All File Changes

v351_preview2 to v351_base (2017-06-19 to 2017-06-26) v351

• src/README
  • lines changed 3, context: html, text, full: html, text
    9632e533bf1e99abde7ce09b9abf57f8c314c8b6 Mon Jun 26 08:15:06 2017 -0700
    Addressing command line variable (cl prefix rather than g).
• src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/arrayExpressStormToHcaStorm.c
  • lines changed 48, context: html, text, full: html, text
    cbf20a6cc8b6b751bdbf50d2b17df70206706b0a Mon Jun 26 08:07:48 2017 -0700
    Removing some ifdef OLDs
• src/hca/fromGeo/geoStormToHcaStorm/expected.tags
  • lines changed 137, context: html, text, full: html, text
    29d48c738193b3cfa30ca447a8b73aabda617c48 Mon Jun 26 08:04:52 2017 -0700
    Updating per code review to be more conservative about parsing out accessions at end of URLs. refs#19646
• src/hca/fromGeo/geoStormToHcaStorm/geoStormToHcaStorm.c
  • lines changed 4, context: html, text, full: html, text
    29d48c738193b3cfa30ca447a8b73aabda617c48 Mon Jun 26 08:04:52 2017 -0700
    Updating per code review to be more conservative about parsing out accessions at end of URLs. refs#19646
  • lines changed 50, context: html, text, full: html, text
    cbf20a6cc8b6b751bdbf50d2b17df70206706b0a Mon Jun 26 08:07:48 2017 -0700
    Removing some ifdef OLDs
• src/hca/fromGeo/geoToTagStorm/geoToTagStorm.c
  • lines changed 1, context: html, text, full: html, text
    95a654f3f094dcee3c3a6301743f1cbd4359d828 Mon Jun 26 08:09:24 2017 -0700
    Added a comment in response to code review.
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 37, context: html, text, full: html, text
    473e5a170dfaddfcd4a897f0b40a06ac1ed502bb Thu Jun 22 00:31:43 2017 -0700
    CIRM cdwMakeValidFile. Adding csv file validator. All rows must have same number of columns. Parses with src/lib/csv.c::csvParse()
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 6, context: html, text, full: html, text
    d322dfac875e06a3de869564777741736897d69b Wed Jun 21 15:09:29 2017 -0700
    CIRM: fixing downloads over the https gateway. This breaks downloads over the VPN. Per email from Clay. No redmine.
  • lines changed 3, context: html, text, full: html, text
    0cc03aeda705989933a28505129d1313b4f5e72d Wed Jun 21 15:12:59 2017 -0700
    CIRM: fixing aria2c arguments
• src/hg/cirm/cdw/lib/resetCdw
  • lines changed 131, context: html, text, full: html, text
    0224d9fec00cf13eaf200b6630ee24106434cc03 Tue Jun 20 07:59:44 2017 -0700
    Adding instructions on how to rebuild database.
• src/hg/cirm/cdw/makefile
  • lines changed 1, context: html, text, full: html, text
    cfbf2d8dfcd52224d120ad266f5fb15831de4708 Fri Jun 23 14:40:52 2017 -0700
    adding cdwPublicSubset to utils list.
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 52, context: html, text, full: html, text
    4c389c37d5a42eafb281c81ca6d12271a58f1499 Thu Jun 22 13:18:03 2017 -0700
    hgHubConnect now expands on single click, show results in correct order, and has more intuitive logic for the search/filter text boxes, refs #13625
  • lines changed 24, context: html, text, full: html, text
    191a1172e19c7c124fbb09cbad05fcb2f2c0c726 Thu Jun 22 16:53:10 2017 -0700
    Fixing position issue for hgHubConnect when changing assemblies, refs #13625
• src/hg/hgLinkIn/hgLinkIn.c
  • lines changed 2, context: html, text, full: html, text
    9186224c599aee020869b7ae3f08bc6ca05cdbe2 Tue Jun 20 20:19:01 2017 -0700
    hgLinkIn now uses cgiOptionalString instead of cartOptionalString to fetch variables that are excluded from the cart, refs #19645
• src/hg/hgLogin/hgLogin.c
  • lines changed 3, context: html, text, full: html, text
    b535013b6598af52d63ad9865b8377b83d84fa2d Mon Jun 19 10:25:52 2017 -0700
    fixing a few more things in hgLogin/hgSession: empty returnto url uses the new function, fixing typo in hLoginHostCgiBinUrl removing hgLogin from URL, removing the slash in loginUrl() as hLoginHostCgiBinUrl adds a slash already, refs #19632
  • lines changed 1, context: html, text, full: html, text
    317f70443fd671e78de95a2136c624a5f6c12110 Tue Jun 20 05:44:01 2017 -0700
    fixing my stupid typo in hgLogin
• src/hg/htdocs/goldenPath/help/gbic.html
  • lines changed 1, context: html, text, full: html, text
    feb9548eb9b7ba8fff68f4da32ebfee624f9c51c Fri Jun 23 10:59:38 2017 -0700
    Fixing a minor typo on the GBiC help page, no redmine
  • lines changed 2, context: html, text, full: html, text
    142b482aa4460d131f048397859dbd2e4ee50185 Fri Jun 23 14:05:53 2017 -0700
    Fixing a minor typo on the gbic.html page, no redmine
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
  • lines changed 4, context: html, text, full: html, text
    44bde1c4de72fdbd7c3823417b1ca877dff57984 Tue Jun 20 15:24:21 2017 -0700
    Grammar corrections based on CR, refs #19653
  • lines changed 75, context: html, text, full: html, text
    f0b3d364f15020868363d20f10df489c267a4dcd Thu Jun 22 11:00:38 2017 -0700
    Adding ToC link to Credits section. HTML encoded quotes. Added taget='_blank' to some external links. Most other changes are primarily whitespace to bring character count per line under 100 characters. refs #13634
  • lines changed 3, context: html, text, full: html, text
    e034342232478618820fcee41025d243b833d683 Thu Jun 22 11:14:27 2017 -0700
    Correcting some hgdownload urls on hgGeneGraph help page, refs #13634
  • lines changed 3, context: html, text, full: html, text
    9409a4eede975ac7a29f4cb073c9d2d24a11da01 Thu Jun 22 15:11:26 2017 -0700
    Correcting hgdownload links, refs #13634
  • lines changed 1, context: html, text, full: html, text
    57631a6710ced8ceedbd1aa394cd32843370a2b6 Thu Jun 22 15:13:17 2017 -0700
    Removing extra r, no redmine
  • lines changed 1, context: html, text, full: html, text
    ad515b37509c9a9b8c76b500f22c900073f84fe1 Sun Jun 25 08:14:58 2017 -0700
    changed less than to fewer than
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 180, context: html, text, full: html, text
    12837fed8cc087fcf254e989ecd727bb3825127a Wed Jun 21 08:13:20 2017 -0700
    Adding a help page for authors submitting manuscripts to NAR, refs #19125
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 41, context: html, text, full: html, text
    b66aa409df32ff0aad22fc550e5450032691b8aa Thu Jun 22 15:05:45 2017 -0700
    Adding announcement for hgGeneGraph CGI, uncommenting Tools link for CGI, replacing main CGI image with lower quality version so it loads faster on slow connections, refs #13634
  • lines changed 3, context: html, text, full: html, text
    5b0c986e8b7cce51bbf811429f8e28d9da381bfc Thu Jun 22 15:51:17 2017 -0700
    Fixing minor typos in announcement, refs #13634
• src/hg/htdocs/images/hgGeneGraph.png
  • lines changed 0, context: html, text, full: html, text
    b66aa409df32ff0aad22fc550e5450032691b8aa Thu Jun 22 15:05:45 2017 -0700
    Adding announcement for hgGeneGraph CGI, uncommenting Tools link for CGI, replacing main CGI image with lower quality version so it loads faster on slow connections, refs #13634
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    b66aa409df32ff0aad22fc550e5450032691b8aa Thu Jun 22 15:05:45 2017 -0700
    Adding announcement for hgGeneGraph CGI, uncommenting Tools link for CGI, replacing main CGI image with lower quality version so it loads faster on slow connections, refs #13634
• src/hg/htdocs/indexNews.html
  • lines changed 13, context: html, text, full: html, text
    b66aa409df32ff0aad22fc550e5450032691b8aa Thu Jun 22 15:05:45 2017 -0700
    Adding announcement for hgGeneGraph CGI, uncommenting Tools link for CGI, replacing main CGI image with lower quality version so it loads faster on slow connections, refs #13634
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    45d468a020251066818949cde30a17de3023b927 Mon Jun 26 10:04:49 2017 -0700
    New version number v351
• src/hg/js/hgHubConnect.js
  • lines changed 1, context: html, text, full: html, text
    4c389c37d5a42eafb281c81ca6d12271a58f1499 Thu Jun 22 13:18:03 2017 -0700
    hgHubConnect now expands on single click, show results in correct order, and has more intuitive logic for the search/filter text boxes, refs #13625
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    b535013b6598af52d63ad9865b8377b83d84fa2d Mon Jun 19 10:25:52 2017 -0700
    fixing a few more things in hgLogin/hgSession: empty returnto url uses the new function, fixing typo in hLoginHostCgiBinUrl removing hgLogin from URL, removing the slash in loginUrl() as hLoginHostCgiBinUrl adds a slash already, refs #19632
  • lines changed 2, context: html, text, full: html, text
    a28f852664b23a2c5952b1f6ea4bb47636ddd51e Fri Jun 23 10:22:15 2017 -0700
    Use cgiScriptDirUrl() instead of "/cgi-bin/". refs #19647
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    17ac71b6117c6c4e211aca6415afd0bfffc2dabc Mon Jun 19 14:21:15 2017 -0700
    add support for more big* files to put out file changed times. #19655
• src/hg/lib/wikiLink.c
  • lines changed 1, context: html, text, full: html, text
    b535013b6598af52d63ad9865b8377b83d84fa2d Mon Jun 19 10:25:52 2017 -0700
    fixing a few more things in hgLogin/hgSession: empty returnto url uses the new function, fixing typo in hLoginHostCgiBinUrl removing hgLogin from URL, removing the slash in loginUrl() as hLoginHostCgiBinUrl adds a slash already, refs #19632
• src/hg/makeDb/doc/danRer10/initialBuild.txt
  • lines changed 39, context: html, text, full: html, text
    ef94a845faa09cb4bb6c84700516cb6867160832 Thu Jun 22 14:50:12 2017 -0700
    ensGene v89 build completed refs #19526
• src/hg/makeDb/doc/danRer11/initialBuild.txt
  • lines changed 26, context: html, text, full: html, text
    2755e53d6c92e115ca1a9a0d4ba645faa366c263 Mon Jun 19 15:11:49 2017 -0700
    finishing the last couple things associated with this, refs #19459
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 79, context: html, text, full: html, text
    fc4dcd913db9a41f8980b96cd04640bf05175faa Thu Jun 22 14:47:24 2017 -0700
    ensGene v89 build completed refs #19526
• src/hg/makeDb/doc/mm10.txt
  • lines changed 110, context: html, text, full: html, text
    be6a5d9722c63fcb736c959843fe50e2b4735241 Thu Jun 22 22:20:55 2017 -0700
    lastz chainNet to orcOrc1 and papAnu3 refs #10145 #19660
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.ensGene.html
  • lines changed 3, context: html, text, full: html, text
    ca520426928780172309d926d7817c5e889635f1 Fri Jun 23 16:01:07 2017 -0700
    Fixing typos on the Ensembl track description that were found from my code review, CR #19652
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.ensGene.html
  • lines changed 3, context: html, text, full: html, text
    ca520426928780172309d926d7817c5e889635f1 Fri Jun 23 16:01:07 2017 -0700
    Fixing typos on the Ensembl track description that were found from my code review, CR #19652
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.ensGene.html
  • lines changed 3, context: html, text, full: html, text
    ca520426928780172309d926d7817c5e889635f1 Fri Jun 23 16:01:07 2017 -0700
    Fixing typos on the Ensembl track description that were found from my code review, CR #19652
• src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.ensGene.html
  • lines changed 3, context: html, text, full: html, text
    ca520426928780172309d926d7817c5e889635f1 Fri Jun 23 16:01:07 2017 -0700
    Fixing typos on the Ensembl track description that were found from my code review, CR #19652
• src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/html/GCA_001624475.1_CBA_J_v1.ensGene.html
  • lines changed 3, context: html, text, full: html, text
    ca520426928780172309d926d7817c5e889635f1 Fri Jun 23 16:01:07 2017 -0700
    Fixing typos on the Ensembl track description that were found from my code review, CR #19652
• src/hg/makeDb/doc/mouseStrains/GCA_001624505.1_DBA_2J_v1/html/GCA_001624505.1_DBA_2J_v1.ensGene.html
  • lines changed 3, context: html, text, full: html, text
    ca520426928780172309d926d7817c5e889635f1 Fri Jun 23 16:01:07 2017 -0700
    Fixing typos on the Ensembl track description that were found from my code review, CR #19652
• src/hg/makeDb/doc/mouseStrains/GCA_001624535.1_FVB_NJ_v1/html/GCA_001624535.1_FVB_NJ_v1.ensGene.html
  • lines changed 3, context: html, text, full: html, text
    ca520426928780172309d926d7817c5e889635f1 Fri Jun 23 16:01:07 2017 -0700
    Fixing typos on the Ensembl track description that were found from my code review, CR #19652
• src/hg/makeDb/doc/mouseStrains/GCA_001624675.1_NOD_ShiLtJ_v1/html/GCA_001624675.1_NOD_ShiLtJ_v1.ensGene.html
  • lines changed 3, context: html, text, full: html, text
    ca520426928780172309d926d7817c5e889635f1 Fri Jun 23 16:01:07 2017 -0700
    Fixing typos on the Ensembl track description that were found from my code review, CR #19652
• src/hg/makeDb/doc/mouseStrains/GCA_001624745.1_NZO_HlLtJ_v1/html/GCA_001624745.1_NZO_HlLtJ_v1.ensGene.html
  • lines changed 3, context: html, text, full: html, text
    ca520426928780172309d926d7817c5e889635f1 Fri Jun 23 16:01:07 2017 -0700
    Fixing typos on the Ensembl track description that were found from my code review, CR #19652
• src/hg/makeDb/doc/mouseStrains/GCA_001624775.1_PWK_PhJ_v1/html/GCA_001624775.1_PWK_PhJ_v1.ensGene.html
  • lines changed 3, context: html, text, full: html, text
    ca520426928780172309d926d7817c5e889635f1 Fri Jun 23 16:01:07 2017 -0700
    Fixing typos on the Ensembl track description that were found from my code review, CR #19652
• src/hg/makeDb/doc/mouseStrains/GCA_001624835.1_WSB_EiJ_v1/html/GCA_001624835.1_WSB_EiJ_v1.ensGene.html
  • lines changed 3, context: html, text, full: html, text
    ca520426928780172309d926d7817c5e889635f1 Fri Jun 23 16:01:07 2017 -0700
    Fixing typos on the Ensembl track description that were found from my code review, CR #19652
• src/hg/makeDb/doc/mouseStrains/GCA_001624865.1_SPRET_EiJ_v1/html/GCA_001624865.1_SPRET_EiJ_v1.ensGene.html
  • lines changed 3, context: html, text, full: html, text
    ca520426928780172309d926d7817c5e889635f1 Fri Jun 23 16:01:07 2017 -0700
    Fixing typos on the Ensembl track description that were found from my code review, CR #19652
• src/hg/makeDb/doc/mouseStrains/GCA_001632525.1_BALB_cJ_v1/html/GCA_001632525.1_BALB_cJ_v1.ensGene.html
  • lines changed 3, context: html, text, full: html, text
    ca520426928780172309d926d7817c5e889635f1 Fri Jun 23 16:01:07 2017 -0700
    Fixing typos on the Ensembl track description that were found from my code review, CR #19652
• src/hg/makeDb/doc/mouseStrains/GCA_001632555.1_C57BL_6NJ_v1/html/GCA_001632555.1_C57BL_6NJ_v1.ensGene.html
  • lines changed 3, context: html, text, full: html, text
    ca520426928780172309d926d7817c5e889635f1 Fri Jun 23 16:01:07 2017 -0700
    Fixing typos on the Ensembl track description that were found from my code review, CR #19652
• src/hg/makeDb/doc/mouseStrains/GCA_001632575.1_C3H_HeJ_v1/html/GCA_001632575.1_C3H_HeJ_v1.ensGene.html
  • lines changed 3, context: html, text, full: html, text
    ca520426928780172309d926d7817c5e889635f1 Fri Jun 23 16:01:07 2017 -0700
    Fixing typos on the Ensembl track description that were found from my code review, CR #19652
• src/hg/makeDb/doc/mouseStrains/GCA_001632615.1_LP_J_v1/html/GCA_001632615.1_LP_J_v1.ensGene.html
  • lines changed 3, context: html, text, full: html, text
    ca520426928780172309d926d7817c5e889635f1 Fri Jun 23 16:01:07 2017 -0700
    Fixing typos on the Ensembl track description that were found from my code review, CR #19652
• src/hg/makeDb/doc/mouseStrains/hubIndex.html
  • lines changed 157, context: html, text, full: html, text
    e5609f4458d44ab4198d58f1ba84ec16e33a83e9 Thu Jun 22 07:52:10 2017 -0700
    Updating the mouse strains landing page to use the new html style sheets, refs #13553
• src/hg/makeDb/doc/orcOrc1/initialBuild.txt
  • lines changed 53, context: html, text, full: html, text
    2279f1e5ab6e4804202db626f8c26e6eedbf18ac Thu Jun 22 14:49:17 2017 -0700
    completed build with hg38 and mm10 lastz/chainNet refs #10145
• src/hg/makeDb/doc/ornAna1.txt
  • lines changed 23, context: html, text, full: html, text
    ad20328fafb4624a0c919223a670cec1bc8ba759 Thu Jun 22 14:47:57 2017 -0700
    ensGene v89 build completed refs #19526
• src/hg/makeDb/doc/ornAna2/initialBuild.txt
  • lines changed 23, context: html, text, full: html, text
    ef94a845faa09cb4bb6c84700516cb6867160832 Thu Jun 22 14:50:12 2017 -0700
    ensGene v89 build completed refs #19526
• src/hg/makeDb/doc/papAnu2.txt
  • lines changed 14, context: html, text, full: html, text
    8544a30328a92e972e3821fee757ae7266ee0c4e Fri Jun 23 23:24:51 2017 -0700
    done with papHam3 just in time for it to be obsolete and with papAnu2 liftOvers refs #19660
• src/hg/makeDb/doc/papAnu3/initialBuild.txt
  • lines changed 817, context: html, text, full: html, text
    a88df1bc16f870f81548755d0c964a06ba9da84a Tue Jun 20 15:16:06 2017 -0700
    beginning build for papAnu3 refs #19660
  • lines changed 177, context: html, text, full: html, text
    8544a30328a92e972e3821fee757ae7266ee0c4e Fri Jun 23 23:24:51 2017 -0700
    done with papHam3 just in time for it to be obsolete and with papAnu2 liftOvers refs #19660
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    314353a462cda9040fffcf7a2b75adfc99539c4f Wed Jun 21 22:40:07 2017 -0700
    adding papAnu3 to the update alignments refs #19660
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 19, context: html, text, full: html, text
    02de0399c944e45474e900c30d13a18c0cbaf129 Wed Jun 21 10:01:27 2017 -0700
    adding papAnu3 baboon refs #19660
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    314353a462cda9040fffcf7a2b75adfc99539c4f Wed Jun 21 22:40:07 2017 -0700
    adding papAnu3 to the update alignments refs #19660
• src/hg/makeDb/schema/all.joiner
  • lines changed 9, context: html, text, full: html, text
    2407a24bda328c9759342a48cf25c544365347c4 Fri Jun 23 10:54:06 2017 -0700
    adding papAnu3 rules refs #19660
• src/hg/makeDb/trackDb/baboon/papAnu3/description.html
  • lines changed 64, context: html, text, full: html, text
    fc833c04dbfd859531c4ac3d9ff7e01e84fbb158 Tue Jun 20 13:09:04 2017 -0700
    adding papAnu3 to the build refs #19660makefile
• src/hg/makeDb/trackDb/baboon/papAnu3/gap.html
  • lines changed 31, context: html, text, full: html, text
    fc833c04dbfd859531c4ac3d9ff7e01e84fbb158 Tue Jun 20 13:09:04 2017 -0700
    adding papAnu3 to the build refs #19660makefile
• src/hg/makeDb/trackDb/baboon/papAnu3/gold.html
  • lines changed 34, context: html, text, full: html, text
    fc833c04dbfd859531c4ac3d9ff7e01e84fbb158 Tue Jun 20 13:09:04 2017 -0700
    adding papAnu3 to the build refs #19660makefile
• src/hg/makeDb/trackDb/baboon/papAnu3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    fc833c04dbfd859531c4ac3d9ff7e01e84fbb158 Tue Jun 20 13:09:04 2017 -0700
    adding papAnu3 to the build refs #19660makefile
  • lines changed 5, context: html, text, full: html, text
    9103b5db09531c76b160d6920c1c820ebb0ec3a3 Tue Jun 20 14:10:20 2017 -0700
    adding gold search rule refs #19660
• src/hg/makeDb/trackDb/crispors.html
  • lines changed 26, context: html, text, full: html, text
    9476dc411e687bb2b3af03aeab503aa524e6e456 Sat Jun 24 01:05:41 2017 -0700
    html for crispr composite track refs #19513
• src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra
  • lines changed 2, context: html, text, full: html, text
    dddb53fb92727ff8b3a36cc734df27732b950ec2 Fri Jun 23 08:53:48 2017 -0700
    Fixing issue where the mRNA track was not in alphabetical order on hg19, refs #19187
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    e07d36ff81bdd0db210d1a40b1ea70599568a986 Tue Jun 20 14:10:47 2017 -0700
    adding papAnu3 to the build refs #19660
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    92880d7bf9067fcd53f5fabfad7a6b013947f1f0 Tue Jun 20 12:17:31 2017 -0700
    Changing CpG Island subtrack stanzas from supertrack to parent so qa checks will work, refs #18361
  • lines changed 33, context: html, text, full: html, text
    97fa8be8e7ad24266549b6970051d09de2c5f7b7 Tue Jun 20 12:49:50 2017 -0700
    adding crispr10K track refs #18969
  • lines changed 8, context: html, text, full: html, text
    cea4e7a82347bee9e18c11c2137106315852f630 Thu Jun 22 16:01:38 2017 -0700
    taking a look at the crispr track from Ensembl refs #19513
  • lines changed 22, context: html, text, full: html, text
    c67d3507317826da8a2f94751ad4f017a83ee0da Fri Jun 23 15:07:06 2017 -0700
    taking a look at the crispr track from Ensembl and the locally generated kmer track for all crispr sites refs #19513
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 6, context: html, text, full: html, text
    2914267509c11c2eab2cbf4698337b139bfba185 Wed Jun 21 10:41:26 2017 -0700
    update papAnu2 to papAnu3 and ornAna1 to ornAna2 for v89 refs #19526
  • lines changed 6, context: html, text, full: html, text
    4ab3e6850013b520c76257a6607ad638945ce9a1 Thu Jun 22 14:32:44 2017 -0700
    add ornAna1,ornAna2, papAnu2,papAnu3 to the v89 build refs #19526
• src/hg/utils/automation/chromAlias.pl
  • lines changed 144, context: html, text, full: html, text
    502c0e30679e95cc9137837a7394711c3adc3fed Thu Jun 22 09:57:48 2017 -0700
    adding a help script to construct chromAlias table refs #19660
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • lines changed 1, context: html, text, full: html, text
    3c9289aafb0cb3c18d3aeb35416f9c12040d6c49 Thu Jun 22 14:31:09 2017 -0700
    fixup the broken ensemblSource.tab construction refs #19526
• src/hg/utils/hubCrawl/hubCrawl.c
  • lines changed 1, context: html, text, full: html, text
    9101ab13c42813200a09bd089ff3f05665e5ef83 Tue Jun 20 20:17:47 2017 -0700
    Removing pointless sleep(), refs #19645
  • lines changed 49, context: html, text, full: html, text
    ccfbdd7909fa1514365a2a2294aca4094653d816 Thu Jun 22 11:37:23 2017 -0700
    Adding htmlTextStripJavascriptCssAndTags as a library function following code review, refs #19645
• src/inc/common.h
  • lines changed 3, context: html, text, full: html, text
    d4228428913bd26a1031a2acc156a0b0d777ea45 Mon Jun 26 08:11:31 2017 -0700
    Improving comments in csv.h. Make eraseTrailingSpaces keep track of number of spaces erased, and using this to keep a dyString->stringSize accurate.
• src/inc/csv.h
  • lines changed 1, context: html, text, full: html, text
    d4228428913bd26a1031a2acc156a0b0d777ea45 Mon Jun 26 08:11:31 2017 -0700
    Improving comments in csv.h. Make eraseTrailingSpaces keep track of number of spaces erased, and using this to keep a dyString->stringSize accurate.
• src/inc/htmshell.h
  • lines changed 3, context: html, text, full: html, text
    ccfbdd7909fa1514365a2a2294aca4094653d816 Thu Jun 22 11:37:23 2017 -0700
    Adding htmlTextStripJavascriptCssAndTags as a library function following code review, refs #19645
• src/lib/common.c
  • lines changed 8, context: html, text, full: html, text
    d4228428913bd26a1031a2acc156a0b0d777ea45 Mon Jun 26 08:11:31 2017 -0700
    Improving comments in csv.h. Make eraseTrailingSpaces keep track of number of spaces erased, and using this to keep a dyString->stringSize accurate.
• src/lib/csv.c
  • lines changed 5, context: html, text, full: html, text
    d4228428913bd26a1031a2acc156a0b0d777ea45 Mon Jun 26 08:11:31 2017 -0700
    Improving comments in csv.h. Make eraseTrailingSpaces keep track of number of spaces erased, and using this to keep a dyString->stringSize accurate.
• src/lib/htmshell.c
  • lines changed 46, context: html, text, full: html, text
    ccfbdd7909fa1514365a2a2294aca4094653d816 Thu Jun 22 11:37:23 2017 -0700
    Adding htmlTextStripJavascriptCssAndTags as a library function following code review, refs #19645
• src/product/installer/README.md
  • lines changed 1, context: html, text, full: html, text
    142b482aa4460d131f048397859dbd2e4ee50185 Fri Jun 23 14:05:53 2017 -0700
    Fixing a minor typo on the gbic.html page, no redmine
• src/tagStorm/makefile
  • lines changed 4, context: html, text, full: html, text
    c81b9d0e412e65c9bf35abe82a813477ed87f204 Fri Jun 23 12:38:52 2017 -0700
    Making a tag value renaming program.
• src/tagStorm/tagStormCheck/tagStormCheck.c
  • lines changed 23, context: html, text, full: html, text
    286acef256a2c9184166e0ad4b136e9a39c3281d Mon Jun 26 08:13:15 2017 -0700
    Works on comma separated values now.
• src/tagStorm/tagStormCheck/test.schema
  • lines changed 2, context: html, text, full: html, text
    286acef256a2c9184166e0ad4b136e9a39c3281d Mon Jun 26 08:13:15 2017 -0700
    Works on comma separated values now.
• src/tagStorm/tagStormCheck/test.tags
  • lines changed 1, context: html, text, full: html, text
    286acef256a2c9184166e0ad4b136e9a39c3281d Mon Jun 26 08:13:15 2017 -0700
    Works on comma separated values now.
• src/tagStorm/tagStormInfo/tagStormInfo.c
  • lines changed 7, context: html, text, full: html, text
    582f9a568c34a562851a3561845f15945be860be Mon Jun 26 08:13:47 2017 -0700
    Adding 'tag' option to restict things to a single tag.
• src/tagStorm/tagStormJoinTab/tagStormJoinTab.c
  • lines changed 8, context: html, text, full: html, text
    f976fa0d9ee4d21594ddd87a5518382810c67f93 Mon Jun 26 08:17:22 2017 -0700
    Added noneOk option so can use in scripts against files that don't need joining. Also made it so that joining tag doesn't need to have unique values, which I needed for some ontology stuff.
• src/tagStorm/tagStormRenameTags/tagStormRenameTags.c
  • lines changed 12, context: html, text, full: html, text
    c1301fcc986b4f85193dc9279ecb582bf2754621 Fri Jun 23 12:41:54 2017 -0700
    Making it so that you can have same source and dest.
• src/tagStorm/tagStormRenameVals/makefile
  • lines changed 3, context: html, text, full: html, text
    c81b9d0e412e65c9bf35abe82a813477ed87f204 Fri Jun 23 12:38:52 2017 -0700
    Making a tag value renaming program.
• src/tagStorm/tagStormRenameVals/tagStormRenameVals.c
  • lines changed 145, context: html, text, full: html, text
    c81b9d0e412e65c9bf35abe82a813477ed87f204 Fri Jun 23 12:38:52 2017 -0700
    Making a tag value renaming program.
  • lines changed 2, context: html, text, full: html, text
    0550596afcd3618f80cd556b984d03008bfb289b Mon Jun 26 08:18:02 2017 -0700
    Editing out -xxx=XXX option since there were none.
• src/tagStorm/tagStormRenameVals/test.3col
  • lines changed 3, context: html, text, full: html, text
    c81b9d0e412e65c9bf35abe82a813477ed87f204 Fri Jun 23 12:38:52 2017 -0700
    Making a tag value renaming program.
• src/tagStorm/tagStormRenameVals/test.in
  • lines changed 249, context: html, text, full: html, text
    c81b9d0e412e65c9bf35abe82a813477ed87f204 Fri Jun 23 12:38:52 2017 -0700
    Making a tag value renaming program.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    bb452818d7cb36511be4569335e6e927c08e3ca0 Mon Jun 26 10:03:26 2017 -0700
    v351 final build

• lines changed: 3409
• files changed: 105