All File Changes

v392_preview to v392_preview2 (2019-12-09 to 2019-12-16) v392

• confs/asia.hg.conf
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    981a56e061a1e3e9a54904f09eb17832151d20be Sun Dec 15 01:11:31 2019 -0800
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
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    981a56e061a1e3e9a54904f09eb17832151d20be Sun Dec 15 01:11:31 2019 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
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    981a56e061a1e3e9a54904f09eb17832151d20be Sun Dec 15 01:11:31 2019 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
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    981a56e061a1e3e9a54904f09eb17832151d20be Sun Dec 15 01:11:31 2019 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgGene/domains.c
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    cb49c73587a465b9ab57052430ee2e39e7311467 Wed Dec 11 15:23:49 2019 -0800
    Updating chimera help link to mupit, refs Bob email
• src/hg/hgTracks/hgTracks.c
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    742b807bec5f518fc190023cc619c61103c2b5b6 Thu Dec 12 09:48:07 2019 -0800
    support _sel and _hideKids in multiwigs #24544
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    984ba3b31499263d5e71deff44dbf7f23abc2bda Fri Dec 13 12:01:13 2019 -0800
    hgTrack makes a color key for the pLI track, refs #20394
• src/hg/hgTracks/hgTracks.h
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    984ba3b31499263d5e71deff44dbf7f23abc2bda Fri Dec 13 12:01:13 2019 -0800
    hgTrack makes a color key for the pLI track, refs #20394
• src/hg/hgTracks/simpleTracks.c
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    984ba3b31499263d5e71deff44dbf7f23abc2bda Fri Dec 13 12:01:13 2019 -0800
    hgTrack makes a color key for the pLI track, refs #20394
• src/hg/hgc/bigDbSnpClick.c
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    716d08695b3bc2a41b82348559e7ad234d09e1c4 Fri Dec 13 14:28:34 2019 -0800
    Adding hReplaceGbdb to bigDataUrl (gbdb path) for GBiB. refs #23283 note-197
• src/hg/hgc/geneReviewsClick.c
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    9c77dc1794e0885d85417037b5e49dc0fa1c9154 Fri Dec 13 06:27:44 2019 -0800
    adding link to geneReviews page from geneReviews track, suggested by Anna, no redmine (yet)
• src/hg/hgc/hgc.c
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    06c58384321c0d1737b23969036e3a417e137285 Wed Dec 11 10:47:19 2019 -0800
    Forgot to check for NULL tdb -- 'trackTable' can be refSeqAli. Thx Chris Lee for finding problem. refs #24630, #24554
• src/hg/hgc/vcfClick.c
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    d68c0ac5daa333dcaa7a9f49e0b554bfd91f05f5 Thu Dec 12 14:52:56 2019 -0800
    Report genotype allele counts and genotype counts correctly when there are more than two alleles. refs #24623
• src/hg/htdocs/FAQ/FAQblat.html
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    a088083189a07e9d1304023f7370f27c713642c7 Tue Dec 10 02:04:47 2019 -0800
    adding note to blat FAQ after refs #24595
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    5667676c9a55330c839f223b9c0cfefa691390d4 Thu Dec 12 02:19:09 2019 -0800
    adding a section to the BLAT FAQ, refs #24595
• src/hg/htdocs/FAQ/FAQgenes.html
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    9ee755e1977934400656229a22c6aaa369eb1c4e Thu Dec 12 02:08:06 2019 -0800
    adding a section gene FAQ, refs #24624
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
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    cd65e033b5235282813dc40fe93c79fcc5a90510 Tue Dec 10 10:01:54 2019 -0800
    Commenting out link to quickStart page, will comment back when completed refs #24327
• src/hg/htdocs/goldenPath/newsarch.html
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    c03fa88273d2b008a51da7bb4e792d0d3ef91fad Fri Dec 13 15:13:25 2019 -0800
    News announcement for dbSNP changes refs #23283
• src/hg/htdocs/images/bigDbSnpNewsArch.png
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    80b87a1d33c3ae99252a263be578e49c081417ca Fri Dec 13 11:39:46 2019 -0800
    Adding image for newsArch dbSNP release refs #23283
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    886b6ef442ed356c2f9c21e5ad98c0b2b2f41ffe Fri Dec 13 11:54:08 2019 -0800
    Fine tuning image for dbSNP release refs #23283
• src/hg/htdocs/indexNews.html
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    c03fa88273d2b008a51da7bb4e792d0d3ef91fad Fri Dec 13 15:13:25 2019 -0800
    News announcement for dbSNP changes refs #23283
• src/hg/lib/hui.c
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    742b807bec5f518fc190023cc619c61103c2b5b6 Thu Dec 12 09:48:07 2019 -0800
    support _sel and _hideKids in multiwigs #24544
• src/hg/makeDb/doc/hg19.txt
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    d52cbc57618c1635024918518f864f9a5f79ca12 Tue Dec 10 03:52:17 2019 -0800
    updating HGMD to 2019 version, refs #24625
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    23dbede5f4f4414a5f1c0d2d9b5ee586ea6a7094 Tue Dec 10 15:25:37 2019 -0800
    Staging gnomAD predicted loss of function track on genome-test, refs #20394
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    612a9d7fa6c688800bedf54ef3f9052e6bf93bbf Wed Dec 11 02:53:13 2019 -0800
    makedoc update for refs #24626
• src/hg/makeDb/doc/hg38/hgmd.txt
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    d52cbc57618c1635024918518f864f9a5f79ca12 Tue Dec 10 03:52:17 2019 -0800
    updating HGMD to 2019 version, refs #24625
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
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    d52cbc57618c1635024918518f864f9a5f79ca12 Tue Dec 10 03:52:17 2019 -0800
    updating HGMD to 2019 version, refs #24625
• src/hg/makeDb/trackDb/drosophila/droVir2/gap.html
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    92f0c70e34a0726e075013ab23f18f87d8c9f61a Mon Dec 9 10:19:29 2019 -0800
    Updating a broken link for droVir2, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/liftHg38.html
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    d1dffba43c4ec03a7fe4094987d266b62d3e96f1 Mon Dec 16 04:50:28 2019 -0800
    docs page for lift over track, refs #24449
• src/hg/makeDb/trackDb/human/hg19/problematic.html
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    bcea72b85c09ea0362c4df36693cc0f98afbe9ff Tue Dec 10 08:46:09 2019 -0800
    problematic regions track, refs #24245
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
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    23dbede5f4f4414a5f1c0d2d9b5ee586ea6a7094 Tue Dec 10 15:25:37 2019 -0800
    Staging gnomAD predicted loss of function track on genome-test, refs #20394
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    9aa5f118ee7504a02d571d8ec6e548053ea7f83d Fri Dec 13 15:38:11 2019 -0800
    Turning off useScore setting for pLI track, refs #20394
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    bcea72b85c09ea0362c4df36693cc0f98afbe9ff Tue Dec 10 08:46:09 2019 -0800
    problematic regions track, refs #24245
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    72696baf7fcc6652995ac9f22e9abdf789478324 Mon Dec 16 04:27:59 2019 -0800
    adding Angies ncbi remap tracks and also our liftover chains, refs #24245
• src/hg/makeDb/trackDb/human/hgmd.html
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    d52cbc57618c1635024918518f864f9a5f79ca12 Tue Dec 10 03:52:17 2019 -0800
    updating HGMD to 2019 version, refs #24625
• src/hg/utils/automation/doAssemblyHub.pl
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    663d3c8c2095473aeb96b0d24849a2b793795d40 Wed Dec 11 14:00:57 2019 -0800
    now correctly processin alternate haplotype and patch sequences refs #23891
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    dbdb4c9fb976266d03316b80d53c54a65784f1b9 Thu Dec 12 13:06:05 2019 -0800
    can verify the name lists have the correct number refs #23891
• src/hg/utils/automation/doCrispr.pl
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    24447c2527a64414060fc472626c0ae6a64f673c Thu Dec 12 13:06:47 2019 -0800
    correctly eliminate dead machines from the rsync copies refs #23891
• src/utils/qa/weeklybld/buildEnv.csh
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    6a4cf917cc3d02102bf6d868b080158fa72fed4f Mon Dec 16 10:06:24 2019 -0800
    v392 preview2, refs #24628

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• files changed: 39