All File Changes

v335_preview2 to v335_base (2016-06-27 to 2016-07-04) v335

• src/blat/version.doc
  • lines changed 2, context: html, text, full: html, text
    cf293df150f4b256d195e90b5a20817d8479ece0 Sat Jul 2 13:17:59 2016 -0700
    fixes #17624. -maxIntron= was broken in blat whenever a non-default value was used causing it to run cutAtBigIntrons() which did not support protein. The fix was using trans3GenoPos() to get correct coordinates handling 3 frames, and also calling ffScoreProtein() instead of ffScore() when it is a protein query.
    
• src/hg/cirm/cdw/cdwDumpManiFiles/cdwDumpManiFiles.c
  • lines changed 181, context: html, text, full: html, text
    3f760544c01bdb2327fd49d8a6088db12bd303a0 Wed Jun 29 12:02:34 2016 -0700
    A program that copies the distinct manifest files and most recent meta files for a cirm submission into a specified directory, refs #17619
    
• src/hg/cirm/cdw/cdwDumpManiFiles/makefile
  • lines changed 4, context: html, text, full: html, text
    3f760544c01bdb2327fd49d8a6088db12bd303a0 Wed Jun 29 12:02:34 2016 -0700
    A program that copies the distinct manifest files and most recent meta files for a cirm submission into a specified directory, refs #17619
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwFlowCharts.c
  • lines changed 297, context: html, text, full: html, text
    6aed8f439c634b658068f823c6b82194c29c9d30 Fri Jun 24 12:14:40 2016 -0700
    Major revisions, new recursion for looking forward and a bunch of robustness checks added. The code is still not up to production level but it is working correctly in this state, refs #17544
    
  • lines changed 64, context: html, text, full: html, text
    4748a978569a66642e5713c7e56eacbd69f89362 Mon Jun 27 13:08:20 2016 -0700
    Fixing comment and variable names, refs #17544
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 7, context: html, text, full: html, text
    a1a81e4aeb6b7d37897686223d1d23468cdb7238 Mon Jun 27 10:49:15 2016 -0700
    Going through and bringing the code up to standards, commenting variable names etc, refs #17544
    
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    98bf562f63bb05060d786d24d797b9ca86746d84 Mon Jun 27 15:42:20 2016 -0700
    Reverting a change that should not have been pushed, refs #17544
    
• src/hg/hgCustom/hgCustom.c
  • lines changed 4, context: html, text, full: html, text
    49dd3ac0e030676ecf09c80494f5a652352a7520 Thu Jun 30 16:00:34 2016 -0700
    Adding hgCustom.c links to new track formats refs #14717
    
• src/hg/hgGene/hgGeneData/Human/hg15/otherOrgs.ra
  • lines changed 18, context: html, text, full: html, text
    19dbed83451bec7177ac6ebbbd17b161e1609c32 Wed Jun 29 12:23:18 2016 -0700
    fix up hg38 otherOrgs.ra to delete links to other species without hgGene
    
• src/hg/hgGene/hgGeneData/Human/hg16/otherOrgs.ra
  • lines changed 17, context: html, text, full: html, text
    19dbed83451bec7177ac6ebbbd17b161e1609c32 Wed Jun 29 12:23:18 2016 -0700
    fix up hg38 otherOrgs.ra to delete links to other species without hgGene
    
• src/hg/hgGene/hgGeneData/Human/hg17/otherOrgs.ra
  • lines changed 15, context: html, text, full: html, text
    19dbed83451bec7177ac6ebbbd17b161e1609c32 Wed Jun 29 12:23:18 2016 -0700
    fix up hg38 otherOrgs.ra to delete links to other species without hgGene
    
• src/hg/hgGene/hgGeneData/Human/hg18/otherOrgs.ra
  • lines changed 15, context: html, text, full: html, text
    19dbed83451bec7177ac6ebbbd17b161e1609c32 Wed Jun 29 12:23:18 2016 -0700
    fix up hg38 otherOrgs.ra to delete links to other species without hgGene
    
• src/hg/hgGene/hgGeneData/Human/hg19/otherOrgs.ra
  • lines changed 15, context: html, text, full: html, text
    19dbed83451bec7177ac6ebbbd17b161e1609c32 Wed Jun 29 12:23:18 2016 -0700
    fix up hg38 otherOrgs.ra to delete links to other species without hgGene
    
• src/hg/hgGene/hgGeneData/Human/hg38/otherOrgs.ra
  • lines changed 7, context: html, text, full: html, text
    19dbed83451bec7177ac6ebbbd17b161e1609c32 Wed Jun 29 12:23:18 2016 -0700
    fix up hg38 otherOrgs.ra to delete links to other species without hgGene
    
• src/hg/hgGene/hgGeneData/Human/otherOrgs.ra
  • lines changed 24, context: html, text, full: html, text
    bce4fe1b88cbe14c14ba8292ee15fa420cf908bb Wed Jun 29 12:24:19 2016 -0700
    delete Human otherOrgs.ra
    
• src/hg/hgMenubar/hgMenubar.c
  • lines changed 22, context: html, text, full: html, text
    5dab84a761280b1155aa58b756fa2c4ecf4baef5 Thu Jun 30 09:13:50 2016 -0700
    Added optional CGI param to hgMenubar to specify a file other than inc/globalNavBar.inc, so the same correction of relative links can be applied to other files such as inc/jWestFooter.html. refs #17470
    
• src/hg/hgTables/identifiers.c
  • lines changed 6, context: html, text, full: html, text
    d229ccd25b8ed02ab143f8cfc2e174ebd749a03b Tue Jun 28 17:37:20 2016 -0700
    deal with table names in idXref statements of the form db.table
    
• src/hg/hgTablesTest/hgTablesTest.c
  • lines changed 127, context: html, text, full: html, text
    8ba435bdd1a1fda7d9f05e027477b6b9d8bdc7f4 Wed Jun 29 11:18:08 2016 -0700
    About to remove findExpectedIntersectingRows() because it seems less necessary now.
    
  • lines changed 70, context: html, text, full: html, text
    90048b6df4aec62edab4c7f49f7a5084776db6a8 Wed Jun 29 11:23:00 2016 -0700
    hgTablesTest, cleaned up. hgTablesTest now supports new options -seed=N and -noShuffle.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 33, context: html, text, full: html, text
    e3fb0aba1be876cee6d93465cc0e585dac75529a Thu Jun 30 17:40:34 2016 -0700
    fixes #17617. Just changed customUrl mode to act like em and gm. instead of trying to have the user switch to a full-virt-chrom view, it simply tries to find the nearest position, which is just what em and gm modes do.
    
  • lines changed 1, context: html, text, full: html, text
    d4d8f531049ad83078fb6130e3d6a341abb5c97b Fri Jul 1 16:38:21 2016 -0700
    Adding hgTracks keyboard shortcut to Public Sessions CGI, refs #17469
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 10, context: html, text, full: html, text
    1f113a15a2cbcbdfeb4040188432cd3d013a57be Mon Jun 27 14:56:13 2016 -0700
    allow chain/net coloring of contig based assemblies with WGS naming schemes refs #17580
    
  • lines changed 1, context: html, text, full: html, text
    52638bd89b284d3d524cc2a5d978032759a90c96 Mon Jun 27 15:41:46 2016 -0700
    do not need the regexHelper.h refs #1758
    
  • lines changed 30, context: html, text, full: html, text
    a50ed53aff81d6fb3e34e6913ce18578292bc24e Tue Jun 28 15:00:42 2016 -0700
    implement an arbitrary 10-color palette scheme for scaffold/contig coloring refs #17580
    
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 90, context: html, text, full: html, text
    c2d7c5a8bf11f342681d0520bba429e739a140ce Tue Jun 28 13:28:22 2016 -0700
    Adding FAQ about evicted tables now residing in hgFixed, refs #17611
    
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 40, context: html, text, full: html, text
    4615346960de407d01970bc97b45c2bb9236c189 Wed Jun 29 13:02:06 2016 -0700
    Adding links to new cram format page #14717
    
• src/hg/htdocs/contacts.html
  • lines changed 2, context: html, text, full: html, text
    a3e7d2ccfd82475284b19db7187ad6ba5e414a01 Thu Jun 30 09:27:27 2016 -0700
    Updated staff picture.
    
• src/hg/htdocs/goldenPath/help/bigChain.html
  • lines changed 4, context: html, text, full: html, text
    2ece489e250370c3ea798eb3000821fc409b6d0b Tue Jun 28 10:10:46 2016 -0700
    Adding changes suggested by code review, refs #17604
    
  • lines changed 2, context: html, text, full: html, text
    b39e0faf9c053b302f088ec8da25db2b43761b3b Tue Jun 28 13:47:16 2016 -0700
    Fixing custom track links to load in correct position and viz, refs #17325
    
• src/hg/htdocs/goldenPath/help/bigMaf.html
  • lines changed 5, context: html, text, full: html, text
    2ece489e250370c3ea798eb3000821fc409b6d0b Tue Jun 28 10:10:46 2016 -0700
    Adding changes suggested by code review, refs #17604
    
  • lines changed 1, context: html, text, full: html, text
    ca181173652db5ba85dc107ff6d59b0c10b2ca8f Tue Jun 28 12:06:06 2016 -0700
    Fixing typo in link to gene pred file, refs #17325
    
  • lines changed 2, context: html, text, full: html, text
    b39e0faf9c053b302f088ec8da25db2b43761b3b Tue Jun 28 13:47:16 2016 -0700
    Fixing custom track links to load in correct position and viz, refs #17325
    
• src/hg/htdocs/goldenPath/help/bigPsl.html
  • lines changed 4, context: html, text, full: html, text
    52bcc9380addad4c3f9de607a0f22f5e4fe5f651 Mon Jun 27 15:46:32 2016 -0700
    Fixing typos suggested by code review, refs #17604
    
  • lines changed 2, context: html, text, full: html, text
    b39e0faf9c053b302f088ec8da25db2b43761b3b Tue Jun 28 13:47:16 2016 -0700
    Fixing custom track links to load in correct position and viz, refs #17325
    
• src/hg/htdocs/goldenPath/help/cram.html
  • lines changed 201, context: html, text, full: html, text
    5947d1ab9f8d22c4347867fe2fe17c71ee92093f Tue Jun 28 16:22:11 2016 -0700
    Adding new cram.html page ref #14717
    
  • lines changed 1, context: html, text, full: html, text
    4615346960de407d01970bc97b45c2bb9236c189 Wed Jun 29 13:02:06 2016 -0700
    Adding links to new cram format page #14717
    
  • lines changed 81, context: html, text, full: html, text
    3d574f0f87e3eafaf550db935cb23ba6c66b0d7b Thu Jun 30 11:51:11 2016 -0700
    Adding changes to cram.html based on feedback, refUrl example added refs #14717
    
  • lines changed 1, context: html, text, full: html, text
    3ea09d4f819c0d245a79714575c35336c4ec7bfe Fri Jul 1 09:19:23 2016 -0700
    Correcting typo on cram.html
    
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 4, context: html, text, full: html, text
    4615346960de407d01970bc97b45c2bb9236c189 Wed Jun 29 13:02:06 2016 -0700
    Adding links to new cram format page #14717
    
• src/hg/htdocs/goldenPath/help/genomeEuro.html
  • lines changed 1, context: html, text, full: html, text
    79c21d9289bf749a55ef270cdfee92e7d5a45bfd Tue Jun 28 14:35:00 2016 -0700
    changed the image so the pulldown now has genome-asia, too. also it now has the new gateway n the background. fixed a broken umlaut on Univeristat Bielefeld. refs #17402
    
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 11, context: html, text, full: html, text
    1049f89fb6ee870b2686aa8558189f9bf4c81c1a Tue Jun 28 09:17:27 2016 -0700
    Updating some text about our session expiration policy ahead of Public Sessions announcement, refs #15312 #14724
    
  • lines changed 1, context: html, text, full: html, text
    1af4515151c25ae880efc23781931d9a7f587aa8 Fri Jul 1 10:51:30 2016 -0700
    Minor change based on CR, refs #17602
    
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 19, context: html, text, full: html, text
    a768b1468d081895d9d41c93ce6b90da71215c8c Tue Jun 28 09:59:16 2016 -0700
    Adding section about bigStar tracks to hgTrackHubHelp, adding bigStar info to trackDbLibrary, refs #17325
    
  • lines changed 18, context: html, text, full: html, text
    4615346960de407d01970bc97b45c2bb9236c189 Wed Jun 29 13:02:06 2016 -0700
    Adding links to new cram format page #14717
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 3, context: html, text, full: html, text
    de54944c94ffcb78a67a1cb3c5ec93bd11af1c7b Fri Jul 1 15:06:00 2016 -0700
    documenting mouseOverField trackDb option, as per Kate, no redmine
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v1.html
  • lines changed 3, context: html, text, full: html, text
    de54944c94ffcb78a67a1cb3c5ec93bd11af1c7b Fri Jul 1 15:06:00 2016 -0700
    documenting mouseOverField trackDb option, as per Kate, no redmine
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 3, context: html, text, full: html, text
    a768b1468d081895d9d41c93ce6b90da71215c8c Tue Jun 28 09:59:16 2016 -0700
    Adding section about bigStar tracks to hgTrackHubHelp, adding bigStar info to trackDbLibrary, refs #17325
    
  • lines changed 2, context: html, text, full: html, text
    de54944c94ffcb78a67a1cb3c5ec93bd11af1c7b Fri Jul 1 15:06:00 2016 -0700
    documenting mouseOverField trackDb option, as per Kate, no redmine
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 41, context: html, text, full: html, text
    9f07556e8f11d2e3778a73064ce58367a6bff812 Tue Jun 28 10:47:42 2016 -0700
    Adding announcement for Public Sessions page, removing older announcements, refs #15312
    
  • lines changed 58, context: html, text, full: html, text
    8f54eba62d6f5805969fe36a58e1a4c970903a64 Thu Jun 30 13:41:06 2016 -0700
    Announcing UCSC Genes release, refs #15315 and #10968
    
  • lines changed 27, context: html, text, full: html, text
    4d66c70ec97d6efbed1dac76f1b617752f8a7b00 Thu Jun 30 15:01:37 2016 -0700
    Adding news release about CRAM file refs #17499
    
  • lines changed 1, context: html, text, full: html, text
    49dd3ac0e030676ecf09c80494f5a652352a7520 Thu Jun 30 16:00:34 2016 -0700
    Adding hgCustom.c links to new track formats refs #14717
    
  • lines changed 1, context: html, text, full: html, text
    ca6d979e4c48448764af58f243a59c79241909c1 Fri Jul 1 12:54:31 2016 -0700
    Change news item links so they go to the correct place, no redmine
    
• src/hg/htdocs/images/dna-163466_960_720_rotated.jpg
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    c43bcc0e7251182c280ed8c1a1fdf592ccf827c4 Tue Apr 12 13:56:18 2016 -0700
    New home page designed by Jim & others, using styles from the new gateway page design. refs #17470, #15277
    
• src/hg/htdocs/images/gbstaff16.jpg
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    242e89742860c5a722d950b0f97148de41d8758f Thu Jun 30 09:25:36 2016 -0700
    Adding new Staff Image refs #17616
    
  • lines changed 0, context: html, text, full: html, text
    a3e7d2ccfd82475284b19db7187ad6ba5e414a01 Thu Jun 30 09:27:27 2016 -0700
    Updated staff picture.
    
  • lines changed 0, context: html, text, full: html, text
    3788a75a3c83d79317886a59a57a2fc865cf5a10 Thu Jun 30 10:25:10 2016 -0700
    made the image lighter, and smaller to fit actual display size
    
• src/hg/htdocs/images/server_selector.jpg
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    79c21d9289bf749a55ef270cdfee92e7d5a45bfd Tue Jun 28 14:35:00 2016 -0700
    changed the image so the pulldown now has genome-asia, too. also it now has the new gateway n the background. fixed a broken umlaut on Univeristat Bielefeld. refs #17402
    
• src/hg/htdocs/images/session.hg19.cramExample.png
  • lines changed 0, context: html, text, full: html, text
    b82741486c2278116fa9286a798c7facc0381da4 Tue Jun 28 14:35:22 2016 -0700
    Adding image of cram density graph refs #14717
    
• src/hg/htdocs/inc/jWestFooter.html
  • lines changed 1, context: html, text, full: html, text
    c43bcc0e7251182c280ed8c1a1fdf592ccf827c4 Tue Apr 12 13:56:18 2016 -0700
    New home page designed by Jim & others, using styles from the new gateway page design. refs #17470, #15277
    
• src/hg/htdocs/index.html
  • lines changed 134, context: html, text, full: html, text
    c43bcc0e7251182c280ed8c1a1fdf592ccf827c4 Tue Apr 12 13:56:18 2016 -0700
    New home page designed by Jim & others, using styles from the new gateway page design. refs #17470, #15277
    
  • lines changed 3, context: html, text, full: html, text
    5dab84a761280b1155aa58b756fa2c4ecf4baef5 Thu Jun 30 09:13:50 2016 -0700
    Added optional CGI param to hgMenubar to specify a file other than inc/globalNavBar.inc, so the same correction of relative links can be applied to other files such as inc/jWestFooter.html. refs #17470
    
• src/hg/htdocs/indexInfo.html
  • lines changed 30, context: html, text, full: html, text
    c43bcc0e7251182c280ed8c1a1fdf592ccf827c4 Tue Apr 12 13:56:18 2016 -0700
    New home page designed by Jim & others, using styles from the new gateway page design. refs #17470, #15277
    
• src/hg/htdocs/indexIntro.html
  • lines changed 114, context: html, text, full: html, text
    c43bcc0e7251182c280ed8c1a1fdf592ccf827c4 Tue Apr 12 13:56:18 2016 -0700
    New home page designed by Jim & others, using styles from the new gateway page design. refs #17470, #15277
    
• src/hg/htdocs/indexNews.html
  • lines changed 100, context: html, text, full: html, text
    9f07556e8f11d2e3778a73064ce58367a6bff812 Tue Jun 28 10:47:42 2016 -0700
    Adding announcement for Public Sessions page, removing older announcements, refs #15312
    
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    58fb9113b8b10faa7af5d9e16b732b2df40dc8de Tue Jun 28 11:31:08 2016 -0700
    Adding missing link to news snippet, no redmine
    
  • lines changed 36, context: html, text, full: html, text
    3a6dc821ef2479752364336c33bd0c96c95f4148 Thu Jun 30 12:44:06 2016 -0700
    staged gencode genes v24 announcement, refs #10968
    
  • lines changed 41, context: html, text, full: html, text
    8f54eba62d6f5805969fe36a58e1a4c970903a64 Thu Jun 30 13:41:06 2016 -0700
    Announcing UCSC Genes release, refs #15315 and #10968
    
  • lines changed 14, context: html, text, full: html, text
    4d66c70ec97d6efbed1dac76f1b617752f8a7b00 Thu Jun 30 15:01:37 2016 -0700
    Adding news release about CRAM file refs #17499
    
  • lines changed 1, context: html, text, full: html, text
    49dd3ac0e030676ecf09c80494f5a652352a7520 Thu Jun 30 16:00:34 2016 -0700
    Adding hgCustom.c links to new track formats refs #14717
    
  • lines changed 234, context: html, text, full: html, text
    c43bcc0e7251182c280ed8c1a1fdf592ccf827c4 Tue Apr 12 13:56:18 2016 -0700
    New home page designed by Jim & others, using styles from the new gateway page design. refs #17470, #15277
    
  • lines changed 4, context: html, text, full: html, text
    138b03b9f70a5e253b7cd82334131cb4c621520b Thu Jun 30 16:49:25 2016 -0700
    Prevent news headlines from wrapping onto next line. refs #17470
    
  • lines changed 6, context: html, text, full: html, text
    d3eadc6bb254b37d4559970a15eb99766acc2a2f Thu Jun 30 17:07:56 2016 -0700
    Added some style comments to file instructions. Edited news headlines to conform to style.
    
  • lines changed 1, context: html, text, full: html, text
    ca6d979e4c48448764af58f243a59c79241909c1 Fri Jul 1 12:54:31 2016 -0700
    Change news item links so they go to the correct place, no redmine
    
  • lines changed 1, context: html, text, full: html, text
    8d281a5b34a9d90ad3253c5b73113bbd2c88e55d Fri Jul 1 14:14:53 2016 -0700
    Changed caps for Public Sessions.
    
• src/hg/htdocs/indexStory.html
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    c43bcc0e7251182c280ed8c1a1fdf592ccf827c4 Tue Apr 12 13:56:18 2016 -0700
    New home page designed by Jim & others, using styles from the new gateway page design. refs #17470, #15277
    
• src/hg/htdocs/indexTools.html
  • lines changed 60, context: html, text, full: html, text
    c43bcc0e7251182c280ed8c1a1fdf592ccf827c4 Tue Apr 12 13:56:18 2016 -0700
    New home page designed by Jim & others, using styles from the new gateway page design. refs #17470, #15277
    
• src/hg/htdocs/mirror.html
  • lines changed 3, context: html, text, full: html, text
    880f5c89d43062297e5762ecfd760b9ef383c140 Tue Jun 28 13:43:12 2016 -0700
    commenting out the Aarhus mirror while they are in transition to a server and rsponsible party
    
  • lines changed 12, context: html, text, full: html, text
    fe12919772c66a1f4bc4794e35f57bef08d1ea37 Fri Jul 1 13:31:14 2016 -0700
    added genome-asia to list of mirror sites, refs #17402
    
  • lines changed 1, context: html, text, full: html, text
    34003250927a260447406afcc73f560655546326 Fri Jul 1 13:33:16 2016 -0700
    added a line break
    
• src/hg/htdocs/style/jWest.css
  • lines changed 12, context: html, text, full: html, text
    c43bcc0e7251182c280ed8c1a1fdf592ccf827c4 Tue Apr 12 13:56:18 2016 -0700
    New home page designed by Jim & others, using styles from the new gateway page design. refs #17470, #15277
    
  • lines changed 1, context: html, text, full: html, text
    138b03b9f70a5e253b7cd82334131cb4c621520b Thu Jun 30 16:49:25 2016 -0700
    Prevent news headlines from wrapping onto next line. refs #17470
    
• src/hg/htdocs/training/index.html
  • lines changed 21, context: html, text, full: html, text
    7afaeedf0bfd1b94f10394e691c5e017d539df42 Mon Jun 27 17:52:45 2016 -0700
    removed denmark workshops. adding tuskegee
    
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    204e1de0b664a180e9ef7d6f7ae05e3130051679 Tue Jun 28 08:02:43 2016 -0700
    they changed the date of my talk in Bar Harbor
    
• src/hg/inc/chromColors.h
  • lines changed 49, context: html, text, full: html, text
    a50ed53aff81d6fb3e34e6913ce18578292bc24e Tue Jun 28 15:00:42 2016 -0700
    implement an arbitrary 10-color palette scheme for scaffold/contig coloring refs #17580
    
• src/hg/inc/trackDb.h
  • lines changed 1, context: html, text, full: html, text
    65aee15f89102180ee10261f0da584856bac6ee4 Fri Jul 1 14:18:10 2016 -0700
    add bigChain to the list of bigBed formats in trackDb.h
    
• src/hg/inc/versionInfo.h
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    2618c345307ad1f19a28d54865ed9709114978f7 Mon Jul 4 11:13:50 2016 -0700
    New version number v335
    
• src/hg/js/hgTracks.js
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    d4d8f531049ad83078fb6130e3d6a341abb5c97b Fri Jul 1 16:38:21 2016 -0700
    Adding hgTracks keyboard shortcut to Public Sessions CGI, refs #17469
    
• src/hg/lib/customTrack.c
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    fdac7b7290cf0005e19debb0a8759e2c8cdc4976 Tue Jun 28 11:36:26 2016 -0700
    adding cram auto-detect so no track line is needed in hgCustom, refs #14717
    
• src/hg/lib/hdb.c
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    323c01a235a8b6c9c88c9c7ba7532db2e165b86c Mon Jun 27 17:03:34 2016 -0700
    Allow command-line CGIs to find js/css when run on genome-preview
    
• src/hg/lib/web.c
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    8e566fe74dab83fee7b705d1084871094065c68d Tue Jun 28 13:36:01 2016 -0700
    add print out of host name in error message about versioned js/style files no redmine
    
• src/hg/makeDb/doc/hg18.txt
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    91b791ed4110a92f0b80c1ae73612f17e46846a3 Wed Jun 29 10:19:36 2016 -0700
    lastz runs per user request gorGor4 refs #17581
    
• src/hg/makeDb/doc/hg19.txt
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    fef43d40a51eb99f7abb3f289fac9218c7c7c24e Tue Jun 28 00:52:49 2016 -0700
    redo refGene CDS Fasta alignments with hg19 multiz100way
    
• src/hg/makeDb/doc/hg38/lastzRuns.txt
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    d4cf4e65eee46690aba5e9128068b9ed3ac68c55 Wed Jun 29 10:05:13 2016 -0700
    lastz run hg38 to gorGor5 refs #17580
    
• src/hg/makeDb/doc/hg38/multiz100way.txt
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    12e63280f4c2dac4dcba582d94dfdedc731f342a Mon Jun 27 15:39:13 2016 -0700
    rebuild CDS FASTA downloads for hg38 knownGene and knownCanonical
    
• src/hg/makeDb/doc/mm10Patch4/mm10Patch4.txt
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    2554b2eb761e879f56893122daca7fe2e03c3ca5 Wed Jun 29 16:52:59 2016 -0700
    need -inclHap on the noClass.net file creation refs #16414
    
• src/hg/makeDb/doc/panTro4.txt
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    2475f2b48ac1d5718541391f3338b151740b2787 Wed Jun 29 10:20:47 2016 -0700
    lastz runs per user request gorGor4 refs #17581
    
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes17.sh
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    6602ea77fd2e1cf9d0b993076805f551dd735c62 Mon Jun 27 15:44:00 2016 -0700
    formatting fix in doc
    
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    113f2763842116b69b0bdb4d6acc05f006cc5dc9 Wed Jun 29 10:27:13 2016 -0700
    add isPcr gfServer for hg38 knownGene
    
• src/hg/makeDb/trackDb/augustusGene.html
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    cece6b7f7907dcf32f7af1dc62a1355e9fd43bc0 Mon Jun 27 17:23:07 2016 -0700
    track description .html errors found by hgTablesTest.
    
• src/hg/makeDb/trackDb/human/chainNetGorGor4.ra
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    3d98fa29168afc1e3d54f91c396d4fcb1356e263 Mon Jun 27 13:59:16 2016 -0700
    adding gorGor5 to the composite Primate refs #17580
    
• src/hg/makeDb/trackDb/human/chainNetGorGor5.ra
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    3d98fa29168afc1e3d54f91c396d4fcb1356e263 Mon Jun 27 13:59:16 2016 -0700
    adding gorGor5 to the composite Primate refs #17580
    
• src/hg/makeDb/trackDb/human/chainNetLegacy.ra
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    3d98fa29168afc1e3d54f91c396d4fcb1356e263 Mon Jun 27 13:59:16 2016 -0700
    adding gorGor5 to the composite Primate refs #17580
    
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
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    3d98fa29168afc1e3d54f91c396d4fcb1356e263 Mon Jun 27 13:59:16 2016 -0700
    adding gorGor5 to the composite Primate refs #17580
    
• src/hg/makeDb/trackDb/human/hg38/cons7way.html
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    cece6b7f7907dcf32f7af1dc62a1355e9fd43bc0 Mon Jun 27 17:23:07 2016 -0700
    track description .html errors found by hgTablesTest.
    
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.html
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    e95ff71818d554f4a49bedf79065198aec93cfe5 Tue Jun 28 13:16:20 2016 -0700
    made correction to gencode version on description page, refs #10968
    
• src/hg/makeDb/trackDb/human/hg38/knownGene.html
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    7f65a14186dc8b755eef961c5869e775fd034ba8 Tue Jun 28 13:18:20 2016 -0700
    made correction to gencode version in description
    
• src/hg/makeDb/trackDb/human/hg38/knownGeneOld9.html
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    e2bad0b45e1e163a9f4b84fb3c76e93994e9a208 Mon Jun 27 15:36:28 2016 -0700
    Old UCSC Genes description
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    5341302faa951decefffd1cae9646c8c87b886e5 Mon Jun 27 15:12:52 2016 -0700
    staging gencode v24 on beta, refs #10968
    
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    008e8022d3ebd9fc6391ad89d30ab09bce1f8c15 Mon Jun 27 15:14:52 2016 -0700
    removed beta tag from gencode v22, refs #10968
    
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    ec876e55b8680adf564f5d2910330a58e4c92925 Tue Jun 28 13:09:26 2016 -0700
    adding alpha tag back to gencode v24
    
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    b1a24c8a7c615fb8bcd10e2cae646937bf66a6b4 Wed Jun 29 15:21:23 2016 -0700
    removed tags for gencode v24 release
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
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    1248813e7f575aadb2bd5781eddf1535f521c838 Tue Jun 28 14:13:17 2016 -0700
    fixed inccorect or missing documentation for GENCODE V24
    
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    32acfe87d17190f63ff9bf2d17aa34b7fb61061e Tue Jun 28 14:26:19 2016 -0700
    made a correction to gencode super track description, refs #10968
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV24.html
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    1248813e7f575aadb2bd5781eddf1535f521c838 Tue Jun 28 14:13:17 2016 -0700
    fixed inccorect or missing documentation for GENCODE V24
    
• src/hg/makeDb/trackDb/human/trackDb.ra
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    35e6ad77d48f262ec1fa6e609dd558ab4d0e77cf Fri Jul 1 14:56:02 2016 -0700
    small changes to clinvar: link to main report, change order of fields.
    Based on feedback by Kate, no redmine.
    
• src/hg/makeDb/trackDb/mouse/mm10/mm10Patch4.html
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    dff86c3bab3c95d3afa2ecd6cbebc0789473949b Tue Jun 28 14:07:03 2016 -0700
    minor updates to mm10 Patch 4 description page, refs #16414
    
• src/hg/makeDb/trackDb/mouse/mm10/mm10Patch4.ra
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    1486e4871920562d08d0d4f03e220815d72a8e8d Thu Jun 30 15:48:03 2016 -0700
    fixup search rules for haplotypes and patches names refs #16414
    
• src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra
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    e9a08f6fde15a5e1c734cf172010d6cec738003a Mon Jun 27 13:18:20 2016 -0700
    adding gorGor5 and moving all gorGor to primates.ra refs #17580
    
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
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    e9a08f6fde15a5e1c734cf172010d6cec738003a Mon Jun 27 13:18:20 2016 -0700
    adding gorGor5 and moving all gorGor to primates.ra refs #17580
    
• src/hg/utils/otto/clinvar/clinVarToBed
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    35e6ad77d48f262ec1fa6e609dd558ab4d0e77cf Fri Jul 1 14:56:02 2016 -0700
    small changes to clinvar: link to main report, change order of fields.
    Based on feedback by Kate, no redmine.
    
• src/hg/utils/otto/clinvar/clinvar.as
  • lines changed 1, context: html, text, full: html, text
    31e30611c81fce0ab3e57f6dd4268ba1134c42ad Fri Jul 1 14:13:26 2016 -0700
    fixing typo in clinvar autoSql
    
  • lines changed 4, context: html, text, full: html, text
    35e6ad77d48f262ec1fa6e609dd558ab4d0e77cf Fri Jul 1 14:56:02 2016 -0700
    small changes to clinvar: link to main report, change order of fields.
    Based on feedback by Kate, no redmine.
    
• src/hg/utils/otto/isca/buildISCA.csh
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    5df82b0b553a450eb4a34f5b323849fad60eaeac Thu Jun 30 13:40:40 2016 -0700
    ISCA pipeline output streamlined, recovers more gracefully from error, refs #14465
    
• src/hg/utils/otto/isca/checkISCA.sh
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    5df82b0b553a450eb4a34f5b323849fad60eaeac Thu Jun 30 13:40:40 2016 -0700
    ISCA pipeline output streamlined, recovers more gracefully from error, refs #14465
    
• src/hg/utils/pslToBigPsl/pslToBigPsl.c
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    10fba1d5b5154cae1299fd79f55d9d582815a207 Wed Jun 29 15:10:35 2016 -0700
    make sure CDS field is null and error out with message on protein psl
    
• src/inc/common.h
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    1f113a15a2cbcbdfeb4040188432cd3d013a57be Mon Jun 27 14:56:13 2016 -0700
    allow chain/net coloring of contig based assemblies with WGS naming schemes refs #17580
    
• src/inc/genoFind.h
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    cf293df150f4b256d195e90b5a20817d8479ece0 Sat Jul 2 13:17:59 2016 -0700
    fixes #17624. -maxIntron= was broken in blat whenever a non-default value was used causing it to run cutAtBigIntrons() which did not support protein. The fix was using trans3GenoPos() to get correct coordinates handling 3 frames, and also calling ffScoreProtein() instead of ffScore() when it is a protein query.
    
• src/jkOwnLib/supStitch.c
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    cf293df150f4b256d195e90b5a20817d8479ece0 Sat Jul 2 13:17:59 2016 -0700
    fixes #17624. -maxIntron= was broken in blat whenever a non-default value was used causing it to run cutAtBigIntrons() which did not support protein. The fix was using trans3GenoPos() to get correct coordinates handling 3 frames, and also calling ffScoreProtein() instead of ffScore() when it is a protein query.
    
• src/lib/common.c
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    1f113a15a2cbcbdfeb4040188432cd3d013a57be Mon Jun 27 14:56:13 2016 -0700
    allow chain/net coloring of contig based assemblies with WGS naming schemes refs #17580
    
• src/product/installer/README.md
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    93a95ead5809259df0dc9faf08acf2a3e375ba5d Fri Jul 1 15:29:50 2016 -0700
    minor updates to gbic README, refs #14399
    
• src/utils/qa/weeklybld/buildEnv.csh
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    1fce3d03051ecda682f9d79aacdb56124cad06c3 Mon Jul 4 11:12:39 2016 -0700
    v335 final build refs #17576
    

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• files changed: 132