All File Changes

v377_base to v378_preview (2019-02-04 to 2019-02-11) v378

• src/hg/hgGene/hgGeneData/Mouse/mm7/links.ra
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    2cf11ade317a13b5eb7fe5bd24bfaded8357ec13 Tue Feb 5 13:09:17 2019 -0800
    fully removing commented exonPrimer links from mm7 and mm8, refs #15342
• src/hg/hgGene/hgGeneData/Mouse/mm8/links.ra
  • lines changed 8, context: html, text, full: html, text
    2cf11ade317a13b5eb7fe5bd24bfaded8357ec13 Tue Feb 5 13:09:17 2019 -0800
    fully removing commented exonPrimer links from mm7 and mm8, refs #15342
• src/hg/hgSession/backupRestore.c
  • lines changed 2163, context: html, text, full: html, text
    05094dabf3d005ab35a998ff225443fc4255611f Mon Feb 4 23:07:42 2019 -0800
    Adding ability to backup and restore the cart and its custom tracks in hgSession.
  • lines changed 4, context: html, text, full: html, text
    ba9df66e76908e3e1d2e3a16c9df0e74bd420eaf Tue Feb 5 18:01:43 2019 -0800
    oops. needs to save using id from userDb table, not the sessionDb table.
  • lines changed 4, context: html, text, full: html, text
    9c0ff0119cc46b2ef1fa191cb64657de78824b64 Tue Feb 5 23:22:10 2019 -0800
    fixing it to use LOCAL in load data infile -- would not work for separate RR and custom trash server anyways.
  • lines changed 23, context: html, text, full: html, text
    fa80307492d13ebdd1c86ef1231fd0f3fc7bbd73 Fri Feb 8 16:41:29 2019 -0800
    Tweaking .sql security. My testing found no way to break it. Mysql and jksql currently do not allow multiple statements, which is good since that is a big weakness otherwise.
  • lines changed 1, context: html, text, full: html, text
    b0ffebb10d016222d9e21975b4d7aaf1c2fb9425 Fri Feb 8 18:20:41 2019 -0800
    oops, missing newline in hubList archive file
• src/hg/hgSession/hgSession.c
  • lines changed 275, context: html, text, full: html, text
    05094dabf3d005ab35a998ff225443fc4255611f Mon Feb 4 23:07:42 2019 -0800
    Adding ability to backup and restore the cart and its custom tracks in hgSession.
• src/hg/hgSession/hgSession.h
  • lines changed 51, context: html, text, full: html, text
    05094dabf3d005ab35a998ff225443fc4255611f Mon Feb 4 23:07:42 2019 -0800
    Adding ability to backup and restore the cart and its custom tracks in hgSession.
• src/hg/hgSession/makefile
  • lines changed 1, context: html, text, full: html, text
    05094dabf3d005ab35a998ff225443fc4255611f Mon Feb 4 23:07:42 2019 -0800
    Adding ability to backup and restore the cart and its custom tracks in hgSession.
• src/hg/hgTables/bigWig.c
  • lines changed 14, context: html, text, full: html, text
    79c5090c373a449c3fa3e83949736e7515f03da2 Tue Feb 5 09:36:59 2019 -0800
    support schemas on bigWigs within composites. #22885
• src/hg/hgTables/hgTables.h
  • lines changed 4, context: html, text, full: html, text
    79c5090c373a449c3fa3e83949736e7515f03da2 Tue Feb 5 09:36:59 2019 -0800
    support schemas on bigWigs within composites. #22885
• src/hg/hgTables/schema.c
  • lines changed 1, context: html, text, full: html, text
    79c5090c373a449c3fa3e83949736e7515f03da2 Tue Feb 5 09:36:59 2019 -0800
    support schemas on bigWigs within composites. #22885
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    27afc5a5182ee8614bcb8ec2ef7eaaa1152040a3 Wed Jan 9 16:06:49 2019 -0800
    Add setting to collapse empty subtracks, for Regeneron AA display, but others may find useful. refs #22739
  • lines changed 4, context: html, text, full: html, text
    75ffe3b6a127bec72fdb44290af9b98a14eb79dc Fri Jan 11 15:27:03 2019 -0800
    Partial implementation of 'centerLabelsPack' setting, to suppress center labels in pack mode (when setting is 'off'). This checkin suppresses center labels but doesn't show left labels. refs #22739
  • lines changed 24, context: html, text, full: html, text
    f7504e4db88de54c3a438f70a0acc4cddb41f148 Sat Jan 12 18:23:15 2019 -0800
    Finish regeneron feature to display left labels instead of center labels in pack mode (setting centerLabelsPack off). refs #22739
  • lines changed 20, context: html, text, full: html, text
    58502ff9a4db966bdad267df1bc713fcc1b660b3 Wed Feb 6 17:47:52 2019 -0800
    Cleanup regeneron features. refs #22739
  • lines changed 11, context: html, text, full: html, text
    c5e7f5a7ca22c7e4cd3fc692ecab55c10a04dce4 Fri Feb 8 14:07:20 2019 -0800
    use _hideKids instead of _sel to hide the children of composites and supertracks
• src/hg/hgTracks/hgTracks.h
  • lines changed 6, context: html, text, full: html, text
    75ffe3b6a127bec72fdb44290af9b98a14eb79dc Fri Jan 11 15:27:03 2019 -0800
    Partial implementation of 'centerLabelsPack' setting, to suppress center labels in pack mode (when setting is 'off'). This checkin suppresses center labels but doesn't show left labels. refs #22739
  • lines changed 3, context: html, text, full: html, text
    f7504e4db88de54c3a438f70a0acc4cddb41f148 Sat Jan 12 18:23:15 2019 -0800
    Finish regeneron feature to display left labels instead of center labels in pack mode (setting centerLabelsPack off). refs #22739
  • lines changed 7, context: html, text, full: html, text
    58502ff9a4db966bdad267df1bc713fcc1b660b3 Wed Feb 6 17:47:52 2019 -0800
    Cleanup regeneron features. refs #22739
• src/hg/hgTracks/interactTrack.c
  • lines changed 1, context: html, text, full: html, text
    34640b8bb26a2f43097ff65d9b2555a79b8335f5 Thu Feb 7 11:59:13 2019 -0800
    Fix display problem with interchromosomal items in non-full modes (introduced with new pack/dense/cluster display code for Genehancer). refs #22910
  • lines changed 9, context: html, text, full: html, text
    9020b599f0a4960ef55d43477f28fca83e6dc162 Thu Feb 7 13:09:41 2019 -0800
    add score filtering to interact type
• src/hg/hgTracks/simpleTracks.c
  • lines changed 3, context: html, text, full: html, text
    ace7d6c2a03c2ad76c14134546785b8c3fa61ac2 Tue Jan 8 11:39:09 2019 -0800
    Implement 'packDense' setting (tentative name) to support Regeneron 2nd contract amino acide display. This setting will pack items on a single line if they are adjacent (suppresses padding between packed items). refs #22739
  • lines changed 37, context: html, text, full: html, text
    75ffe3b6a127bec72fdb44290af9b98a14eb79dc Fri Jan 11 15:27:03 2019 -0800
    Partial implementation of 'centerLabelsPack' setting, to suppress center labels in pack mode (when setting is 'off'). This checkin suppresses center labels but doesn't show left labels. refs #22739
  • lines changed 60, context: html, text, full: html, text
    f7504e4db88de54c3a438f70a0acc4cddb41f148 Sat Jan 12 18:23:15 2019 -0800
    Finish regeneron feature to display left labels instead of center labels in pack mode (setting centerLabelsPack off). refs #22739
  • lines changed 6, context: html, text, full: html, text
    08414ac23ba7fd2d7298ad5502053cc94b0834b0 Mon Jan 14 16:48:37 2019 -0800
    Allow very short labels to be used with labelsOnFeature setting. Needed for Regeneron (and no reason not to). refs #22739
  • lines changed 35, context: html, text, full: html, text
    58502ff9a4db966bdad267df1bc713fcc1b660b3 Wed Feb 6 17:47:52 2019 -0800
    Cleanup regeneron features. refs #22739
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 2, context: html, text, full: html, text
    d2449eba09b11a205f060161b95a363063a323bf Tue Feb 5 11:41:01 2019 -0800
    Fixing a link in documentation ref#22904
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 38, context: html, text, full: html, text
    e3439d269044509fbe350880a93d92db0c640409 Tue Feb 5 09:08:25 2019 -0800
    more gencode docs, as per Braney
  • lines changed 33, context: html, text, full: html, text
    ae157e3199a91b4c4310954dd00b11b8b1c3c596 Wed Feb 6 16:35:51 2019 -0800
    updates to FAQ genes page, after gencode ensembl comparison
  • lines changed 6, context: html, text, full: html, text
    bbedeb1f82df498632977642932de0947c7cdf2b Wed Feb 6 16:40:21 2019 -0800
    more faq genes updates
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 39, context: html, text, full: html, text
    05094dabf3d005ab35a998ff225443fc4255611f Mon Feb 4 23:07:42 2019 -0800
    Adding ability to backup and restore the cart and its custom tracks in hgSession.
• src/hg/htdocs/goldenPath/help/interact.html
  • lines changed 5, context: html, text, full: html, text
    a6412bb73fe3d586c2a2364b3c06b6d47a6d87d0 Thu Feb 7 16:25:47 2019 -0800
    Changing interact documentation to have capitalized titles and explain confusing optional step presented before as mandatory
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 136, context: html, text, full: html, text
    ed9c28e39a6542fcc59aee1dd05bc309ae0f415f Thu Feb 7 15:15:36 2019 -0800
    Adding ens95 release article to newarch.html, refs #22761
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    5b7259d9d96a48a1b976b9a01e293bdccfb22f06 Wed Feb 6 14:39:49 2019 -0800
    Fix merge conflict
• src/hg/htdocs/indexNews.html
  • lines changed 17, context: html, text, full: html, text
    a85c8c3613ca38e4d31cd4a4322736589e124db4 Thu Feb 7 15:25:12 2019 -0800
    updating indexNews.html to include ens95 release, refs #22761
• src/hg/htdocs/training/index.html
  • lines changed 19, context: html, text, full: html, text
    0b05f88cd751d2d4684d93803d59ae379c9548e9 Thu Feb 7 13:09:55 2019 -0800
    moving singpore into active list. adding grand rapids to future list
  • lines changed 10, context: html, text, full: html, text
    3ebee356de8a717fc8c2561407544b5e7de450d1 Thu Feb 7 14:17:51 2019 -0800
    fix typo
• src/hg/hubApi/hubApi.c
  • lines changed 84, context: html, text, full: html, text
    002a02e0a481cb3f1f06c7f848adfdc7940844cf Tue Feb 5 11:24:36 2019 -0800
    return dbDb contents /list/ucscGenomes function refs #18869
  • lines changed 19, context: html, text, full: html, text
    497f88a03fd3e257b9acff6b315f45c7b67a6786 Tue Feb 5 14:09:39 2019 -0800
    now returning track list for any UCSC database genome refs #18869
  • lines changed 17, context: html, text, full: html, text
    3f92bea76f09e3b46d8f1ebc44db19d9e508b67e Tue Feb 5 14:41:23 2019 -0800
    correctly returning track list for any UCSC database genome refs #18869
  • lines changed 10, context: html, text, full: html, text
    e3dccad035436b2b7a76b8e3112b0b06de37fe93 Tue Feb 5 15:03:31 2019 -0800
    not sure why it returns a short track list for a database refs @8869
  • lines changed 70, context: html, text, full: html, text
    8aba55de743fd795f8c26d730567ff8a359254e8 Tue Feb 5 15:58:07 2019 -0800
    beginning to show everything about a track in ucsc database refs #18869
  • lines changed 77, context: html, text, full: html, text
    9614cd02adbffc856bc229ae7c88a2440cc616f1 Wed Feb 6 10:26:35 2019 -0800
    returning chrom list from ucsc chromInfo table refs #18869
  • lines changed 63, context: html, text, full: html, text
    e06aca36b8d5f820603188308c7bec8749427fe0 Wed Feb 6 14:32:14 2019 -0800
    chrom list from specific track on ucsc database output and jsonErr output refs #18869
  • lines changed 126, context: html, text, full: html, text
    d00cd1b5dd768c8edf09b8a2f2ccb48786c8d1ff Fri Feb 8 14:01:15 2019 -0800
    beginning to use "desc" SQL query on table to get column header names refs #18869
  • lines changed 63, context: html, text, full: html, text
    03680a45cb9806e93bc784905fbdb4f6e9ac063e Fri Feb 8 14:26:15 2019 -0800
    output column names for dbDb table refs #18869
  • lines changed 136, context: html, text, full: html, text
    80c13ab201d59baa021d5c1a2222872ecbdf196f Fri Feb 8 16:17:16 2019 -0800
    now using functions in src/lib/jsonWrite.c refs #18869 #22859
  • lines changed 88, context: html, text, full: html, text
    4cb493ab92afe6c13f5592880c4f5fbfa371d84c Sun Feb 10 18:48:32 2019 -0800
    make the chromosome list a sub-list from the top level refs #18869
  • lines changed 53, context: html, text, full: html, text
    09b542fe035a233ec45d2092e4a0ab38e99c3e32 Mon Feb 11 09:50:37 2019 -0800
    adding dataTime and dataTimeStamp to the outputs refs #18869
• src/hg/hubApi/tests/expected.json.gz
  • lines changed 0, context: html, text, full: html, text
    95966f9426d2b06029f2d48a46a9a28f0cd866ba Fri Feb 8 15:20:51 2019 -0800
    updated to do specific test on publicHubs and ucscGenomes refs #18869
• src/hg/hubApi/tests/jsonConsumer.pl
  • lines changed 153, context: html, text, full: html, text
    95966f9426d2b06029f2d48a46a9a28f0cd866ba Fri Feb 8 15:20:51 2019 -0800
    updated to do specific test on publicHubs and ucscGenomes refs #18869
• src/hg/inc/cart.h
  • lines changed 8, context: html, text, full: html, text
    05094dabf3d005ab35a998ff225443fc4255611f Mon Feb 4 23:07:42 2019 -0800
    Adding ability to backup and restore the cart and its custom tracks in hgSession.
  • lines changed 3, context: html, text, full: html, text
    ba9df66e76908e3e1d2e3a16c9df0e74bd420eaf Tue Feb 5 18:01:43 2019 -0800
    oops. needs to save using id from userDb table, not the sessionDb table.
• src/hg/inc/customFactory.h
  • lines changed 1, context: html, text, full: html, text
    05094dabf3d005ab35a998ff225443fc4255611f Mon Feb 4 23:07:42 2019 -0800
    Adding ability to backup and restore the cart and its custom tracks in hgSession.
• src/hg/inc/hdb.h
  • lines changed 7, context: html, text, full: html, text
    79c5090c373a449c3fa3e83949736e7515f03da2 Tue Feb 5 09:36:59 2019 -0800
    support schemas on bigWigs within composites. #22885
  • lines changed 13, context: html, text, full: html, text
    cac8c67d46544187d0fb28cf78060d9d2cb97a5d Tue Feb 5 14:09:20 2019 -0800
    Update chrSlNameCmpWithAltRandom to handle _fix and _hap sequence names. refs #18855 note-70
• src/hg/inc/jksql.h
  • lines changed 9, context: html, text, full: html, text
    05094dabf3d005ab35a998ff225443fc4255611f Mon Feb 4 23:07:42 2019 -0800
    Adding ability to backup and restore the cart and its custom tracks in hgSession.
• src/hg/lib/cart.c
  • lines changed 52, context: html, text, full: html, text
    05094dabf3d005ab35a998ff225443fc4255611f Mon Feb 4 23:07:42 2019 -0800
    Adding ability to backup and restore the cart and its custom tracks in hgSession.
  • lines changed 6, context: html, text, full: html, text
    ba9df66e76908e3e1d2e3a16c9df0e74bd420eaf Tue Feb 5 18:01:43 2019 -0800
    oops. needs to save using id from userDb table, not the sessionDb table.
• src/hg/lib/customFactory.c
  • lines changed 12, context: html, text, full: html, text
    05094dabf3d005ab35a998ff225443fc4255611f Mon Feb 4 23:07:42 2019 -0800
    Adding ability to backup and restore the cart and its custom tracks in hgSession.
• src/hg/lib/hdb.c
  • lines changed 11, context: html, text, full: html, text
    79c5090c373a449c3fa3e83949736e7515f03da2 Tue Feb 5 09:36:59 2019 -0800
    support schemas on bigWigs within composites. #22885
  • lines changed 13, context: html, text, full: html, text
    cac8c67d46544187d0fb28cf78060d9d2cb97a5d Tue Feb 5 14:09:20 2019 -0800
    Update chrSlNameCmpWithAltRandom to handle _fix and _hap sequence names. refs #18855 note-70
• src/hg/lib/jksql.c
  • lines changed 72, context: html, text, full: html, text
    05094dabf3d005ab35a998ff225443fc4255611f Mon Feb 4 23:07:42 2019 -0800
    Adding ability to backup and restore the cart and its custom tracks in hgSession.
• src/hg/makeDb/genbank/etc/build-genbank
  • lines changed 1, context: html, text, full: html, text
    96c92630c503fd2d6e6896af94fdb18343134c64 Thu Feb 7 14:30:00 2019 -0800
    oops... fix rm command to remove directory
• src/hg/makeDb/genbank/etc/mkdownload
  • lines changed 1, context: html, text, full: html, text
    462d5686feeb87245650b673e1637375b985c25c Wed Feb 6 13:17:44 2019 -0800
    moving mkdownload to the genbank machine
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    89c08b05c19cab2e1ae289bf1233821aa7e3ea10 Thu Feb 7 07:54:15 2019 -0800
    oops.. putting mkdownload back on dev
• src/hg/makeDb/trackDb/bacteria/staAur2/aaCounts.ra
  • lines changed 27, context: html, text, full: html, text
    1c31a4919d26da45a76c5dd8355b8312c8ae04ad Mon Jan 14 13:47:42 2019 -0800
    Add new settings for implemented for Regeneron AA display. refs #20377
  • lines changed 2, context: html, text, full: html, text
    9f594b688dbccc173794ef82a264284665965bba Sun Feb 3 20:32:53 2019 -0800
    Add score filter (ala Hiram). refs #20377
  • lines changed 12, context: html, text, full: html, text
    4ea4720251ee4652a7948cf4ba8c1fc0170a2527 Sun Feb 3 20:33:41 2019 -0800
    Add score filter (ala Hiram). refs #20377
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    5e72f9391924a337e2b569658f35dee58874544e Mon Feb 4 14:35:52 2019 -0800
    Fix trackDb for regn
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    a217e96d74faf9343306eba1de0f38e2ed040100 Mon Feb 4 23:12:36 2019 -0800
    ncbiGene is now a bigGenePred with NCBI URL outlinks for protein name and added description page for ncbiGene and fixed score filter max value for aaCounts refs #19937
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    58502ff9a4db966bdad267df1bc713fcc1b660b3 Wed Feb 6 17:47:52 2019 -0800
    Cleanup regeneron features. refs #22739
• src/hg/makeDb/trackDb/bacteria/staAur2/cons369way.html
  • lines changed 2316, context: html, text, full: html, text
    92746c40aacb7137b5b8bee81b4f413e83d2ed9f Mon Feb 4 14:26:22 2019 -0800
    catch up html page now with NCBI assembly outlinks refs #19937
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    b0cb85de5f3669ad674939c60c90191dcd86cd0a Tue Feb 5 08:33:26 2019 -0800
    add link to downloads directory on htdocs-hgdownload refs #19937
• src/hg/makeDb/trackDb/bacteria/staAur2/ncbiGene.html
  • lines changed 25, context: html, text, full: html, text
    36323c910dd2b3e2f1bcbafc5a939f45fd0616ad Mon Feb 4 22:59:16 2019 -0800
    ncbiGene track is no bigGenePred and has NCBI protein name URL outlink refs #19937
  • lines changed 25, context: html, text, full: html, text
    a217e96d74faf9343306eba1de0f38e2ed040100 Mon Feb 4 23:12:36 2019 -0800
    ncbiGene is now a bigGenePred with NCBI URL outlinks for protein name and added description page for ncbiGene and fixed score filter max value for aaCounts refs #19937
• src/hg/makeDb/trackDb/bacteria/staAur2/trackDb.ra
  • lines changed 32, context: html, text, full: html, text
    36323c910dd2b3e2f1bcbafc5a939f45fd0616ad Mon Feb 4 22:59:16 2019 -0800
    ncbiGene track is no bigGenePred and has NCBI protein name URL outlink refs #19937
  • lines changed 11, context: html, text, full: html, text
    a217e96d74faf9343306eba1de0f38e2ed040100 Mon Feb 4 23:12:36 2019 -0800
    ncbiGene is now a bigGenePred with NCBI URL outlinks for protein name and added description page for ncbiGene and fixed score filter max value for aaCounts refs #19937
• src/hg/makeDb/trackDb/chimp/panTro2/gold.html
  • lines changed 1, context: html, text, full: html, text
    0ba1792741e1c7b28ec76650e519656554aa698f Fri Feb 8 10:25:03 2019 -0800
    Updating redirected links for panTro2, uiLinks cronjob.
• src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra
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    12201b9a3be3009a066019d3171d186d16515ad1 Tue Feb 5 15:36:42 2019 -0800
    removing pennantIcon from fr3, refs #22761
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
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    a1240bdef28b973d822768154e4eab64bcdf77f2 Tue Feb 5 14:44:53 2019 -0800
    Removing stale pennantIcons
• src/hg/makeDb/trackDb/human/hg38/nonCodingRNAs.ra
  • lines changed 1, context: html, text, full: html, text
    a1240bdef28b973d822768154e4eab64bcdf77f2 Tue Feb 5 14:44:53 2019 -0800
    Removing stale pennantIcons
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    a1240bdef28b973d822768154e4eab64bcdf77f2 Tue Feb 5 14:44:53 2019 -0800
    Removing stale pennantIcons
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    a1240bdef28b973d822768154e4eab64bcdf77f2 Tue Feb 5 14:44:53 2019 -0800
    Removing stale pennantIcons
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    87e0a09f85192a066a9814afe5ba88925398305a Tue Feb 5 20:09:25 2019 -0800
    adding converter and first demo trackDb (only Breast cancer), refs #22742
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    86e60d009207a61d2f46c9849d10a04ebc26ed79 Thu Feb 7 07:18:41 2019 -0800
    adding pancan33 track, #22742
• src/hg/makeDb/trackDb/mouse/mm10/singleCell.html
  • lines changed 2, context: html, text, full: html, text
    e63ab05d916ec958cfdf7056b11b00753b0e921f Thu Feb 7 15:56:46 2019 -0800
    Removing a duplicate section of a paper reference, refs #22895
• src/hg/makeDb/trackDb/mouse/mm10/tabulamuris.ra
  • lines changed 1, context: html, text, full: html, text
    c89157f031488310d0351e5582cceeb9c7c0c1e3 Tue Feb 5 15:31:55 2019 -0800
    Hiding the splice junction tracks by default, refs #21811
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    d389ae00cb0ccb93fdbdd6f50aa1b814456b9a12 Wed Feb 6 11:51:15 2019 -0800
    Adding missing shortLabel descriptions, refs #21811
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    4b28b9643c71ce1894e3e7567a61573bc0f12351 Tue Feb 5 17:13:44 2019 -0800
    Turning off ucscRetroAli6 ref#22905
• src/hg/makeDb/trackDb/ntSeqContigs.html
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    0ba1792741e1c7b28ec76650e519656554aa698f Fri Feb 8 10:25:03 2019 -0800
    Updating redirected links for panTro2, uiLinks cronjob.
• src/hg/makeDb/trackDb/ntSeqReads.html
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    0ba1792741e1c7b28ec76650e519656554aa698f Fri Feb 8 10:25:03 2019 -0800
    Updating redirected links for panTro2, uiLinks cronjob.
• src/hg/makeDb/trackDb/tagTypes.tab
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    ace7d6c2a03c2ad76c14134546785b8c3fa61ac2 Tue Jan 8 11:39:09 2019 -0800
    Implement 'packDense' setting (tentative name) to support Regeneron 2nd contract amino acide display. This setting will pack items on a single line if they are adjacent (suppresses padding between packed items). refs #22739
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    a3badf9209cb200878acc8ae0cb74d2695032e83 Tue Jan 8 16:57:26 2019 -0800
    Exploratory work for Regeneron. refs #22739
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    459d5ecb521f2127de635683101db94ca4f5c5d5 Fri Jan 11 15:28:48 2019 -0800
    Setting to collapse empty subtracks. refs #22739
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    811c0ec699b51e705fe2364ad5c2c7f0981ac3f8 Mon Jan 14 16:50:58 2019 -0800
    Add setting for Regeneron. refs #22739
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    ebab466d2e7b25ce28a31f3fad3071762f2f162c Mon Feb 4 23:07:33 2019 -0800
    ncbiGene track is no bigGenePred and requires tagTypes.tab entries refs #19937
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    a217e96d74faf9343306eba1de0f38e2ed040100 Mon Feb 4 23:12:36 2019 -0800
    ncbiGene is now a bigGenePred with NCBI URL outlinks for protein name and added description page for ncbiGene and fixed score filter max value for aaCounts refs #19937
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    58502ff9a4db966bdad267df1bc713fcc1b660b3 Wed Feb 6 17:47:52 2019 -0800
    Cleanup regeneron features. refs #22739
• src/hg/makeDb/trackDb/worm/ce11/trackDb.135way.ra
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    a1240bdef28b973d822768154e4eab64bcdf77f2 Tue Feb 5 14:44:53 2019 -0800
    Removing stale pennantIcons
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
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    05094dabf3d005ab35a998ff225443fc4255611f Mon Feb 4 23:07:42 2019 -0800
    Adding ability to backup and restore the cart and its custom tracks in hgSession.
• src/inc/bigWig.h
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    79c5090c373a449c3fa3e83949736e7515f03da2 Tue Feb 5 09:36:59 2019 -0800
    support schemas on bigWigs within composites. #22885
• src/inc/common.mk
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    32de817ec809cc4edf2598e03c0a1c3f202d984c Sat Feb 9 14:07:30 2019 -0800
    new library locations for libssl and libcrypto on Mac OSX Mojave no redmine
• src/inc/spaceSaver.h
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    ace7d6c2a03c2ad76c14134546785b8c3fa61ac2 Tue Jan 8 11:39:09 2019 -0800
    Implement 'packDense' setting (tentative name) to support Regeneron 2nd contract amino acide display. This setting will pack items on a single line if they are adjacent (suppresses padding between packed items). refs #22739
• src/lib/bwgQuery.c
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    79c5090c373a449c3fa3e83949736e7515f03da2 Tue Feb 5 09:36:59 2019 -0800
    support schemas on bigWigs within composites. #22885
• src/lib/metaWig.c
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    79c5090c373a449c3fa3e83949736e7515f03da2 Tue Feb 5 09:36:59 2019 -0800
    support schemas on bigWigs within composites. #22885
• src/lib/spaceSaver.c
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    ace7d6c2a03c2ad76c14134546785b8c3fa61ac2 Tue Jan 8 11:39:09 2019 -0800
    Implement 'packDense' setting (tentative name) to support Regeneron 2nd contract amino acide display. This setting will pack items on a single line if they are adjacent (suppresses padding between packed items). refs #22739
• src/product/mirrorDocs/makefile
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    cdc9db24a93cf9bed359b213533860aab2de6e4b Fri Feb 8 08:50:00 2019 -0800
    Adding a test print command so we can see if pandoc will convert correctly, no refs
• src/utils/cancerMafToBigBed
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    1b2aa0c4e8b1b40a303328da21830a253749a57e Sat Feb 2 19:11:35 2019 +0100
    adding small tool to convert MAF files to bigBed. refs #22742
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    174946a4b501d43409f582bfe2ef0838a30acd6e Sat Feb 2 19:35:11 2019 +0100
    adding annotations to cancerMafToBigBed
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    87e0a09f85192a066a9814afe5ba88925398305a Tue Feb 5 20:09:25 2019 -0800
    adding converter and first demo trackDb (only Breast cancer), refs #22742
• src/utils/makefile
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    1b2aa0c4e8b1b40a303328da21830a253749a57e Sat Feb 2 19:11:35 2019 +0100
    adding small tool to convert MAF files to bigBed. refs #22742
• src/utils/qa/copyHgcentral
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    aee8ef5ddbb8cabd33efa4767fcf761aff0be5a5 Wed Feb 6 12:06:12 2019 -0800
    Fixing quoting error in copyHgcentral so chuck wills widow genome can be updated
• src/utils/qa/weeklybld/buildEnv.csh
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    e1844122763a7690ee729e1d7ddc080723247239 Mon Feb 11 09:56:56 2019 -0800
    v378 preview1, refs #22835

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