All File Changes

v339_preview2 to v339_base (2016-09-19 to 2016-09-26) v339

• src/hg/cirm/cdw/cdwWebBrowse/cdwHelp.html
  • lines changed 157, context: html, text, full: html, text
    8c8a44527ab1b6b94438ba96da7d1cd8c444693d Wed Sep 21 11:06:07 2016 -0700
    Making cdwWebBrowse help use Clay's new page.
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 9, context: html, text, full: html, text
    8c8a44527ab1b6b94438ba96da7d1cd8c444693d Wed Sep 21 11:06:07 2016 -0700
    Making cdwWebBrowse help use Clay's new page.
    
• src/hg/cirm/cdw/cdwWebBrowse/makefile
  • lines changed 4, context: html, text, full: html, text
    fe3b5ff79979fcf271abf2789924e8c29f0d35f9 Wed Sep 21 11:37:00 2016 -0700
    Adding steps to create cdwHelp.h
    
• src/hg/hgBlat/hgBlat.c
  • lines changed 1, context: html, text, full: html, text
    4f1aaa591d14ef02e785e2ae05f86c49129104af Wed Sep 21 14:27:01 2016 -0700
    fix XSS textarea in hgBlat. refs #17782.
    
• src/hg/hgTracks/cds.c
  • lines changed 1, context: html, text, full: html, text
    b41fc14e54398ab40c4141e6931df0693cb4b019 Wed Sep 21 11:08:40 2016 -0700
    recognize refSeqAli as a genbank table when grabbing sequence
    
• src/hg/hgTracks/lrgTrack.c
  • lines changed 1, context: html, text, full: html, text
    c7588c8db4889dbc5b03ae36c70a05b57af033b8 Thu Sep 22 10:19:09 2016 -0700
    Matt noticed that LRG items displayed backwards in full mode -- oops! Added the missing slReverse. refs #13359
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    00c3b2c9fdcd83c851db8f9c12fc47551dabdcd1 Wed Sep 21 12:20:58 2016 -0700
    fix the order of items in bigGenePred driven knownGene display
    
• src/hg/hgc/bigBedClick.c
  • lines changed 1, context: html, text, full: html, text
    547fafff699e3b2f00cd111de91ba560e29b5442 Fri Sep 23 16:07:28 2016 -0700
    crispr track: fixing a link problem visible only on firefox, refs #17235
    
• src/hg/htdocs/goldenPath/help/blatSpec.html
  • lines changed 2, context: html, text, full: html, text
    850b7d8ce4c1b5f779a7eaddd51ae3da9122d6a4 Mon Sep 19 13:37:32 2016 -0700
    adding missing detail in webBlat.cfg example
    
  • lines changed 11, context: html, text, full: html, text
    e771ca271fbf50808a1496fe610fbd6cb4342d2e Mon Sep 19 13:51:58 2016 -0700
    updated webBlat, made it more consistent.
    
  • lines changed 1, context: html, text, full: html, text
    562e47735c0fdd9253baa08310e74fdc9df5386e Tue Sep 20 12:19:06 2016 -0700
    Fixing small typo in blatSpec.html refs #18091
    
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 25, context: html, text, full: html, text
    1af41bf45358b845180f0a50e0abd72075ffb1d8 Mon Sep 19 13:50:15 2016 -0700
    doc'ing a few more CGI arguments, refs #18090
    
• src/hg/htdocs/images/cdwImages/createAccount.png
  • lines changed 0, context: html, text, full: html, text
    c58320471b388a9b6ad3d0cce66aa42739ec2c38 Wed Sep 21 10:59:59 2016 -0700
    Adding some binary files in support of the new help pages for cdwWebBrowse.
    
• src/hg/htdocs/images/cdwImages/dropdown.png
  • lines changed 0, context: html, text, full: html, text
    c58320471b388a9b6ad3d0cce66aa42739ec2c38 Wed Sep 21 10:59:59 2016 -0700
    Adding some binary files in support of the new help pages for cdwWebBrowse.
    
• src/hg/htdocs/images/cdwImages/files.png
  • lines changed 0, context: html, text, full: html, text
    c58320471b388a9b6ad3d0cce66aa42739ec2c38 Wed Sep 21 10:59:59 2016 -0700
    Adding some binary files in support of the new help pages for cdwWebBrowse.
    
• src/hg/htdocs/images/cdwImages/filter.png
  • lines changed 0, context: html, text, full: html, text
    c58320471b388a9b6ad3d0cce66aa42739ec2c38 Wed Sep 21 10:59:59 2016 -0700
    Adding some binary files in support of the new help pages for cdwWebBrowse.
    
• src/hg/htdocs/images/cdwImages/filtered.png
  • lines changed 0, context: html, text, full: html, text
    c58320471b388a9b6ad3d0cce66aa42739ec2c38 Wed Sep 21 10:59:59 2016 -0700
    Adding some binary files in support of the new help pages for cdwWebBrowse.
    
• src/hg/htdocs/images/cdwImages/loginScreen.png
  • lines changed 0, context: html, text, full: html, text
    c58320471b388a9b6ad3d0cce66aa42739ec2c38 Wed Sep 21 10:59:59 2016 -0700
    Adding some binary files in support of the new help pages for cdwWebBrowse.
    
• src/hg/htdocs/images/cdwImages/navigation.png
  • lines changed 0, context: html, text, full: html, text
    c58320471b388a9b6ad3d0cce66aa42739ec2c38 Wed Sep 21 10:59:59 2016 -0700
    Adding some binary files in support of the new help pages for cdwWebBrowse.
    
• src/hg/htdocs/inc/encodeProject.topbar.html
  • lines changed 2, context: html, text, full: html, text
    0a9325a5150a1f3715dddfc3449518399e850cd5 Thu Sep 22 14:18:29 2016 -0700
    Adding message about ENCODE data portal to topbar refs #18111
    
• src/hg/htdocs/training/index.html
  • lines changed 31, context: html, text, full: html, text
    fba3bc9e32aba201e37fb16d95ea2ebf71abfbc5 Sat Sep 24 09:32:14 2016 -0700
    fixed format of an item on vid index page. dropped workshops in GA, AL, and CO. added VEP/VAI workshop in Greece
    
• src/hg/htdocs/training/vids/index.html
  • lines changed 1, context: html, text, full: html, text
    fba3bc9e32aba201e37fb16d95ea2ebf71abfbc5 Sat Sep 24 09:32:14 2016 -0700
    fixed format of an item on vid index page. dropped workshops in GA, AL, and CO. added VEP/VAI workshop in Greece
    
• src/hg/htdocs/util.html
  • lines changed 2, context: html, text, full: html, text
    23006734e4b7badfcdce018f6af09e68c6bb8026 Mon Sep 19 17:23:43 2016 -0700
    Renamed phyloGif to phloPng. Fixes #18104.
    
• src/hg/inc/chainDb.h
  • lines changed 2, context: html, text, full: html, text
    8a3fc031d9181ba2448473ad8029042dcb9ae26e Sun Sep 18 21:28:22 2016 -0700
    initial pass at program to merge split table to remove need to support them
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    e45747fa3be910c892981352b9cac298178cfd27 Mon Sep 26 09:58:48 2016 -0700
    New version number v339
    
• src/hg/lib/bigPsl.c
  • lines changed 2, context: html, text, full: html, text
    2e206d7863e94079e3defe181a0c9a6599ff6600 Mon Sep 19 23:18:25 2016 -0700
    changed assert to errAbort so get useful message on invalid bigPsl
    
• src/hg/lib/jksql.c
  • lines changed 1, context: html, text, full: html, text
    8a3fc031d9181ba2448473ad8029042dcb9ae26e Sun Sep 18 21:28:22 2016 -0700
    initial pass at program to merge split table to remove need to support them
    
  • lines changed 3, context: html, text, full: html, text
    cf1c012cd06342fb0a5db804847dcc90c3cd3b66 Wed Sep 21 14:09:19 2016 -0700
    revert change made to sqlListTablesLike done due to my lame missunderstanding of how it worked
    
• src/hg/makeDb/doc/dm6.txt
  • lines changed 2, context: html, text, full: html, text
    29c8bf71cef86b2444f7de78d213d527b78081be Tue Sep 20 09:44:08 2016 -0700
    make makeDoc entry for Pfam track follow undocumented standards. ;-)
    
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 3, context: html, text, full: html, text
    3f048ceda64727796667d807cec1d478b124593d Thu Sep 22 10:12:15 2016 -0700
    fixup comment for gorGor5 lastz section refs #17580
    
• src/hg/makeDb/genbank/etc/ignore.idx
  • lines changed 24, context: html, text, full: html, text
    0ca843e479b32307898a24a0538e9478834e7cab Wed Sep 21 16:48:03 2016 -0700
    more thinks I have to pay attention to in order for them to be ignored
    
• src/hg/makeDb/hgMergeSplitTables/hgMergeSplitTables.c
  • lines changed 791, context: html, text, full: html, text
    8a3fc031d9181ba2448473ad8029042dcb9ae26e Sun Sep 18 21:28:22 2016 -0700
    initial pass at program to merge split table to remove need to support them
    
  • lines changed 1, context: html, text, full: html, text
    cf1c012cd06342fb0a5db804847dcc90c3cd3b66 Wed Sep 21 14:09:19 2016 -0700
    revert change made to sqlListTablesLike done due to my lame missunderstanding of how it worked
    
• src/hg/makeDb/hgMergeSplitTables/makefile
  • lines changed 4, context: html, text, full: html, text
    8a3fc031d9181ba2448473ad8029042dcb9ae26e Sun Sep 18 21:28:22 2016 -0700
    initial pass at program to merge split table to remove need to support them
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    00454ff955d7032804b47ea8d97c73a62f331d27 Tue Sep 20 15:10:54 2016 -0700
    Adding pfam table to tables ignored for dm6 since there are no current joins, refs #18094
    
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    0b17ba7da17eccf7f7d5f4e915e96b5809011e48 Wed Sep 21 10:30:21 2016 -0700
    Adding snp148 entries to all.joiner, refs #16846
    
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
  • lines changed 1, context: html, text, full: html, text
    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/cat/felCat3/multiz4way.html
  • lines changed 1, context: html, text, full: html, text
    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
  • lines changed 1, context: html, text, full: html, text
    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/chicken/galGal3/multiz7way.html
  • lines changed 1, context: html, text, full: html, text
    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
  • lines changed 1, context: html, text, full: html, text
    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/chimp/panTro5/defaultPriority.ra
  • lines changed 6, context: html, text, full: html, text
    a43948a60b10302e1c9a09dd10a56030fee10fbf Thu Sep 22 15:06:05 2016 -0700
    changing default tracks for panTro5
    
• src/hg/makeDb/trackDb/chimp/panTro5/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    a43948a60b10302e1c9a09dd10a56030fee10fbf Thu Sep 22 15:06:05 2016 -0700
    changing default tracks for panTro5
    
  • lines changed 1, context: html, text, full: html, text
    89b2c6ac24dbefc8fc813af1cb669b6526920d41 Thu Sep 22 15:16:29 2016 -0700
    change default track setting panTro5
    
• src/hg/makeDb/trackDb/chimp/panTro5/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    89b2c6ac24dbefc8fc813af1cb669b6526920d41 Thu Sep 22 15:16:29 2016 -0700
    change default track setting panTro5
    
• src/hg/makeDb/trackDb/chlorocebus/chlSab2/description.html
  • lines changed 1, context: html, text, full: html, text
    730b6a7e0e5a85215ca0ecfbeac38881f61f3b1e Fri Sep 23 09:03:23 2016 -0700
    Fixing up vervet description page, refs #11172
    
• src/hg/makeDb/trackDb/cow/bosTau4/multiz5way.html
  • lines changed 1, context: html, text, full: html, text
    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/cow/snp148.html
  • lines changed 16, context: html, text, full: html, text
    82adbc5c26c7fd0cb1d5a2f79a788afc6690ba31 Wed Sep 21 09:44:29 2016 -0700
    removing common and flagged snp info, refs #16846
    
• src/hg/makeDb/trackDb/cow/snp148.shared.html
  • lines changed 13, context: html, text, full: html, text
    82adbc5c26c7fd0cb1d5a2f79a788afc6690ba31 Wed Sep 21 09:44:29 2016 -0700
    removing common and flagged snp info, refs #16846
    
• src/hg/makeDb/trackDb/crispr.html
  • lines changed 1, context: html, text, full: html, text
    9dee11139a7501815177e4074d358fe3157a0175 Fri Sep 23 14:53:30 2016 -0700
    Making description page match shortLabel for crispr regions track, refs #17235
    
  • lines changed 3, context: html, text, full: html, text
    5ad76834a408d93a2f9395767335c670f17d5bd5 Fri Sep 23 16:08:24 2016 -0700
    renaming crispr track ranges to regions, refs #71235
    
  • lines changed 1, context: html, text, full: html, text
    c7510928697ac791c5dc833e25546ee0f2d72f0c Fri Sep 23 16:13:20 2016 -0700
    typo
    
• src/hg/makeDb/trackDb/drosophila/dm6/cons27way.html
  • lines changed 1, context: html, text, full: html, text
    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/ebola/bunEbo1/cons160way.html
  • lines changed 1, context: html, text, full: html, text
    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/ebola/eboVir2/cons49way.html
  • lines changed 1, context: html, text, full: html, text
    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
  • lines changed 1, context: html, text, full: html, text
    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/ebola/resEbo1/cons160way.html
  • lines changed 1, context: html, text, full: html, text
    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/ebola/sudEbo1/cons160way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/ebola/taiEbo1/cons160way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/ebola/zaiEbo1/cons160way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/fugu/fr2/multiz5way.html
  • lines changed 1, context: html, text, full: html, text
    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/fugu/fr3/cons8way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/galVar/galVar1/cons5way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/gorilla/gorGor3/cons11way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/gorilla/gorGor5/description.html
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    a7ffc565995fe15966231e79c1ea4dbb0ac77b0d Thu Sep 22 14:43:36 2016 -0700
    Fixed broken links on gateway page, refs #17580
    
• src/hg/makeDb/trackDb/gorilla/gorGor5/gap.html
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    fd331485f67c4260b738021bee4126140a29f498 Tue Sep 20 15:06:47 2016 -0700
    correct technology discussion for gold and gap tracks refs #17580
    
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    c382a888c03bb42dec7990ea657e12fbb10082fa Thu Sep 22 14:09:06 2016 -0700
    Changed the order of the references, refs #17580
    
• src/hg/makeDb/trackDb/gorilla/gorGor5/gold.html
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    fd331485f67c4260b738021bee4126140a29f498 Tue Sep 20 15:06:47 2016 -0700
    correct technology discussion for gold and gap tracks refs #17580
    
  • lines changed 16, context: html, text, full: html, text
    c382a888c03bb42dec7990ea657e12fbb10082fa Thu Sep 22 14:09:06 2016 -0700
    Changed the order of the references, refs #17580
    
• src/hg/makeDb/trackDb/gorilla/gorGor5/trackDb.ra
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    2d32d14c3a6c69ee163ce78c8bc0b4af22149ba2 Thu Sep 22 15:23:17 2016 -0700
    Changing xenoRefGene track to pack by default, refs #17580
    
• src/hg/makeDb/trackDb/guineaPig/cavPor3/cons5way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/horse/equCab2/multiz6way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/human/dgvPlus.html
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    1db293471cccdda01232c3de29d7cc73efe6d78b Tue Sep 20 10:51:21 2016 -0700
    Putting references in alphabetical order, refs #17351
    
• src/hg/makeDb/trackDb/human/hg17/multiz10way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/human/hg17/multiz17way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/human/hg17/multiz7way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/human/hg18/cons44way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/human/hg18/defaultPriority.ra
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    841f8596a14376775454a3f6c1f4d2eacc3a2dfd Wed Sep 21 17:00:40 2016 -0700
    Adding release tags to knownGene in hg18,hg19,hg38,mm10,mm9 where alpha,beta have new bigGeneDataUrl and public does not refs #15259
    
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    886021f4c3f836ebba6a973c01030ac45d0c1b1a Thu Sep 22 09:34:47 2016 -0700
    Adjusting public priority status for knownGene mm9,mm10,hg18 refs #15259
    
• src/hg/makeDb/trackDb/human/hg18/multiz28way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/human/hg18/multizPrimate.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
  • lines changed 1, context: html, text, full: html, text
    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    841f8596a14376775454a3f6c1f4d2eacc3a2dfd Wed Sep 21 17:00:40 2016 -0700
    Adding release tags to knownGene in hg18,hg19,hg38,mm10,mm9 where alpha,beta have new bigGeneDataUrl and public does not refs #15259
    
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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    841f8596a14376775454a3f6c1f4d2eacc3a2dfd Wed Sep 21 17:00:40 2016 -0700
    Adding release tags to knownGene in hg18,hg19,hg38,mm10,mm9 where alpha,beta have new bigGeneDataUrl and public does not refs #15259
    
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    f964b14dff2b59b626586c2a6e89c18006669f90 Mon Sep 19 10:05:56 2016 -0700
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    86987338868c089ac07378d440a5c245d6ef654a Wed Sep 21 19:36:10 2016 -0700
    remove test 100way default species track
    
• src/hg/makeDb/trackDb/human/trackDb.ra
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    18c81815392e17176e47b085cbfaf2f63ca42315 Tue Sep 20 14:15:37 2016 -0700
    Changing release tags for dgv track, refs #17351
    
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    1c12b250e294a2d29e35d12dbb8a988f502f4811 Tue Sep 20 14:50:43 2016 -0700
    Removed old dgv stanza, refs #17351
    
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    ce2680afd6c993d112e01296b3b36eb1147b9604 Tue Sep 20 18:45:28 2016 -0700
    changed name of omim allele track to drop word SNPs, per Ada Hamosh. refs #17831
    
• src/hg/makeDb/trackDb/lamprey/petMar1/multiz6way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/lancelet/braFlo1/multiz5way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/medaka/oryLat1/multiz5way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/mouse/mm10/defaultPriority.ra
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    841f8596a14376775454a3f6c1f4d2eacc3a2dfd Wed Sep 21 17:00:40 2016 -0700
    Adding release tags to knownGene in hg18,hg19,hg38,mm10,mm9 where alpha,beta have new bigGeneDataUrl and public does not refs #15259
    
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    886021f4c3f836ebba6a973c01030ac45d0c1b1a Thu Sep 22 09:34:47 2016 -0700
    Adjusting public priority status for knownGene mm9,mm10,hg18 refs #15259
    
• src/hg/makeDb/trackDb/mouse/mm8/multiz17way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/mouse/mm9/defaultPriority.ra
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    841f8596a14376775454a3f6c1f4d2eacc3a2dfd Wed Sep 21 17:00:40 2016 -0700
    Adding release tags to knownGene in hg18,hg19,hg38,mm10,mm9 where alpha,beta have new bigGeneDataUrl and public does not refs #15259
    
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    886021f4c3f836ebba6a973c01030ac45d0c1b1a Thu Sep 22 09:34:47 2016 -0700
    Adjusting public priority status for knownGene mm9,mm10,hg18 refs #15259
    
• src/hg/makeDb/trackDb/mouse/mm9/multiz30way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/opossum/monDom4/multiz7way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/opossum/monDom5/multiz9way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/platypus/ornAna1/multiz6way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/rat/rn4/multiz9way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/rat/rn5/cons13way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/refGenePfam.html
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    58457bc18da6a8c2868b375b4265ae40fba2cad4 Mon Sep 19 10:35:26 2016 -0700
    add detail page for refGenePfam track
    
• src/hg/makeDb/trackDb/stickleback/gasAcu1/multiz8way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons17way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons20way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/trackDb.ra
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    153fade3fa83f36495ca5995bb6fdbcbd09eb2d6 Tue Sep 20 15:45:08 2016 -0700
    Capitlizing S in RefSeq for Pfam in RefSeq Genes track, refs #18094
    
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    6d8fa858d5720957b2994f3b941b4d2b30517ef7 Wed Sep 21 08:01:20 2016 -0700
    Shortening shortLabel of refGenePfam track on dm6, refs #18094
    
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    547fafff699e3b2f00cd111de91ba560e29b5442 Fri Sep 23 16:07:28 2016 -0700
    crispr track: fixing a link problem visible only on firefox, refs #17235
    
• src/hg/makeDb/trackDb/worm/ce10/cons7way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makeDb/trackDb/worm/ce10/cons9way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/worm/ce11/cons26way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/worm/ce6/multiz6way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/zebrafish/danRer3/multiz5way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
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• src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html
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    42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700
    renamed phyloGif to phyloPng. refs #18104.
    
• src/hg/makefile
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    aa2868d81e0ceb67d971112ee42118e298c3ee08 Mon Sep 19 17:35:48 2016 -0700
    Renamed phyloGif to phloPng. Refs #18104.
    
• src/hg/mrnaToGene/mrnaToGene.c
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    2124d33552ad625470e6136295530e804a2ed8c7 Fri Sep 23 22:30:04 2016 -0700
    fixed confused help message (that I wrote)
    
• src/hg/phyloGif/17way.nh
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    6894b3e9c5590a37147afd1485f21f07285c7ed1 Mon Sep 19 17:10:21 2016 -0700
    Renamed phyloGif to phloPng for greater accuracy in the name. Because when we switched to PNG, only 16-bit color palettes are supported now. We lost the ability to do 8-bit color palette which is needed by GIF.
    
• src/hg/phyloGif/makefile
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    6894b3e9c5590a37147afd1485f21f07285c7ed1 Mon Sep 19 17:10:21 2016 -0700
    Renamed phyloGif to phloPng for greater accuracy in the name. Because when we switched to PNG, only 16-bit color palettes are supported now. We lost the ability to do 8-bit color palette which is needed by GIF.
    
• src/hg/phyloGif/phyloGif.c
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    fixing XSS problem in phyloGif
    
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    6894b3e9c5590a37147afd1485f21f07285c7ed1 Mon Sep 19 17:10:21 2016 -0700
    Renamed phyloGif to phloPng for greater accuracy in the name. Because when we switched to PNG, only 16-bit color palettes are supported now. We lost the ability to do 8-bit color palette which is needed by GIF.
    
• src/hg/phyloPng/17way.nh
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    6894b3e9c5590a37147afd1485f21f07285c7ed1 Mon Sep 19 17:10:21 2016 -0700
    Renamed phyloGif to phloPng for greater accuracy in the name. Because when we switched to PNG, only 16-bit color palettes are supported now. We lost the ability to do 8-bit color palette which is needed by GIF.
    
• src/hg/phyloPng/makefile
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    6894b3e9c5590a37147afd1485f21f07285c7ed1 Mon Sep 19 17:10:21 2016 -0700
    Renamed phyloGif to phloPng for greater accuracy in the name. Because when we switched to PNG, only 16-bit color palettes are supported now. We lost the ability to do 8-bit color palette which is needed by GIF.
    
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    165031e4604f8cd4905100753c686a3e66d1ff91 Fri Sep 23 11:29:16 2016 -0700
    rename phyloGif to phyloPng
    
• src/hg/phyloPng/phyloPng.c
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    6894b3e9c5590a37147afd1485f21f07285c7ed1 Mon Sep 19 17:10:21 2016 -0700
    Renamed phyloGif to phloPng for greater accuracy in the name. Because when we switched to PNG, only 16-bit color palettes are supported now. We lost the ability to do 8-bit color palette which is needed by GIF.
    
• src/hg/utils/automation/makePushQSql.pl
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    aa2868d81e0ceb67d971112ee42118e298c3ee08 Mon Sep 19 17:35:48 2016 -0700
    Renamed phyloGif to phloPng. Refs #18104.
    
• src/hg/utils/genePredToBigGenePred/makeBigKnown
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    1490b71d8c02bdcc0690fc472bdcaada4496471f Thu Sep 22 12:14:45 2016 -0700
    modify how bigGenePreds are made from knownGene
    
• src/hg/utils/otto/isca/buildISCA.csh
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    75bebe2c8e43137b522b2a02af7385dc7302b9ab Fri Sep 23 15:09:00 2016 -0700
    A better glob skips all patch mappings in ClinGen processing
    
• src/hg/visiGene/hgVisiGene/hgVisiGene.c
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    285c2491df2e77edf845a763afb008a3a733220f Mon Sep 19 16:52:41 2016 -0700
    fixing XSS problem in VisiGene search box
    
• src/lib/cheapcgi.c
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    86516ebc28dc4b6c7c96067e66469308880d7502 Wed Sep 21 12:55:16 2016 -0700
    Fixes XSS problem found in hgVisiGene. refs #17782.
    
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    324f433e00cd05daeba5403195601ba0a03cdbeb Wed Sep 21 16:56:46 2016 -0700
    Fixes oops and adds comment about unfinished XSS issues for javascript parameters. refs #17782.
    
• src/utils/bdfToGem/menlo/README
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    aa2868d81e0ceb67d971112ee42118e298c3ee08 Mon Sep 19 17:35:48 2016 -0700
    Renamed phyloGif to phloPng. Refs #18104.
    
• src/utils/bedBetween
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    557415034ca7f233f8f4b5be7201261136ed80ae Wed Sep 21 16:13:31 2016 -0700
    small fix to two crispr-related utils
    
• src/utils/doLocusName
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    557415034ca7f233f8f4b5be7201261136ed80ae Wed Sep 21 16:13:31 2016 -0700
    small fix to two crispr-related utils
    
• src/utils/qa/weeklybld/buildEnv.csh
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    fb715de270a9372e6243d6b5121c2bde91dfcddd Mon Sep 26 09:56:53 2016 -0700
    v339 final build refs #17782
    
• src/webBlat/install.txt
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    4f059beb788c0f7685ae2c95958d45e649f2f805 Mon Sep 19 14:10:25 2016 -0700
    updating webBlat docs and making consistent
    
• src/webBlat/webBlat.cfg
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    4f059beb788c0f7685ae2c95958d45e649f2f805 Mon Sep 19 14:10:25 2016 -0700
    updating webBlat docs and making consistent
    

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