All File Changes

v352_base to v353_preview (2017-07-17 to 2017-07-24) v353

• src/hg/cirm/gateway/htdocs/cescgOrg.html
  • lines changed 39, context: html, text, full: html, text
    4a94d2b3853667992e137748d43bb03bd4ca8170 Fri Jul 21 15:10:08 2017 -0700
    Initial commit of tools, projects and cescg organization pages, refs #19709
• src/hg/cirm/gateway/htdocs/footer.html
  • lines changed 118, context: html, text, full: html, text
    2d6fcc5006f239f46b0a76c5196a5b027556fb7d Thu Jul 20 11:31:59 2017 -0700
    First commit of new CIRM site HTML files. Currently only header, footer and basic index page. More coming later. refs #19709
  • lines changed 0, context: html, text, full: html, text
    af84257c6050efda77e0eae1339c83bd4e82a0de Thu Jul 20 11:35:03 2017 -0700
    Correcting permissions. Making files executeable. refs #19709
  • lines changed 1, context: html, text, full: html, text
    b7106b2a6e4e20b90444bf4b7685da0c2563fca0 Fri Jul 21 15:11:34 2017 -0700
    Minor changes to footer and index.html files, nor redmine
• src/hg/cirm/gateway/htdocs/header.html
  • lines changed 63, context: html, text, full: html, text
    2d6fcc5006f239f46b0a76c5196a5b027556fb7d Thu Jul 20 11:31:59 2017 -0700
    First commit of new CIRM site HTML files. Currently only header, footer and basic index page. More coming later. refs #19709
  • lines changed 0, context: html, text, full: html, text
    af84257c6050efda77e0eae1339c83bd4e82a0de Thu Jul 20 11:35:03 2017 -0700
    Correcting permissions. Making files executeable. refs #19709
• src/hg/cirm/gateway/htdocs/index.html
  • lines changed 13, context: html, text, full: html, text
    2d6fcc5006f239f46b0a76c5196a5b027556fb7d Thu Jul 20 11:31:59 2017 -0700
    First commit of new CIRM site HTML files. Currently only header, footer and basic index page. More coming later. refs #19709
  • lines changed 0, context: html, text, full: html, text
    af84257c6050efda77e0eae1339c83bd4e82a0de Thu Jul 20 11:35:03 2017 -0700
    Correcting permissions. Making files executeable. refs #19709
  • lines changed 3, context: html, text, full: html, text
    b7106b2a6e4e20b90444bf4b7685da0c2563fca0 Fri Jul 21 15:11:34 2017 -0700
    Minor changes to footer and index.html files, nor redmine
• src/hg/cirm/gateway/htdocs/projects.html
  • lines changed 1074, context: html, text, full: html, text
    4a94d2b3853667992e137748d43bb03bd4ca8170 Fri Jul 21 15:10:08 2017 -0700
    Initial commit of tools, projects and cescg organization pages, refs #19709
• src/hg/cirm/gateway/htdocs/style/cirmStyle.css
  • lines changed 264, context: html, text, full: html, text
    2d6fcc5006f239f46b0a76c5196a5b027556fb7d Thu Jul 20 11:31:59 2017 -0700
    First commit of new CIRM site HTML files. Currently only header, footer and basic index page. More coming later. refs #19709
• src/hg/cirm/gateway/htdocs/tools.html
  • lines changed 44, context: html, text, full: html, text
    4a94d2b3853667992e137748d43bb03bd4ca8170 Fri Jul 21 15:10:08 2017 -0700
    Initial commit of tools, projects and cescg organization pages, refs #19709
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 62, context: html, text, full: html, text
    15aca5da7562e7314e110729f6b5e85f3b77371b Mon Jul 24 08:57:28 2017 -0700
    hgHubConnect now requires all search terms and supports term expansion, refs #19758
• src/hg/hgTables/schema.c
  • lines changed 1, context: html, text, full: html, text
    570b4217afcf77a3435db55a2083716e8ebe61b5 Tue Jul 18 11:16:27 2017 -0700
    Fix for related tables schema crashing build patch, refs #19810
• src/hg/hgTracks/gtexEqtlClusterTrack.c
  • lines changed 1, context: html, text, full: html, text
    321309e057df857daf2b00099ded02864dc77d2f Tue Jul 18 16:06:20 2017 -0700
    1. Fix problem in full mode. 2. Make tissue track item labels black (too many colors o/w). refs #15646
• src/hg/hgTracks/gtexTracks.c
  • lines changed 6, context: html, text, full: html, text
    321309e057df857daf2b00099ded02864dc77d2f Tue Jul 18 16:06:20 2017 -0700
    1. Fix problem in full mode. 2. Make tissue track item labels black (too many colors o/w). refs #15646
• src/hg/hgTracks/hgTracks.h
  • lines changed 6, context: html, text, full: html, text
    321309e057df857daf2b00099ded02864dc77d2f Tue Jul 18 16:06:20 2017 -0700
    1. Fix problem in full mode. 2. Make tissue track item labels black (too many colors o/w). refs #15646
• src/hg/hgTracks/simpleTracks.c
  • lines changed 8, context: html, text, full: html, text
    89065c3677b833bb80467057e0d54c367ea9600a Tue Jul 18 15:38:41 2017 -0700
    Set item color for GTEx eqtl tissue tracks to black. O/w there's too much color going on!
• src/hg/hgc/bigBedClick.c
  • lines changed 1, context: html, text, full: html, text
    74d52dbd8919f57e9fe3effdc49a2b49bfd928b5 Tue Jul 18 14:19:57 2017 -0700
    fixing crispr track on gbib, refs #19789
• src/hg/hgc/gtexEqtlClusterClick.c
  • lines changed 133, context: html, text, full: html, text
    4e04099939e8c5351d07cd086a3a5140cb678532 Mon Jul 17 16:36:35 2017 -0700
    1. Print MAF (instead of allele freqs). Code cleanup. refs #15646
• src/hg/hgc/hgc.c
  • lines changed 3, context: html, text, full: html, text
    7d4c975fa4ecda9baa76ebf9f88fda72a8ff52f2 Sun Jul 23 13:16:30 2017 -0700
    adding link to RepBase from rmsk hgc page, no redmine
• src/hg/htdocs/images/mouse_tree.png
  • lines changed 0, context: html, text, full: html, text
    4bdd46371d9bd9c6bf4414827b5adea61fe82981 Tue Jul 18 08:37:04 2017 -0700
    Adding the mouse tree image into source control, refs #13553
  • lines changed 0, context: html, text, full: html, text
    0d44dd7b223b5f4aeaf94a9fabb33b8134b77745 Tue Jul 18 09:23:16 2017 -0700
    Removing the image from the htdocs/images/ directory, refs #13553
• src/hg/htdocs/images/phylo/mouseStrains_18way.png
  • lines changed 0, context: html, text, full: html, text
    6298ec1c37c297189e74a9acc218397be6afc72a Tue Jul 18 10:22:38 2017 -0700
    adding 18-way phylo tree for mouse strains refs #13553
• src/hg/inc/gtexUi.h
  • lines changed 1, context: html, text, full: html, text
    07d69821a29e5862d56812e2cb3bc10bf9d903f7 Mon Jul 17 15:37:50 2017 -0700
    Set default probability to .5, by request of JK (observing many single-tissue items, indicative of noise). refs #15646
• src/hg/js/hgTracks.js
  • lines changed 6, context: html, text, full: html, text
    357131c4e27b8116f9930bdf600b53403a581556 Mon Jul 17 15:07:22 2017 -0700
    Fix trackUi popup position. Fixes bugs where popup moves around and sometimes disappears after using Apply button. Credit to Joe Thomas for troubleshooting. refs #16948
• src/hg/lib/fullBed.as
  • lines changed 1, context: html, text, full: html, text
    7e8d5489a05a56f1a6ba0f1f56bf2e21a350c3dc Mon Jul 17 15:54:00 2017 -0700
    Editing 'score' to be more specifc in schema desc, refs #19793
• src/hg/lib/gtexUi.c
  • lines changed 1, context: html, text, full: html, text
    188c181cec969cc105bf72c9138360ea5c4f78c3 Mon Jul 17 15:35:19 2017 -0700
    Set default probability to .5, by request of JK (observing many single-tissue items, indicative of noise). refs #15646
• src/hg/lib/rmskJoined.as
  • lines changed 1, context: html, text, full: html, text
    7e8d5489a05a56f1a6ba0f1f56bf2e21a350c3dc Mon Jul 17 15:54:00 2017 -0700
    Editing 'score' to be more specifc in schema desc, refs #19793
• src/hg/makeDb/doc/hg19.txt
  • lines changed 8, context: html, text, full: html, text
    5df02c210c5cf652a8338c17fcbe866669f2cbcf Mon Jul 17 14:57:43 2017 -0700
    adding snpedia track, refs #19811
• src/hg/makeDb/doc/mouseStrains/mouseStrains.18way.nh
  • lines changed 18, context: html, text, full: html, text
    6298ec1c37c297189e74a9acc218397be6afc72a Tue Jul 18 10:22:38 2017 -0700
    adding 18-way phylo tree for mouse strains refs #13553
• src/hg/makeDb/doc/mouseStrains/mouseStrains.html
  • lines changed 97, context: html, text, full: html, text
    d367d589ad912b4cbe974e79ea97b2680c1d6b01 Tue Jul 18 15:39:34 2017 -0700
    Fixing up the track description page for the mice strains track on the alternative mouse strain hub. The underlying data for the track are bigMaf files; not HAL files, CR #19806
  • lines changed 6, context: html, text, full: html, text
    7d8e39a1fc748028c42a536432ad511757d7b316 Wed Jul 19 09:30:31 2017 -0700
    Replacing relative links with direct links since they were broken when viewing the hub, refs #13553 #19806
• src/hg/makeDb/makefile
  • lines changed 1, context: html, text, full: html, text
    98a9e74cefbb5946e7e5a14f0efced56eee34e71 Mon Jul 24 09:14:54 2017 -0700
    adding hgFakeAgp to userApps per user request refs #19843
• src/hg/makeDb/trackDb/human/hg19/barCharts.ra
  • lines changed 68, context: html, text, full: html, text
    fa480f6533ed4083d15733839b9aceb92782c97b Wed Jul 12 12:45:07 2017 -0700
    Adding in gtex transcript track for hg19, refs #19350
• src/hg/makeDb/trackDb/human/hg19/gtexEqtl.ra
  • lines changed 51, context: html, text, full: html, text
    649c42550d482f3264b55265e9d3b1a0c7c92c94 Tue Jul 18 15:39:25 2017 -0700
    Switch some settings and move to expression group, as per JK
  • lines changed 415, context: html, text, full: html, text
    dd1c233b61b1877907f465a80a7bfb1c6677a70a Tue Jul 18 16:08:16 2017 -0700
    Add GTEx eQTL Tissues composite track. refs #15646
• src/hg/makeDb/trackDb/human/hg19/snpedia.html
  • lines changed 34, context: html, text, full: html, text
    5df02c210c5cf652a8338c17fcbe866669f2cbcf Mon Jul 17 14:57:43 2017 -0700
    adding snpedia track, refs #19811
  • lines changed 7, context: html, text, full: html, text
    e332166912f7996761ba751464936f60e82569cd Mon Jul 17 15:28:45 2017 -0700
    fixing up snpedia page, refs #19811
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    fa480f6533ed4083d15733839b9aceb92782c97b Wed Jul 12 12:45:07 2017 -0700
    Adding in gtex transcript track for hg19, refs #19350
  • lines changed 4, context: html, text, full: html, text
    5df02c210c5cf652a8338c17fcbe866669f2cbcf Mon Jul 17 14:57:43 2017 -0700
    adding snpedia track, refs #19811
  • lines changed 1, context: html, text, full: html, text
    8acf6adb3a1209b0207c91819df9a49665cd029f Tue Jul 18 15:11:56 2017 -0700
    Restricting cosmic to non-genome-wide queries for now, refs #18919
  • lines changed 3, context: html, text, full: html, text
    9fc0c821c4290aec70704ec473fa79bb9afd0319 Tue Jul 18 15:40:09 2017 -0700
    Switch some settings and move to expression group, as per JK
  • lines changed 1, context: html, text, full: html, text
    dd1c233b61b1877907f465a80a7bfb1c6677a70a Tue Jul 18 16:08:16 2017 -0700
    Add GTEx eQTL Tissues composite track. refs #15646
• src/hg/makeDb/trackDb/human/hg38/description.html.bk
  • lines changed 349, context: html, text, full: html, text
    d42cba9764a7c1f0fb12ca629e306f31e0db70c4 Tue Jul 18 12:49:22 2017 -0700
    Deleting temp files accidentally commited, see Note 10 refs #19704
• src/hg/makeDb/trackDb/human/hg38/description.html.bk2
  • lines changed 81, context: html, text, full: html, text
    d42cba9764a7c1f0fb12ca629e306f31e0db70c4 Tue Jul 18 12:49:22 2017 -0700
    Deleting temp files accidentally commited, see Note 10 refs #19704
• src/hg/makeDb/trackDb/human/hg38/description.mod
  • lines changed 80, context: html, text, full: html, text
    d42cba9764a7c1f0fb12ca629e306f31e0db70c4 Tue Jul 18 12:49:22 2017 -0700
    Deleting temp files accidentally commited, see Note 10 refs #19704
• src/hg/makeDb/trackDb/human/hg38/description.new.html
  • lines changed 81, context: html, text, full: html, text
    d42cba9764a7c1f0fb12ca629e306f31e0db70c4 Tue Jul 18 12:49:22 2017 -0700
    Deleting temp files accidentally commited, see Note 10 refs #19704
• src/hg/makeDb/trackDb/human/hg38/description.orig
  • lines changed 218, context: html, text, full: html, text
    d42cba9764a7c1f0fb12ca629e306f31e0db70c4 Tue Jul 18 12:49:22 2017 -0700
    Deleting temp files accidentally commited, see Note 10 refs #19704
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    8acf6adb3a1209b0207c91819df9a49665cd029f Tue Jul 18 15:11:56 2017 -0700
    Restricting cosmic to non-genome-wide queries for now, refs #18919
• src/hg/makeDb/trackDb/worm/ce10/trackDb.ra
  • lines changed 33, context: html, text, full: html, text
    cf40145885582f6573880bce3f123679f61cb5a1 Fri Jul 21 22:32:58 2017 -0700
    taking a look at the crisprKmer track refs #18969
• src/hg/protein/kgAliasM/kgAliasM.c
  • lines changed 3, context: html, text, full: html, text
    52829699ad71924c98fa85cf38e78345b9a6458b Mon Jul 24 08:34:48 2017 -0700
    Removing unused variable
• src/hg/protein/pbHgnc/pbHgnc.c
  • lines changed 2, context: html, text, full: html, text
    3813053294824f9e909ffab34f172876ac695f67 Mon Jul 24 08:36:32 2017 -0700
    Commenting out unused variable
• src/hg/utils/hubCrawl/hubCrawl.c
  • lines changed 38, context: html, text, full: html, text
    b183bf8d8d8509569d0f64d663f6fe375a9bd6c7 Mon Jul 24 08:56:34 2017 -0700
    hubCrawl now correctly omits empty superTracks, refs #19758
• src/lib/osunix.c
  • lines changed 3, context: html, text, full: html, text
    85e85f6d49fc60e860faa858d522f30dbb1597e4 Mon Jul 17 15:12:21 2017 -0700
    maybeTouchFile() will now succeed at updating mtime/atime to now on files owned by another, but for which the user has write permisson, refs #19812
• src/utils/crisprKmers/crisprKmers.c
  • lines changed 186, context: html, text, full: html, text
    118ed185e6dd714a9896cfbc8287ca81d9decfbb Mon Jul 17 23:14:43 2017 -0700
    adding the CFD score calculations refs #18969
  • lines changed 63, context: html, text, full: html, text
    d821d48d0f454a343f806d2567929bad4be1a09c Tue Jul 18 13:03:50 2017 -0700
    looks like MIT and CFD scores are functioning correctly now refs #18969
  • lines changed 160, context: html, text, full: html, text
    3f6442f9cbf277adf44d00d78a5aaf53e5b0e4c7 Thu Jul 20 12:47:20 2017 -0700
    failed experiment to utilize CPU caching, does not help, just for the record checked in, refs #18969
  • lines changed 49, context: html, text, full: html, text
    083833e1f84528f923fde137a041657635f4564e Thu Jul 20 22:29:00 2017 -0700
    remove the CPU cache experiment and change memLimit option to threads refs #18969
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    a0d80a4f6d675eee8020ac9ed4d613ec40d74d9e Mon Jul 24 09:55:48 2017 -0700
    v353 preview1 refs #19715
• src/utils/qa/weeklybld/summaryEmail.sh
  • lines changed 1, context: html, text, full: html, text
    b2b1b6303df0a95750126a29c6e96f115f23b674 Fri Jul 21 09:22:45 2017 -0700
    change Ann to Brian in email message no redmine

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• files changed: 61