: html, text, full: html, text
    d539859f1af69b7128762420cafe128cf8e20fc1 Mon Nov 12 09:05:59 2018 -0800
    making news announcement for BLAT ALL
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 4, context: html, text, full: html, text
    b1f75ee8ac887fc627d5d5dac516cda9e44a76dd Fri Nov 9 15:44:11 2018 -0800
    Adding a hint about parent myCompite on in the track Inheritance blurb based on input from Sol refs #22418
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 42, context: html, text, full: html, text
    ab10bbc0f630bce030bbf3cb683833fb6279edeb Tue Nov 6 15:39:43 2018 -0800
    Creating ponAbe3 news artcile in newsarch.html and adding link to indexNews.html, refs #20980
  • lines changed 32, context: html, text, full: html, text
    7466b46636ef48a8adb2ee275e6bd38a5deae05f Tue Nov 6 16:03:27 2018 -0800
    Adding GH announcement to news/newsfeed ref#22048
  • lines changed 3, context: html, text, full: html, text
    649ee09e02ff89cd0c814df6f2751cee3074bd69 Wed Nov 7 09:24:34 2018 -0800
    Fixing release dates and changing supporting URL for GH ref#22048
  • lines changed 2, context: html, text, full: html, text
    4e45b46f333af031fa7417e0deb4551cbba02f86 Thu Nov 8 11:02:43 2018 -0800
    adding db=hg19 to the news release URLs to prevent errors
  • lines changed 2, context: html, text, full: html, text
    5abae6651d3a9b5f21bfbc0b8cf8f6cfc0c24b04 Thu Nov 8 14:40:41 2018 -0800
    added a few more internal contributors to the interact work
  • lines changed 36, context: html, text, full: html, text
    7942e327e24d6ef43f005a1b3bbceb727add3c08 Sat Nov 10 18:15:23 2018 -0800
    staging announcemenet for new video
  • lines changed 10, context: html, text, full: html, text
    563857623d23dec0158377bcc06a4afc2592f854 Sat Nov 10 19:53:00 2018 -0800
    adding link to YouTube vid on announcement and on training page
  • lines changed 1, context: html, text, full: html, text
    a8f4adb92e213c8eff0a6ca5a51c08470a15c2a5 Sat Nov 10 20:00:15 2018 -0800
    tiny edit. added one word
  • lines changed 1, context: html, text, full: html, text
    b2de5c6d740989b438da62ab75b4e479a1fc1e01 Sat Nov 10 20:23:06 2018 -0800
    fixed spelling of transcript
  • lines changed 9, context: html, text, full: html, text
    d539859f1af69b7128762420cafe128cf8e20fc1 Mon Nov 12 09:05:59 2018 -0800
    making news announcement for BLAT ALL
  • lines changed 50, context: html, text, full: html, text
    477dd29a38e92f7bd2dc0b07527625a152ce2c77 Mon Nov 12 09:14:33 2018 -0800
    committing BLAT ALL to newsarch.html and indexNews.html, refs #18992
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 12, context: html, text, full: html, text
    32e334f62dc9324ce4ba208ac985cd4549b19ba2 Thu Nov 8 12:31:24 2018 -0800
    early release of 2019 NAR (advance article)
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    ab10bbc0f630bce030bbf3cb683833fb6279edeb Tue Nov 6 15:39:43 2018 -0800
    Creating ponAbe3 news artcile in newsarch.html and adding link to indexNews.html, refs #20980
  • lines changed 13, context: html, text, full: html, text
    7466b46636ef48a8adb2ee275e6bd38a5deae05f Tue Nov 6 16:03:27 2018 -0800
    Adding GH announcement to news/newsfeed ref#22048
  • lines changed 24, context: html, text, full: html, text
    0fa55d10ca092017b4d3b7dfe7c14ce1186f5291 Tue Nov 6 16:11:39 2018 -0800
    Adding GH announcement to index/news, also resolving conflicts with ponAbe3 news release ref#22048
  • lines changed 2, context: html, text, full: html, text
    649ee09e02ff89cd0c814df6f2751cee3074bd69 Wed Nov 7 09:24:34 2018 -0800
    Fixing release dates and changing supporting URL for GH ref#22048
  • lines changed 11, context: html, text, full: html, text
    7942e327e24d6ef43f005a1b3bbceb727add3c08 Sat Nov 10 18:15:23 2018 -0800
    staging announcemenet for new video
  • lines changed 9, context: html, text, full: html, text
    d539859f1af69b7128762420cafe128cf8e20fc1 Mon Nov 12 09:05:59 2018 -0800
    making news announcement for BLAT ALL
  • lines changed 17, context: html, text, full: html, text
    477dd29a38e92f7bd2dc0b07527625a152ce2c77 Mon Nov 12 09:14:33 2018 -0800
    committing BLAT ALL to newsarch.html and indexNews.html, refs #18992
• src/hg/htdocs/staff.html
  • lines changed 1, context: html, text, full: html, text
    dc21ac608a892d3b0ac40aa2565fb339d58c076d Wed Nov 7 09:20:28 2018 -0800
    Updating the staff.html page, no Redmine.
• src/hg/htdocs/training/index.html
  • lines changed 32, context: html, text, full: html, text
    44f75350effe28df8e94affedd62816104f4a0c5 Tue Nov 6 12:13:39 2018 -0800
    dropping completed Cincinnati Med workshop. adding City of Hope and some others to the future list
  • lines changed 11, context: html, text, full: html, text
    16f8d0d789dfdd47741cc432629fc315b0cbdddb Wed Nov 7 15:43:38 2018 -0800
    adding links for City of Hope workshop. dropping ref to inactive OpenHelix link found by link checker
  • lines changed 17, context: html, text, full: html, text
    563857623d23dec0158377bcc06a4afc2592f854 Sat Nov 10 19:53:00 2018 -0800
    adding link to YouTube vid on announcement and on training page
• src/hg/inc/encode/wgEncodeGencodeGeneSymbol.h
  • lines changed 64, context: html, text, full: html, text
    0bba06928b53c75f8f04c13f50319650982938b8 Sat Nov 10 15:47:34 2018 -0800
    renamed new gencode table for hgnc to geneSymbol, since mouse has MGI not HGNC. Import of GENCODE mouse VM19;
• src/hg/inc/encode/wgEncodeGencodeHgnc.h
  • lines changed 64, context: html, text, full: html, text
    00a0d93a2032a4547ae62657fb98edd8247888ce Fri Nov 9 18:24:43 2018 -0800
    added gencode V29 final
  • lines changed 64, context: html, text, full: html, text
    0bba06928b53c75f8f04c13f50319650982938b8 Sat Nov 10 15:47:34 2018 -0800
    renamed new gencode table for hgnc to geneSymbol, since mouse has MGI not HGNC. Import of GENCODE mouse VM19;
• src/hg/inc/hubConnect.h
  • lines changed 3, context: html, text, full: html, text
    dc10e2f415c03138342729c5d7667bf38bdae534 Tue Nov 6 14:03:29 2018 -0800
    use udcTimeout instead of hub.timeToCheck as timeout before rechecking the hubs after an error.
• src/hg/inc/hui.h
  • lines changed 2, context: html, text, full: html, text
    7c96305a8cc177ad7792386ab9978f66fc82e0a2 Thu Nov 8 14:26:53 2018 -0800
    make filterBy and labels be smarter about being configured at the view level
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    94ca49469aa9a2c7eb6d58ce0ca45eaa3289db2c Mon Nov 12 10:02:08 2018 -0800
    New version number v374
• src/hg/lib/barChartUi.c
  • lines changed 1, context: html, text, full: html, text
    5dea522615a407b872263372cc02e848f1ce03a3 Thu Nov 8 14:34:28 2018 -0800
    oops... some functions needed modifying from label change
• src/hg/lib/customFactory.c
  • lines changed 21, context: html, text, full: html, text
    bde74890d08e6f51bccf7bcbb8f8e75955682b9f Tue Nov 6 12:37:39 2018 -0800
    New version #39 fixes somes some access-time touching issues. For a long time Hiram has made the case that touching cts with bigDataUrl in cache is not needed. And skipping it might help the trash cleaner run faster, and keep from locking up unused udc cache space. So I have removed the touchUdc routine in customFactory.c since it is no longer needed. Also, the multiRegionsBedUrl and customComposite files were not getting access time touched correctly.
• src/hg/lib/encode/wgEncodeGencodeGeneSymbol.as
  • lines changed 6, context: html, text, full: html, text
    0bba06928b53c75f8f04c13f50319650982938b8 Sat Nov 10 15:47:34 2018 -0800
    renamed new gencode table for hgnc to geneSymbol, since mouse has MGI not HGNC. Import of GENCODE mouse VM19;
• src/hg/lib/encode/wgEncodeGencodeGeneSymbol.c
  • lines changed 126, context: html, text, full: html, text
    0bba06928b53c75f8f04c13f50319650982938b8 Sat Nov 10 15:47:34 2018 -0800
    renamed new gencode table for hgnc to geneSymbol, since mouse has MGI not HGNC. Import of GENCODE mouse VM19;
  • lines changed 1, context: html, text, full: html, text
    22e980eb254f6bfc8c6b5c9ef7a067297d96bcd4 Sun Nov 11 04:52:32 2018 -0800
    missed manual edit of genereated file
• src/hg/lib/encode/wgEncodeGencodeGeneSymbol.sql
  • lines changed 12, context: html, text, full: html, text
    0bba06928b53c75f8f04c13f50319650982938b8 Sat Nov 10 15:47:34 2018 -0800
    renamed new gencode table for hgnc to geneSymbol, since mouse has MGI not HGNC. Import of GENCODE mouse VM19;
• src/hg/lib/encode/wgEncodeGencodeHgnc.as
  • lines changed 6, context: html, text, full: html, text
    00a0d93a2032a4547ae62657fb98edd8247888ce Fri Nov 9 18:24:43 2018 -0800
    added gencode V29 final
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    0bba06928b53c75f8f04c13f50319650982938b8 Sat Nov 10 15:47:34 2018 -0800
    renamed new gencode table for hgnc to geneSymbol, since mouse has MGI not HGNC. Import of GENCODE mouse VM19;
• src/hg/lib/encode/wgEncodeGencodeHgnc.c
  • lines changed 126, context: html, text, full: html, text
    00a0d93a2032a4547ae62657fb98edd8247888ce Fri Nov 9 18:24:43 2018 -0800
    added gencode V29 final
  • lines changed 126, context: html, text, full: html, text
    0bba06928b53c75f8f04c13f50319650982938b8 Sat Nov 10 15:47:34 2018 -0800
    renamed new gencode table for hgnc to geneSymbol, since mouse has MGI not HGNC. Import of GENCODE mouse VM19;
• src/hg/lib/encode/wgEncodeGencodeHgnc.sql
  • lines changed 12, context: html, text, full: html, text
    00a0d93a2032a4547ae62657fb98edd8247888ce Fri Nov 9 18:24:43 2018 -0800
    added gencode V29 final
  • lines changed 12, context: html, text, full: html, text
    0bba06928b53c75f8f04c13f50319650982938b8 Sat Nov 10 15:47:34 2018 -0800
    renamed new gencode table for hgnc to geneSymbol, since mouse has MGI not HGNC. Import of GENCODE mouse VM19;
• src/hg/lib/hubConnect.c
  • lines changed 4, context: html, text, full: html, text
    ba7ae795dae786e94a5e131ddf85b84e90c7c06e Tue Nov 6 08:49:24 2018 -0800
    don't open hubs that aren't connected.
  • lines changed 4, context: html, text, full: html, text
    dc10e2f415c03138342729c5d7667bf38bdae534 Tue Nov 6 14:03:29 2018 -0800
    use udcTimeout instead of hub.timeToCheck as timeout before rechecking the hubs after an error.
• src/hg/lib/hui.c
  • lines changed 20, context: html, text, full: html, text
    7c96305a8cc177ad7792386ab9978f66fc82e0a2 Thu Nov 8 14:26:53 2018 -0800
    make filterBy and labels be smarter about being configured at the view level
• src/hg/lib/interactUi.c
  • lines changed 1, context: html, text, full: html, text
    a4766721c2b45fc57b270df079c57f86b60e430d Wed Nov 7 17:05:10 2018 -0800
    fix scoreFilter'ing in bigInteract tracks.
  • lines changed 1, context: html, text, full: html, text
    5dea522615a407b872263372cc02e848f1ce03a3 Thu Nov 8 14:34:28 2018 -0800
    oops... some functions needed modifying from label change
• src/hg/lib/makefile
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    0bba06928b53c75f8f04c13f50319650982938b8 Sat Nov 10 15:47:34 2018 -0800
    renamed new gencode table for hgnc to geneSymbol, since mouse has MGI not HGNC. Import of GENCODE mouse VM19;
• src/hg/makeDb/doc/bosTau9/initialBuild.txt
  • lines changed 993, context: html, text, full: html, text
    abfb32782fdf69479add4c6425693aa6843da1e6 Tue Nov 6 12:00:49 2018 -0800
    beginning bosTau9 refs #22425
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    aeb72ec96ea4bd581db5f9bc2ce68863aadee06b Tue Nov 6 15:44:29 2018 -0800
    running repeat masker refs #22425
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    7c9234b9239a9c8223b7b82ee176fa16fca41b95 Thu Nov 8 13:35:40 2018 -0800
    genbank set up running hg38 mm10 lastz chain net refs #22425
• src/hg/makeDb/doc/hg19.txt
  • lines changed 36, context: html, text, full: html, text
    97ce2992da15a56f4bf44c30918586189ebed5d4 Sat Nov 10 08:00:59 2018 -0800
    fixed release data label on All GENCODE V29
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    e35316da983301ef1a6fb40490a08e52333e9908 Sat Nov 10 11:34:18 2018 -0800
    import of All GENCODE v29lift37
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    5c47f34eb9751e62455c711c73952bc90878b34e Sun Nov 11 13:31:13 2018 -0800
    crispr 10K run done on hg19 refs #21987
• src/hg/makeDb/doc/hg38/hg38.txt
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    00a0d93a2032a4547ae62657fb98edd8247888ce Fri Nov 9 18:24:43 2018 -0800
    added gencode V29 final
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    97ce2992da15a56f4bf44c30918586189ebed5d4 Sat Nov 10 08:00:59 2018 -0800
    fixed release data label on All GENCODE V29
• src/hg/makeDb/doc/mm10.txt
  • lines changed 76, context: html, text, full: html, text
    e9aebd4215542bcbda89eb0b114d0516488ed945 Thu Nov 8 10:38:41 2018 -0800
    starting mm10 vs. bosTau9 lastz chainNet refs #22425
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    0bba06928b53c75f8f04c13f50319650982938b8 Sat Nov 10 15:47:34 2018 -0800
    renamed new gencode table for hgnc to geneSymbol, since mouse has MGI not HGNC. Import of GENCODE mouse VM19;
  • lines changed 12, context: html, text, full: html, text
    4c34bd001dc210b27e71e8b6075fa22c64286538 Sun Nov 11 13:25:24 2018 -0800
    almost done with bosTau9 lastz chainNet refs #22425
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    75ea5687d7991a8db97bdce360b2887684ecc937 Mon Nov 12 09:15:06 2018 -0800
    done with hg38 lastz chainNet refs #22425
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes17.sh
  • lines changed 2, context: html, text, full: html, text
    4121dfe8f09b481700227d625b28cb5a61962b1a Mon Nov 5 10:12:15 2018 -0800
    add version number to /gbdb/hg38/knownGene.bb
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes19.sh
  • lines changed 2, context: html, text, full: html, text
    4121dfe8f09b481700227d625b28cb5a61962b1a Mon Nov 5 10:12:15 2018 -0800
    add version number to /gbdb/hg38/knownGene.bb
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 22, context: html, text, full: html, text
    9272a6a9b7fe172e30d39dc9a3a4311f629f7220 Fri Nov 9 11:40:14 2018 -0800
    adding bosTau9 refs #22425
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    045052d120686b40311642e526d5c837d0524f13 Thu Nov 8 15:33:22 2018 -0800
    Adding galGal6 to this file list
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    82f255866510c66e9936acca6bd47e5a6ec8f725 Thu Nov 8 13:32:27 2018 -0800
    adding bosTau9 refs #22425
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    70a524b33b2b8bad532866b236a36494c8c976e9 Mon Nov 5 10:35:57 2018 -0800
    Adding ponAbe3 to rr.dbs file, refs #20980
• src/hg/makeDb/outside/gencode/gencodeGenerateTrackDbs
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    00a0d93a2032a4547ae62657fb98edd8247888ce Fri Nov 9 18:24:43 2018 -0800
    added gencode V29 final
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    0bba06928b53c75f8f04c13f50319650982938b8 Sat Nov 10 15:47:34 2018 -0800
    renamed new gencode table for hgnc to geneSymbol, since mouse has MGI not HGNC. Import of GENCODE mouse VM19;
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
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    00a0d93a2032a4547ae62657fb98edd8247888ce Fri Nov 9 18:24:43 2018 -0800
    added gencode V29 final
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    97ce2992da15a56f4bf44c30918586189ebed5d4 Sat Nov 10 08:00:59 2018 -0800
    fixed release data label on All GENCODE V29
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    e35316da983301ef1a6fb40490a08e52333e9908 Sat Nov 10 11:34:18 2018 -0800
    import of All GENCODE v29lift37
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    0bba06928b53c75f8f04c13f50319650982938b8 Sat Nov 10 15:47:34 2018 -0800
    renamed new gencode table for hgnc to geneSymbol, since mouse has MGI not HGNC. Import of GENCODE mouse VM19;
• src/hg/makeDb/schema/all.joiner
  • lines changed 5, context: html, text, full: html, text
    f67ecd77604d1cbf071bb1e598efb9d634652ce7 Thu Nov 8 11:16:41 2018 -0800
    adding mm10 strains1 ext and seq file table rules refs #20280
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    85af5b05fba85ff364442b39139f4592f5862932 Thu Nov 8 11:50:41 2018 -0800
    adding bosTau9 rules refs #22425
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    00a0d93a2032a4547ae62657fb98edd8247888ce Fri Nov 9 18:24:43 2018 -0800
    added gencode V29 final
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    e35316da983301ef1a6fb40490a08e52333e9908 Sat Nov 10 11:34:18 2018 -0800
    import of All GENCODE v29lift37
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    0bba06928b53c75f8f04c13f50319650982938b8 Sat Nov 10 15:47:34 2018 -0800
    renamed new gencode table for hgnc to geneSymbol, since mouse has MGI not HGNC. Import of GENCODE mouse VM19;
• src/hg/makeDb/trackDb/apis/apiMel2/brhInparalog.html
  • lines changed 1, context: html, text, full: html, text
    01e8a2ac231439958cc86cb346724822b4307c3e Wed Nov 7 09:22:20 2018 -0800
    Updating redirected links for apiMel2 found by the uiLinks cronjob, no Redmine
• src/hg/makeDb/trackDb/apis/xenoMrna.html
  • lines changed 1, context: html, text, full: html, text
    01e8a2ac231439958cc86cb346724822b4307c3e Wed Nov 7 09:22:20 2018 -0800
    Updating redirected links for apiMel2 found by the uiLinks cronjob, no Redmine
• src/hg/makeDb/trackDb/blatFugu.html
  • lines changed 1, context: html, text, full: html, text
    ccb003fa2b99c2159fce92814b7f502492ac5bde Fri Nov 9 08:32:15 2018 -0800
    Updating http to https for dm1, uiLinks cronjob.
• src/hg/makeDb/trackDb/cow/bosTau9/description.html
  • lines changed 64, context: html, text, full: html, text
    520d57f838925d11fcf21da4b41eee5359ecc7f4 Tue Nov 6 13:23:46 2018 -0800
    adding bosTau9 to the build refs #22425
• src/hg/makeDb/trackDb/cow/bosTau9/gap.html
  • lines changed 29, context: html, text, full: html, text
    520d57f838925d11fcf21da4b41eee5359ecc7f4 Tue Nov 6 13:23:46 2018 -0800
    adding bosTau9 to the build refs #22425
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    f0c97e8e3eb888112e3ad6287dbbfe04ef11fb62 Thu Nov 8 12:55:40 2018 -0800
    indicate no gaps and hid the gap track refs #22425
• src/hg/makeDb/trackDb/cow/bosTau9/gold.html
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    520d57f838925d11fcf21da4b41eee5359ecc7f4 Tue Nov 6 13:23:46 2018 -0800
    adding bosTau9 to the build refs #22425
• src/hg/makeDb/trackDb/cow/bosTau9/trackDb.ra
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    520d57f838925d11fcf21da4b41eee5359ecc7f4 Tue Nov 6 13:23:46 2018 -0800
    adding bosTau9 to the build refs #22425
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    2b9cfcbece1a18da8d98c50a5d39483035590d6e Tue Nov 6 15:28:03 2018 -0800
    add assembly/gold table search rule refs #22425
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    f0c97e8e3eb888112e3ad6287dbbfe04ef11fb62 Thu Nov 8 12:55:40 2018 -0800
    indicate no gaps and hid the gap track refs #22425
• src/hg/makeDb/trackDb/drosophila/chainDp2.html
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    ccb003fa2b99c2159fce92814b7f502492ac5bde Fri Nov 9 08:32:15 2018 -0800
    Updating http to https for dm1, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/dm1/anophelesEcores.html
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    ccb003fa2b99c2159fce92814b7f502492ac5bde Fri Nov 9 08:32:15 2018 -0800
    Updating http to https for dm1, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/mzDy1Dp2Ag1_phast.html
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    ccb003fa2b99c2159fce92814b7f502492ac5bde Fri Nov 9 08:32:15 2018 -0800
    Updating http to https for dm1, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/netDp2.html
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    ccb003fa2b99c2159fce92814b7f502492ac5bde Fri Nov 9 08:32:15 2018 -0800
    Updating http to https for dm1, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
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    0bba06928b53c75f8f04c13f50319650982938b8 Sat Nov 10 15:47:34 2018 -0800
    renamed new gencode table for hgnc to geneSymbol, since mouse has MGI not HGNC. Import of GENCODE mouse VM19;
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
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    97ce2992da15a56f4bf44c30918586189ebed5d4 Sat Nov 10 08:00:59 2018 -0800
    fixed release data label on All GENCODE V29
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV29lift37.html
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    e35316da983301ef1a6fb40490a08e52333e9908 Sat Nov 10 11:34:18 2018 -0800
    import of All GENCODE v29lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV29lift37.ra
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    e35316da983301ef1a6fb40490a08e52333e9908 Sat Nov 10 11:34:18 2018 -0800
    import of All GENCODE v29lift37
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
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    4121dfe8f09b481700227d625b28cb5a61962b1a Mon Nov 5 10:12:15 2018 -0800
    add version number to /gbdb/hg38/knownGene.bb
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
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    4121dfe8f09b481700227d625b28cb5a61962b1a Mon Nov 5 10:12:15 2018 -0800
    add version number to /gbdb/hg38/knownGene.bb
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    6790025e18f385351106f897480594cd05ca91d5 Wed Nov 7 13:39:46 2018 -0800
    Fixing pennantIcons for GH and miRnaAtlas ref#18508, #22048
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    c399e8d185d6692a3039b0b0b9b6c05ae42db061 Thu Nov 8 10:48:58 2018 -0800
    Removing release tags to hold miRNA track back from RR/Asia/Euro/Public #18508
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV29.html
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    97ce2992da15a56f4bf44c30918586189ebed5d4 Sat Nov 10 08:00:59 2018 -0800
    fixed release data label on All GENCODE V29
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV29.ra
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    97ce2992da15a56f4bf44c30918586189ebed5d4 Sat Nov 10 08:00:59 2018 -0800
    fixed release data label on All GENCODE V29
• src/hg/makeDb/trackDb/human/trackDb.geneHancer.ra
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    4e60a6f7f6b4af392b8d857f67f782ea8e56cfcf Mon Nov 5 17:37:37 2018 -0800
    Disable score filter on GeneHancer interact tracks, as this is not currently working. refs #21917
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    6790025e18f385351106f897480594cd05ca91d5 Wed Nov 7 13:39:46 2018 -0800
    Fixing pennantIcons for GH and miRnaAtlas ref#18508, #22048
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    04250e1501da1173d6596090e0169fa2f04fc0a8 Wed Nov 7 16:16:06 2018 -0800
    Fix bad view settings. refs #22048
• src/hg/makeDb/trackDb/makefile
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    520d57f838925d11fcf21da4b41eee5359ecc7f4 Tue Nov 6 13:23:46 2018 -0800
    adding bosTau9 to the build refs #22425
• src/hg/makeDb/trackDb/miRNA.html
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    ccb003fa2b99c2159fce92814b7f502492ac5bde Fri Nov 9 08:32:15 2018 -0800
    Updating http to https for dm1, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gencode.ra
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    0bba06928b53c75f8f04c13f50319650982938b8 Sat Nov 10 15:47:34 2018 -0800
    renamed new gencode table for hgnc to geneSymbol, since mouse has MGI not HGNC. Import of GENCODE mouse VM19;
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM19.html
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    0bba06928b53c75f8f04c13f50319650982938b8 Sat Nov 10 15:47:34 2018 -0800
    renamed new gencode table for hgnc to geneSymbol, since mouse has MGI not HGNC. Import of GENCODE mouse VM19;
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM19.ra
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    0bba06928b53c75f8f04c13f50319650982938b8 Sat Nov 10 15:47:34 2018 -0800
    renamed new gencode table for hgnc to geneSymbol, since mouse has MGI not HGNC. Import of GENCODE mouse VM19;
• src/hg/makeDb/trackDb/refSeqComposite.html
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    118faf291bda6985bea9a16d2eec7f9d424c64ba Mon Nov 5 10:02:15 2018 -0800
    add space btw number 45 and units kb, missed in CR. Refs #22348
• src/hg/makeDb/trackDb/tagTypes.tab
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    4e60a6f7f6b4af392b8d857f67f782ea8e56cfcf Mon Nov 5 17:37:37 2018 -0800
    Disable score filter on GeneHancer interact tracks, as this is not currently working. refs #21917
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    d5fe3b53cdb1439931f37b5e87e3172472009e75 Sat Nov 10 08:09:13 2018 -0800
    added tagType entry for new GENCODE table
• src/hg/utils/automation/makeGenomeDb.pl
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    0c13306bc9defeac3d959a73c2942e41cf6a6014 Thu Nov 8 13:02:46 2018 -0800
    properly indicate no gaps refs #22425
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.psl
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    bb12e20332ff8cdf45003f41268011e95ca64221 Mon Nov 5 15:30:59 2018 -0800
    In pslFromGff3Cigar, we should not reverse the order of CIGAR operations when strand is +- or -+. I'm not sure if the spec covers the -- case for Gap, so making that an errAbort until we get input with that combo. Tested with BLAT. Discovered the problem when our altSeqLiftOverPsl alignments on the - strand were a sea of mismatches in hgTracks. refs #18854 note-27.
• src/hg/utils/otto/clinvar/clinVarToBed
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    e1b869378b6c55ad8e986652a8ad379ac0f9f3a5 Mon Nov 12 06:08:38 2018 -0800
    adding new clinvar format of names
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
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    bde74890d08e6f51bccf7bcbb8f8e75955682b9f Tue Nov 6 12:37:39 2018 -0800
    New version #39 fixes somes some access-time touching issues. For a long time Hiram has made the case that touching cts with bigDataUrl in cache is not needed. And skipping it might help the trash cleaner run faster, and keep from locking up unused udc cache space. So I have removed the touchUdc routine in customFactory.c since it is no longer needed. Also, the multiRegionsBedUrl and customComposite files were not getting access time touched correctly.
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    e2e7c4659bbd523f7141894149c2dd4aa8275459 Sun Nov 11 11:45:35 2018 -0800
    Version 40 of refreshNamedSessionCustomTracks. Added command-line options to allow testing that various error conditions have taken place in the child process, such as exitCode non-zero, errAbort, timeout, and segfault. Exposed timeout commandline option for flexibility.
• src/inc/srcVersion.h
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    94ca49469aa9a2c7eb6d58ce0ca45eaa3289db2c Mon Nov 12 10:02:08 2018 -0800
    New version number v374
• src/lib/https.c
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    883079a5fc2edb6f85650f3f34fd1eabaed81d25 Sun Nov 11 11:48:09 2018 -0800
    Fixed typo in error message in https.c. It uses sigwait, not sigtimedwait (which is not available on osx).
• src/lib/psl.c
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    bb12e20332ff8cdf45003f41268011e95ca64221 Mon Nov 5 15:30:59 2018 -0800
    In pslFromGff3Cigar, we should not reverse the order of CIGAR operations when strand is +- or -+. I'm not sure if the spec covers the -- case for Gap, so making that an errAbort until we get input with that combo. Tested with BLAT. Discovered the problem when our altSeqLiftOverPsl alignments on the - strand were a sea of mismatches in hgTracks. refs #18854 note-27.
• src/product/README.txt
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    044b7ed97d32f43e1aa2ea6680d0fbfbe50c04d5 Wed Nov 7 09:50:00 2018 -0800
    Removing CentOS broken link ref#22339
• src/utils/qa/qaGbTracks
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    cfb0157aeb4b9858b42baa0cb6a2aac6536ea55e Tue Nov 6 07:25:29 2018 -0800
    Forgot else statement if tables are formatted correctly, refs #22364
• src/utils/qa/weeklybld/buildEnv.csh
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    ca74493524f26c4dc389d376b6ad36940004a8a4 Mon Nov 12 10:01:25 2018 -0800
    v374 final build, refs #22357

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