All File Changes

v360_preview to v360_preview2 (2018-01-08 to 2018-01-16) v360

• src/hg/hgGateway/hgGateway.c
  • lines changed 75, context: html, text, full: html, text
    03803eba90389888a329f1c2ddb16b61fdaac4b3 Wed Jan 10 17:06:08 2018 -0800
    In hgGateway's autocomplete search for assembly hubs, use the new & improved hubSearchText table instead of the no-longer-updated trix search files. refs #20694
• src/hg/hgTables/bigWig.c
  • lines changed 1, context: html, text, full: html, text
    043102a443731a0d579d9766157ff57968d30d02 Tue Jan 9 14:52:24 2018 -0800
    implement missing data and reading of WIB files into mathWigs.
• src/hg/hgTracks/bigWigTrack.c
  • lines changed 18, context: html, text, full: html, text
    043102a443731a0d579d9766157ff57968d30d02 Tue Jan 9 14:52:24 2018 -0800
    implement missing data and reading of WIB files into mathWigs.
• src/hg/hgTracks/extTools.c
  • lines changed 9, context: html, text, full: html, text
    74f7bf30603c7dfe869afcbe63adb6ddd74e9898 Wed Jan 10 12:58:38 2018 -0800
    Link to NCBI's Genome Data Viewer (GDV) using GCA_ accessions from dbDb.sourceName instead of hardcoded GCF_ ids. refs #18671
• src/hg/hgTracks/extTools.ra
  • lines changed 2, context: html, text, full: html, text
    74f7bf30603c7dfe869afcbe63adb6ddd74e9898 Wed Jan 10 12:58:38 2018 -0800
    Link to NCBI's Genome Data Viewer (GDV) using GCA_ accessions from dbDb.sourceName instead of hardcoded GCF_ ids. refs #18671
• src/hg/hgTracks/menu.c
  • lines changed 4, context: html, text, full: html, text
    74f7bf30603c7dfe869afcbe63adb6ddd74e9898 Wed Jan 10 12:58:38 2018 -0800
    Link to NCBI's Genome Data Viewer (GDV) using GCA_ accessions from dbDb.sourceName instead of hardcoded GCF_ ids. refs #18671
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    043102a443731a0d579d9766157ff57968d30d02 Tue Jan 9 14:52:24 2018 -0800
    implement missing data and reading of WIB files into mathWigs.
• src/hg/hgc/hgc.c
  • lines changed 27, context: html, text, full: html, text
    79672605ddcba54a4c42b0b87ac243fc5d86d810 Wed Jan 10 14:04:37 2018 -0800
    Don't use (hgFixed.)trackVersion for NCBI RefSeq anymore -- tdb dataVersion is preferred now and included automatically by printDataVersion. refs #20108, #18997 note-141
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    8fcd19432e3046383de848311dcb453f90f6e635 Mon Jan 8 15:04:48 2018 -0800
    Removing extra 'Bonobo' in the 'species' column for panPan1 as per code review, refs #20793
• src/hg/htdocs/contacts.html
  • lines changed 1, context: html, text, full: html, text
    00fb00a849accd17146065a9e9a08e70bc6c9c3e Mon Jan 8 13:34:55 2018 -0800
    reformatted video section, removing link to vids directory which will be deprecated, and removing (most of) indent. added anchor tag in contacts file so I can link to mailing list
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 25, context: html, text, full: html, text
    fe4abcad40590f19e9d9c862e341b6e1d6e44b28 Thu Jan 11 15:56:49 2018 -0800
    Adding TB User Guide section to get gene symbols from query, no RM
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    e38cbf32b1393b87af0310b5a24e8b773d0f6b3c Mon Jan 8 16:28:07 2018 -0800
    Fixing a typo in Chris Eisenhart's name, no Redmine.
  • lines changed 12, context: html, text, full: html, text
    1f1c65c5f67be78b9d62faf03a7d7cfdb1863f74 Thu Jan 11 08:54:14 2018 -0800
    added section for 2018. fixed old typo
  • lines changed 32, context: html, text, full: html, text
    6c81a3f2bd096bf0774dfc44896e0b939afc2300 Mon Jan 15 12:27:05 2018 -0800
    Publishing news for released hg38 30-way, refs #20216
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 24, context: html, text, full: html, text
    02d321faaed51e27e584f6be623eff1d9872a253 Tue Jan 16 08:28:11 2018 -0800
    adding final info and moving Browser NAR paper to 2018 section
• src/hg/htdocs/images/training/thumbCloud.jpg
  • lines changed 0, context: html, text, full: html, text
    adeae932e1c902daa8875a1ca060914d5082d6a1 Tue Jan 9 15:22:34 2018 -0800
    removing vids/index.html and all its images. will no longer be maintaining this page
• src/hg/htdocs/images/training/thumbGateway.jpg
  • lines changed 0, context: html, text, full: html, text
    adeae932e1c902daa8875a1ca060914d5082d6a1 Tue Jan 9 15:22:34 2018 -0800
    removing vids/index.html and all its images. will no longer be maintaining this page
• src/hg/htdocs/images/training/titleInformatics.gif
  • lines changed 0, context: html, text, full: html, text
    adeae932e1c902daa8875a1ca060914d5082d6a1 Tue Jan 9 15:22:34 2018 -0800
    removing vids/index.html and all its images. will no longer be maintaining this page
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    b9432a52c4e16cba4bb5371e4434a32cc315b69b Tue Jan 9 16:17:44 2018 -0800
    adding back dummy page to hide directory of transcripts coming from htdocsExtras
  • lines changed 0, context: html, text, full: html, text
    a4cef2824d0561593e823539838e95eff64ee940 Tue Jan 9 16:27:42 2018 -0800
    swapping in .jpg for .gif file
• src/hg/htdocs/images/training/titleInformatics.jpg
  • lines changed 0, context: html, text, full: html, text
    adeae932e1c902daa8875a1ca060914d5082d6a1 Tue Jan 9 15:22:34 2018 -0800
    removing vids/index.html and all its images. will no longer be maintaining this page
  • lines changed 0, context: html, text, full: html, text
    a4cef2824d0561593e823539838e95eff64ee940 Tue Jan 9 16:27:42 2018 -0800
    swapping in .jpg for .gif file
• src/hg/htdocs/images/training/vidTitle01.jpg
  • lines changed 0, context: html, text, full: html, text
    adeae932e1c902daa8875a1ca060914d5082d6a1 Tue Jan 9 15:22:34 2018 -0800
    removing vids/index.html and all its images. will no longer be maintaining this page
• src/hg/htdocs/images/training/vidTitle02.jpg
  • lines changed 0, context: html, text, full: html, text
    adeae932e1c902daa8875a1ca060914d5082d6a1 Tue Jan 9 15:22:34 2018 -0800
    removing vids/index.html and all its images. will no longer be maintaining this page
• src/hg/htdocs/images/training/vidTitle03.jpg
  • lines changed 0, context: html, text, full: html, text
    adeae932e1c902daa8875a1ca060914d5082d6a1 Tue Jan 9 15:22:34 2018 -0800
    removing vids/index.html and all its images. will no longer be maintaining this page
• src/hg/htdocs/images/training/vidTitle04.jpg
  • lines changed 0, context: html, text, full: html, text
    adeae932e1c902daa8875a1ca060914d5082d6a1 Tue Jan 9 15:22:34 2018 -0800
    removing vids/index.html and all its images. will no longer be maintaining this page
• src/hg/htdocs/images/training/vidTitle06.jpg
  • lines changed 0, context: html, text, full: html, text
    adeae932e1c902daa8875a1ca060914d5082d6a1 Tue Jan 9 15:22:34 2018 -0800
    removing vids/index.html and all its images. will no longer be maintaining this page
• src/hg/htdocs/images/training/vidTitle07.jpg
  • lines changed 0, context: html, text, full: html, text
    adeae932e1c902daa8875a1ca060914d5082d6a1 Tue Jan 9 15:22:34 2018 -0800
    removing vids/index.html and all its images. will no longer be maintaining this page
• src/hg/htdocs/images/training/vidTitle08.jpg
  • lines changed 0, context: html, text, full: html, text
    adeae932e1c902daa8875a1ca060914d5082d6a1 Tue Jan 9 15:22:34 2018 -0800
    removing vids/index.html and all its images. will no longer be maintaining this page
• src/hg/htdocs/images/training/vidTitle09.jpg
  • lines changed 0, context: html, text, full: html, text
    adeae932e1c902daa8875a1ca060914d5082d6a1 Tue Jan 9 15:22:34 2018 -0800
    removing vids/index.html and all its images. will no longer be maintaining this page
• src/hg/htdocs/images/training/vidTitle10.jpg
  • lines changed 0, context: html, text, full: html, text
    adeae932e1c902daa8875a1ca060914d5082d6a1 Tue Jan 9 15:22:34 2018 -0800
    removing vids/index.html and all its images. will no longer be maintaining this page
• src/hg/htdocs/images/training/vidTitle11.jpg
  • lines changed 0, context: html, text, full: html, text
    adeae932e1c902daa8875a1ca060914d5082d6a1 Tue Jan 9 15:22:34 2018 -0800
    removing vids/index.html and all its images. will no longer be maintaining this page
• src/hg/htdocs/images/training/vidTitle12.jpg
  • lines changed 0, context: html, text, full: html, text
    adeae932e1c902daa8875a1ca060914d5082d6a1 Tue Jan 9 15:22:34 2018 -0800
    removing vids/index.html and all its images. will no longer be maintaining this page
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    6c81a3f2bd096bf0774dfc44896e0b939afc2300 Mon Jan 15 12:27:05 2018 -0800
    Publishing news for released hg38 30-way, refs #20216
• src/hg/htdocs/staticStyle/gbStatic.css
  • lines changed 1, context: html, text, full: html, text
    00fb00a849accd17146065a9e9a08e70bc6c9c3e Mon Jan 8 13:34:55 2018 -0800
    reformatted video section, removing link to vids directory which will be deprecated, and removing (most of) indent. added anchor tag in contacts file so I can link to mailing list
• src/hg/htdocs/training/index.html
  • lines changed 68, context: html, text, full: html, text
    00fb00a849accd17146065a9e9a08e70bc6c9c3e Mon Jan 8 13:34:55 2018 -0800
    reformatted video section, removing link to vids directory which will be deprecated, and removing (most of) indent. added anchor tag in contacts file so I can link to mailing list
  • lines changed 10, context: html, text, full: html, text
    6dfddc618c6085265058080643d103951d565c26 Tue Jan 9 11:11:50 2018 -0800
    adding workshop in Galveston
  • lines changed 2, context: html, text, full: html, text
    3d85ea7ecaae80112ac732ddd2b92aa7d38c8e4d Tue Jan 9 11:39:48 2018 -0800
    added link to signup for Galveston workshop
• src/hg/htdocs/training/vids/index.html
  • lines changed 790, context: html, text, full: html, text
    adeae932e1c902daa8875a1ca060914d5082d6a1 Tue Jan 9 15:22:34 2018 -0800
    removing vids/index.html and all its images. will no longer be maintaining this page
  • lines changed 39, context: html, text, full: html, text
    b9432a52c4e16cba4bb5371e4434a32cc315b69b Tue Jan 9 16:17:44 2018 -0800
    adding back dummy page to hide directory of transcripts coming from htdocsExtras
  • lines changed 1, context: html, text, full: html, text
    5b3d2aeb34218ef1a8028d07cd37fc6d984c8167 Tue Jan 9 16:59:41 2018 -0800
    pointing to .jpg instead of .gif image
• src/hg/inc/hdb.h
  • lines changed 3, context: html, text, full: html, text
    74f7bf30603c7dfe869afcbe63adb6ddd74e9898 Wed Jan 10 12:58:38 2018 -0800
    Link to NCBI's Genome Data Viewer (GDV) using GCA_ accessions from dbDb.sourceName instead of hardcoded GCF_ ids. refs #18671
• src/hg/inc/mathWig.h
  • lines changed 5, context: html, text, full: html, text
    043102a443731a0d579d9766157ff57968d30d02 Tue Jan 9 14:52:24 2018 -0800
    implement missing data and reading of WIB files into mathWigs.
• src/hg/js/dbDbTaxonomy.js
  • lines changed 11, context: html, text, full: html, text
    71f07bcffb4709109d882b2faac5d1811e34040a Thu Jan 11 11:26:32 2018 -0800
    adding cavApe1 and fukDam1 Brazilian guinea pig and Damara mole-rat refs #20770 #20752
• src/hg/lib/hAnno.c
  • lines changed 1, context: html, text, full: html, text
    93d78cb9877d1b22ce6167fc1c0a18d27ca55c85 Tue Jan 9 13:38:10 2018 -0800
    hAnnoStreamerFromTrackDb was erring out if it didn't recognize a bigData track type for an assembly hub -- but even for assembly hubs, custom tracks are still sql-based, so let custom tracks past that check. refs #20798
• src/hg/lib/hdb.c
  • lines changed 23, context: html, text, full: html, text
    74f7bf30603c7dfe869afcbe63adb6ddd74e9898 Wed Jan 10 12:58:38 2018 -0800
    Link to NCBI's Genome Data Viewer (GDV) using GCA_ accessions from dbDb.sourceName instead of hardcoded GCF_ ids. refs #18671
• src/hg/lib/hgFind.c
  • lines changed 8, context: html, text, full: html, text
    15438197526bd4c53ebd64921edc05e266f28a93 Thu Jan 11 11:23:26 2018 -0800
    Apply the limitResults parameter to the number of matching terms collected in hgFind.matches, so a term with thousands of matching results doesn't lead to a cart so big that it's slow. refs #20809
  • lines changed 4, context: html, text, full: html, text
    36d99737da9468220abdd6926d3d60119e7c94be Thu Jan 11 12:18:19 2018 -0800
    Apply the limitResults parameter to hgFindSpec sql searches in doQuery. refs #20809 note-4
• src/hg/lib/hubSearchText.sql
  • lines changed 1, context: html, text, full: html, text
    25727d0f604cdf295c116beef0ad0ce47b5014a1 Wed Jan 10 14:40:42 2018 -0800
    Added index on track field to hubSearchText.sql. refs #20694 note-11
• src/hg/lib/mathWig.c
  • lines changed 137, context: html, text, full: html, text
    043102a443731a0d579d9766157ff57968d30d02 Tue Jan 9 14:52:24 2018 -0800
    implement missing data and reading of WIB files into mathWigs.
  • lines changed 1, context: html, text, full: html, text
    31fffada1e52bfc7318ad52f40e95fae1f53a5b9 Tue Jan 9 15:10:49 2018 -0800
    oops... left in a printf
• src/hg/makeDb/doc/anoGam1.txt
  • lines changed 18, context: html, text, full: html, text
    9c9e11889ba3abf8287c56c5909b5695ab6edf44 Thu Jan 11 11:32:49 2018 -0800
    liftOver to anoGam3 refs #20743
• src/hg/makeDb/doc/anoGam3/initialBuild.txt
  • lines changed 246, context: html, text, full: html, text
    714ffecbab169fb2467b47a323995f95d0b97706 Mon Jan 8 13:30:57 2018 -0800
    adding ensGene and crispr10K tracks refs #20743
• src/hg/makeDb/doc/cavApe1/initialBuild.txt
  • lines changed 954, context: html, text, full: html, text
    bc7564d8e57ba1bb89a3292efbcbc3139c90cd5d Wed Jan 10 17:15:53 2018 -0800
    to catch up with Ensembl release v91, QA Ready refs #20770
  • lines changed 1, context: html, text, full: html, text
    26286f426d7cd5922e2d1e4d098b4cf2a6f55397 Wed Jan 10 17:28:20 2018 -0800
    remove trailing blanks refs #20770
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    631e141c2d368e654de036bc4bd82802ceed6483 Thu Jan 11 11:33:28 2018 -0800
    correct defaultPosition refs #20770
• src/hg/makeDb/doc/cavPor3.txt
  • lines changed 5, context: html, text, full: html, text
    c6e704da62c47b77a828cd8c09f64234c6521b5b Thu Jan 11 11:34:16 2018 -0800
    genomewiki page for 6-way alignment no redmine
• src/hg/makeDb/doc/criGriChoV2/initialBuild.txt
  • lines changed 317, context: html, text, full: html, text
    caf7f66a080240cb343e9e9dabd628f0e6b97fbc Wed Jan 10 17:23:47 2018 -0800
    catching up to Ensembl v91 release refs #20540
• src/hg/makeDb/doc/dbDbTaxonomy.txt
  • lines changed 12, context: html, text, full: html, text
    b574473817079811671096b5cb7fb219530be5dc Thu Jan 11 11:31:56 2018 -0800
    update notes during update 2018-01-11 no redmine
• src/hg/makeDb/doc/dipOrd1.txt
  • lines changed 15, context: html, text, full: html, text
    f4fc51970f35afcba95e138ba7ffbf39e36d9673 Thu Jan 11 11:36:12 2018 -0800
    liftOver to dipOrd2 refs #20751
• src/hg/makeDb/doc/dm6.txt
  • lines changed 67, context: html, text, full: html, text
    252fbe2630ffc34ba67275a78039176a8765f80f Thu Jan 11 11:37:04 2018 -0800
    chainNet to anoGam3 refs #20743
• src/hg/makeDb/doc/ficAlb1/initialBuild.txt
  • lines changed 131, context: html, text, full: html, text
    0db946ddc862c388b463902ced3eaf0f050d3a49 Wed Jan 10 17:19:27 2018 -0800
    attempt catch with Ensembl release v91 but their release was a much older sequence refs #9870
• src/hg/makeDb/doc/galVar1/multiz6way.txt
  • lines changed 5, context: html, text, full: html, text
    ef33c3732a399ef285ce299e8c3bafb1aa360722 Thu Jan 11 11:37:57 2018 -0800
    genomewiki status pages for 6-way alignment no redmine
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 388, context: html, text, full: html, text
    950db5b87a30a254b67c01855de3ee8816ace145 Wed Jan 10 10:59:30 2018 -0800
    run up lastz/chainNet for criGriChoV2 papAnu4 cavApe1 ficAlb1 and panTro3 on hg38 refs #20540 #20769 #20770 #9870 #17504
• src/hg/makeDb/doc/hg38/multiz5way.txt
  • lines changed 5, context: html, text, full: html, text
    b0ee4c4ea80e5f0f1b7d2284d9463fd54303222d Thu Jan 11 11:38:16 2018 -0800
    genomewiki status pages for 5-way alignment no redmine
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
  • lines changed 7, context: html, text, full: html, text
    4375c533fdfb3e651724f19d8173ab93f44b2233 Tue Jan 9 15:34:39 2018 -0800
    Regenerating hg38.ncbiRefSeq* tables and files from latest NCBI download file. refs #20108 note-14
• src/hg/makeDb/doc/mm10.txt
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    950db5b87a30a254b67c01855de3ee8816ace145 Wed Jan 10 10:59:30 2018 -0800
    run up lastz/chainNet for criGriChoV2 papAnu4 cavApe1 ficAlb1 and panTro3 on hg38 refs #20540 #20769 #20770 #9870 #17504
• src/hg/makeDb/doc/papAnu2.txt
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    df7fc755086b35477a73c87463b50ecf33d5b956 Thu Jan 11 11:39:00 2018 -0800
    liftOver to papAnu4 refs #20769
• src/hg/makeDb/doc/papAnu3/initialBuild.txt
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    df7fc755086b35477a73c87463b50ecf33d5b956 Thu Jan 11 11:39:00 2018 -0800
    liftOver to papAnu4 refs #20769
• src/hg/makeDb/doc/papAnu4/initialBuild.txt
  • lines changed 135, context: html, text, full: html, text
    5aeeb014a98558fefa023f237abd29f02d8ae42d Wed Jan 10 17:27:04 2018 -0800
    catching up to Ensembl release v91 refs #20769
• src/hg/makeDb/doc/petMar3/initialBuild.txt
  • lines changed 836, context: html, text, full: html, text
    26c5373d5731d708c0417e81c17d241be3f85c11 Fri Jan 12 22:01:14 2018 -0800
    running up genbank, liftOvers refs #20819
• src/hg/makeDb/doc/tupChi1/multiz5way.txt
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    5ed2d4a3edd913536da9faca9418ae1a54d05cb6 Thu Jan 11 11:39:38 2018 -0800
    genomewiki status page for 5-way no redmine
• src/hg/makeDb/genbank/etc/align.dbs
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    23910020e89fc566f43bbfdfd06552454b221380 Tue Jan 9 09:37:02 2018 -0800
    adding ficAlb1 to the update alignments refs #9870
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    a89bfe4906e124c5d6a0c7dd188650c56a5036a9 Tue Jan 9 10:35:14 2018 -0800
    adding papAnu4 to the update alignments refs #20769
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    37b32f1e7817dcbe7de7d5aa097912a90c9b71a6 Tue Jan 9 14:34:37 2018 -0800
    adding cavApe1 to the update alignments refs #20770
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    dd9925b1305828b4c2a608bb07675794b1f03047 Tue Jan 9 21:41:09 2018 -0800
    adding criGriChoV2 to the update alignments refs #20540
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 22, context: html, text, full: html, text
    4ecbbeb768fa003f3164f0a014ecccf144268c13 Mon Jan 8 18:43:57 2018 -0800
    adding ficAlb1 - Ficedula albicollis - collard flycatcher refs #9870
  • lines changed 18, context: html, text, full: html, text
    73e75eccb6cba0a17ae7abb221148d409bc75751 Mon Jan 8 18:56:45 2018 -0800
    adding papAnu4 Papio anubis - olive baboon refs #20769
  • lines changed 19, context: html, text, full: html, text
    5a92b3984d39408749b1ed37045e810b17c5ee65 Mon Jan 8 22:15:17 2018 -0800
    adding criGriChoV2 Cricetulus griseus cell line CHO-K1 refs #20540
  • lines changed 25, context: html, text, full: html, text
    70282bf14f8a7b30dea908c56fc61cad7279d4ad Mon Jan 8 22:38:02 2018 -0800
    adding cavApe1 Cavia aperea Brizilian guinea pig refs #20770
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    e4e5325b502ebed2dc000fcb28c69cbcb262c78f Tue Jan 9 10:29:31 2018 -0800
    fixing pathnames for cavApe1 refs #20770
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    8d346ba47a6fbec178c8b28f39c2aaed395696dd Fri Jan 12 21:17:47 2018 -0800
    adding petMar3 - Petromyzon marinus - lamprey refs #20819
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    23910020e89fc566f43bbfdfd06552454b221380 Tue Jan 9 09:37:02 2018 -0800
    adding ficAlb1 to the update alignments refs #9870
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    a89bfe4906e124c5d6a0c7dd188650c56a5036a9 Tue Jan 9 10:35:14 2018 -0800
    adding papAnu4 to the update alignments refs #20769
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    37b32f1e7817dcbe7de7d5aa097912a90c9b71a6 Tue Jan 9 14:34:37 2018 -0800
    adding cavApe1 to the update alignments refs #20770
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    dd9925b1305828b4c2a608bb07675794b1f03047 Tue Jan 9 21:41:09 2018 -0800
    adding criGriChoV2 to the update alignments refs #20540
• src/hg/makeDb/genbank/src/lib/gbGenome.c
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    4ecbbeb768fa003f3164f0a014ecccf144268c13 Mon Jan 8 18:43:57 2018 -0800
    adding ficAlb1 - Ficedula albicollis - collard flycatcher refs #9870
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    73e75eccb6cba0a17ae7abb221148d409bc75751 Mon Jan 8 18:56:45 2018 -0800
    adding papAnu4 Papio anubis - olive baboon refs #20769
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    70282bf14f8a7b30dea908c56fc61cad7279d4ad Mon Jan 8 22:38:02 2018 -0800
    adding cavApe1 Cavia aperea Brizilian guinea pig refs #20770
• src/hg/makeDb/schema/all.joiner
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    83d406ebfff2ffad31502f8fac3e681cf258fd75 Wed Jan 10 11:18:04 2018 -0800
    adding rules for ficAlb1 cavApe1 criGriChoV2 papAnu3 refs #9870 #20770 #20540 #20759
• src/hg/makeDb/trackDb/anopheles/anoGam3/trackDb.ra
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    b1b355ce357e00c4eb84739db8f75b95bb078631 Thu Jan 11 11:40:55 2018 -0800
    adding ensGene override for URL to metazoa.ensembl.org refs #20743
• src/hg/makeDb/trackDb/chicken/galGal4/trackDb.ra
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    55ed5573360c54ac085d87f3fb02852798d6a0a1 Wed Jan 10 14:45:03 2018 -0800
    changing default snp on galGal4 to All SNPs (too few in Commmon SNPs)
• src/hg/makeDb/trackDb/chicken/trackDb.ra
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    068493ab4955dc39523f2f4e2d6205534dc454b3 Wed Jan 10 15:37:20 2018 -0800
    moving RefSeq to top priority in its group for chicken
• src/hg/makeDb/trackDb/drosophila/droVir2/gap.html
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    4ff272ca1b5fb9f596bfeb3b9c5745f52e521055 Tue Jan 9 08:14:31 2018 -0800
    Fixing broken links found by the broken link report for droVir2, no Redmine.
• src/hg/makeDb/trackDb/guineaPig/cavApe1/trackDb.ra
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    5baca4fd235d872d4c522ffae9fe26ca9fde341b Thu Jan 11 13:46:51 2018 -0800
    better, more restricted, search termRegex for the gold track to prevent excessive results refs #20770 #20809
• src/hg/makeDb/trackDb/human/chainNetLegacy.ra
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    65a60bdc792a12cd342e719fe38ab0f9975d797b Thu Jan 11 11:43:10 2018 -0800
    no longer needed definitions have been included in other subsets no redmine
• src/hg/makeDb/trackDb/human/chainNetStray.ra
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    65a60bdc792a12cd342e719fe38ab0f9975d797b Thu Jan 11 11:43:10 2018 -0800
    no longer needed definitions have been included in other subsets no redmine
• src/hg/makeDb/trackDb/human/hg38/cons30way.html
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    a878c602b192a71718d6efa7ad42794dcd59cbbd Tue Jan 9 17:49:17 2018 -0800
    Uncommenting released panPan2 for hg38.cons30way Table1, refs #20216
• src/hg/makeDb/trackDb/human/hg38/trackDb.30way.ra
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    352747430d39553d83a3e6ec3e16b03df30a8194 Fri Jan 12 17:17:47 2018 -0800
    Adding 'new' label to hg38 cons30way, refs #20216
• src/hg/makeDb/trackDb/human/newChainNet.ra
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    18fa4aa598e9f71be0e1723ba3b9570f74b52277 Thu Jan 11 11:43:35 2018 -0800
    no longer needed definitions have been included in other subsets no redmine
• src/hg/makeDb/trackDb/human/ntSssSnps.html
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    144dbd87662ea872c53290e724bd3e651a87a96d Tue Jan 9 09:28:29 2018 -0800
    Fixing a broken link on the S SNPs page, no Redmine
• src/hg/makeDb/trackDb/lamprey/petMar3/description.html
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    08c5217ebf53c216f38a9fb641e9b9f601c3946e Fri Jan 12 14:34:21 2018 -0800
    initial set of files refs #20819
• src/hg/makeDb/trackDb/lamprey/petMar3/gap.html
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    08c5217ebf53c216f38a9fb641e9b9f601c3946e Fri Jan 12 14:34:21 2018 -0800
    initial set of files refs #20819
• src/hg/makeDb/trackDb/lamprey/petMar3/gold.html
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    08c5217ebf53c216f38a9fb641e9b9f601c3946e Fri Jan 12 14:34:21 2018 -0800
    initial set of files refs #20819
• src/hg/makeDb/trackDb/lamprey/petMar3/trackDb.ra
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    08c5217ebf53c216f38a9fb641e9b9f601c3946e Fri Jan 12 14:34:21 2018 -0800
    initial set of files refs #20819
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    8d080e8275a37ec089274051eb92266cf4072faf Fri Jan 12 16:27:39 2018 -0800
    adding gold table assembly track search rule refs #20819
• src/hg/makeDb/trackDb/makefile
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    08c5217ebf53c216f38a9fb641e9b9f601c3946e Fri Jan 12 14:34:21 2018 -0800
    initial set of files refs #20819
• src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html
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    a76da48b7fb1d435e26324fd2066a37be39f0f7f Thu Jan 11 07:25:26 2018 -0800
    Fixing broken links for ponAbe2, no Redmine.
• src/hg/makeDb/trackDb/orangutan/ponAbe2/nscanGene.html
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    a76da48b7fb1d435e26324fd2066a37be39f0f7f Thu Jan 11 07:25:26 2018 -0800
    Fixing broken links for ponAbe2, no Redmine.
• src/hg/makeDb/trackDb/orangutan/ponAbe2/phastConsElements8way.html
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    a76da48b7fb1d435e26324fd2066a37be39f0f7f Thu Jan 11 07:25:26 2018 -0800
    Fixing broken links for ponAbe2, no Redmine.
• src/hg/makeDb/trackDb/trackDb.ra
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    14971a27bce60ec145d4dec1fb0b09f249511a76 Mon Jan 8 10:38:44 2018 -0800
    crispr10K tracks can now be seen on ce10 hbv1 mm10 staAur1 anoGam3 refs #0743
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    63f35e0a728226108ba9f18004e3f9047681a545 Tue Jan 9 17:52:53 2018 -0800
    Removing pennantIcon for refSeqFuncElems, refs #19638
• src/hg/mouseStuff/chainPreNet/chainPreNet.c
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    4fde87273f82ff77fc3b3c14e2b39a28ad64d182 Tue Jan 9 13:38:11 2018 -0800
    fix from Michael Hiller to not mark excluded chains as used
• src/hg/utils/automation/doNcbiRefSeq.pl
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    ddc6aa1ff598414619b2b9a122017fbcf53c15e6 Tue Jan 9 15:33:05 2018 -0800
    Use ln -f and gzip -f to avoid file-already-exists errors from reruns.
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    a9575f6e1eaeb3597910b1611fd8f718d58d759c Wed Jan 10 09:25:21 2018 -0800
    Don't compress ncbiRefSeqVersion.txt when cleaning up because there's a link to it from gbdb.
• src/hg/utils/automation/makeGenomeDb.pl
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    4ebd38aaf09a2db1fdbfebad9cc76cae7a2fe9f9 Fri Jan 12 14:55:44 2018 -0800
    new dependent crispr10K.ra file for trackDb build refs #20819
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
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    62689a652c5741683e7042e753e32389c86d7003 Tue Jan 9 13:40:33 2018 -0800
    NCBI's latest RefSeq GFF3 now uses 'pseudogene' in some cases where it previously used 'gene'; treat it the same as before. refs #20108 note-18
• src/inc/gff3.h
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    62689a652c5741683e7042e753e32389c86d7003 Tue Jan 9 13:40:33 2018 -0800
    NCBI's latest RefSeq GFF3 now uses 'pseudogene' in some cases where it previously used 'gene'; treat it the same as before. refs #20108 note-18
• src/inc/hex.h
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    c656295e8e186c77de7c45a34aa5d0f85b1d7265 Thu Jan 11 18:13:39 2018 -0800
    fixing description of hex function.
• src/lib/gff3.c
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    62689a652c5741683e7042e753e32389c86d7003 Tue Jan 9 13:40:33 2018 -0800
    NCBI's latest RefSeq GFF3 now uses 'pseudogene' in some cases where it previously used 'gene'; treat it the same as before. refs #20108 note-18
• src/lib/hex.c
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    c656295e8e186c77de7c45a34aa5d0f85b1d7265 Thu Jan 11 18:13:39 2018 -0800
    fixing description of hex function.
• src/utils/qa/weeklybld/buildEnv.csh
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    6cc89b471714794f170e8e327beda78516d58e5f Tue Jan 16 09:56:53 2018 -0800
    v360 preview2

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