All File Changes

v317_preview2 to v317_base (2015-05-25 to 2015-06-01) v317

• src/hg/hgGene/hgGene.c
  • lines changed 2, context: html, text, full: html, text
    use #define for constant refs #15407
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 8, context: html, text, full: html, text
    support setting transMap track default item labeling in trackDb (#15440)
    
• src/hg/hgTracks/chainTrack.c
  • lines changed 2, context: html, text, full: html, text
    fix score filter on chains refs #15143
    
• src/hg/hgTracks/transMapTracks.c
  • lines changed 37, context: html, text, full: html, text
    support setting transMap track default item labeling in trackDb (#15440)
    
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    print link to other genome assembly on snake tracks that are not assembly hubs
    
• src/hg/htdocs/goldenPath/help/hgIntegratorHelp.html
  • lines changed 56, context: html, text, full: html, text
    Moving the 'quick-reference' contents of hgIntegratorHelp.html to
    hgIntegrator.jsx so Matt can write a proper user's guide in
    hgIntegratorHelp.html. Also, now we don't need to fetch html
    from the server and use React's dangerouslySetInnerHTML.
    refs #14579 note 65
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 47, context: html, text, full: html, text
    1. Get version from doc. 2. Fix err messages. refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js
  • lines changed 9, context: html, text, full: html, text
    1. Get version from doc. 2. Fix err messages. refs #10015
    
  • lines changed 1, context: html, text, full: html, text
    Fix test on doc type. Commit v0 version. refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 44, context: html, text, full: html, text
    1. Get version from doc. 2. Fix err messages. refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v0.html
  • lines changed 785, context: html, text, full: html, text
    Fix test on doc type. Commit v0 version. refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 90, context: html, text, full: html, text
    1. Get version from doc. 2. Fix err messages. refs #10015
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 31, context: html, text, full: html, text
    Adding announcement for new mm10 UCSC Genes track, refs #15145
    
  • lines changed 2, context: html, text, full: html, text
    Correcting typo in annnouncement, refs #15145
    
• src/hg/htdocs/indexNews.html
  • lines changed 37, context: html, text, full: html, text
    Adding announcement for new mm10 UCSC Genes track, refs #15145
    
  • lines changed 2, context: html, text, full: html, text
    Correcting typo in annnouncement, refs #15145
    
• src/hg/inc/hgBam.h
  • lines changed 4, context: html, text, full: html, text
    Add needed include
    
• src/hg/inc/trackHub.h
  • lines changed 34, context: html, text, full: html, text
    1. Add -test option to use genome-test spec file. 2. Remove unneeded errCatch (from code review). 3. Simplify code org (delibify unshared code); bye to lib/trackHubCheck.c. refs #10015
    
• src/hg/inc/transMapStuff.h
  • lines changed 10, context: html, text, full: html, text
    support setting transMap track default item labeling in trackDb (#15440)
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v317
    
• src/hg/js/model/hgIntegrator/hgIntegratorModel.js
  • lines changed 5, context: html, text, full: html, text
    Moving the 'quick-reference' contents of hgIntegratorHelp.html to
    hgIntegrator.jsx so Matt can write a proper user's guide in
    hgIntegratorHelp.html. Also, now we don't need to fetch html
    from the server and use React's dangerouslySetInnerHTML.
    refs #14579 note 65
    
• src/hg/js/react/hgIntegrator/hgIntegrator.jsx
  • lines changed 84, context: html, text, full: html, text
    Moving the 'quick-reference' contents of hgIntegratorHelp.html to
    hgIntegrator.jsx so Matt can write a proper user's guide in
    hgIntegratorHelp.html. Also, now we don't need to fetch html
    from the server and use React's dangerouslySetInnerHTML.
    refs #14579 note 65
    
• src/hg/js/react/lib/Modal.jsx
  • lines changed 8, context: html, text, full: html, text
    Fixed wacky scrolling behavior in pop-up dialog (Modal).
    refs #14579 note 68
    
  • lines changed 6, context: html, text, full: html, text
    When pop-up/Modal closes, return to the original page scroll height
    in case the user has scrolled way down while viewing the Modal.
    refs #14579 note 54
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    1. Add -test option to use genome-test spec file. 2. Remove unneeded errCatch (from code review). 3. Simplify code org (delibify unshared code); bye to lib/trackHubCheck.c. refs #10015
    
• src/hg/lib/tests/expected/annoGrator/bigBedToTabOut.txt
  • lines changed 1, context: html, text, full: html, text
    Updating hg/lib/tests annoGrator files for some recent(ish) changes: full source name in header,
    wiggle chrom shown by default in addition to start and end, and wiggle average shown instead of
    comma-sep list in tab-sep output.
    refs #14579
    
• src/hg/lib/tests/expected/annoGrator/pgSnpDbToTabOut.txt
  • lines changed 1, context: html, text, full: html, text
    Updating hg/lib/tests annoGrator files for some recent(ish) changes: full source name in header,
    wiggle chrom shown by default in addition to start and end, and wiggle average shown instead of
    comma-sep list in tab-sep output.
    refs #14579
    
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 1, context: html, text, full: html, text
    Updating hg/lib/tests annoGrator files for some recent(ish) changes: full source name in header,
    wiggle chrom shown by default in addition to start and end, and wiggle average shown instead of
    comma-sep list in tab-sep output.
    refs #14579
    
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToTabOutShort.txt
  • lines changed 1, context: html, text, full: html, text
    Updating hg/lib/tests annoGrator files for some recent(ish) changes: full source name in header,
    wiggle chrom shown by default in addition to start and end, and wiggle average shown instead of
    comma-sep list in tab-sep output.
    refs #14579
    
• src/hg/lib/tests/expected/annoGrator/snpBigWigToTabOut.txt
  • lines changed 288, context: html, text, full: html, text
    Updating hg/lib/tests annoGrator files for some recent(ish) changes: full source name in header,
    wiggle chrom shown by default in addition to start and end, and wiggle average shown instead of
    comma-sep list in tab-sep output.
    refs #14579
    
• src/hg/lib/tests/expected/annoGrator/snpConsDbToTabOutShort.txt
  • lines changed 38, context: html, text, full: html, text
    Updating hg/lib/tests annoGrator files for some recent(ish) changes: full source name in header,
    wiggle chrom shown by default in addition to start and end, and wiggle average shown instead of
    comma-sep list in tab-sep output.
    refs #14579
    
• src/hg/lib/tests/expected/annoGrator/vcfEx1.txt
  • lines changed 1, context: html, text, full: html, text
    Updating hg/lib/tests annoGrator files for some recent(ish) changes: full source name in header,
    wiggle chrom shown by default in addition to start and end, and wiggle average shown instead of
    comma-sep list in tab-sep output.
    refs #14579
    
• src/hg/lib/tests/expected/annoGrator/vcfEx2.txt
  • lines changed 1, context: html, text, full: html, text
    Updating hg/lib/tests annoGrator files for some recent(ish) changes: full source name in header,
    wiggle chrom shown by default in addition to start and end, and wiggle average shown instead of
    comma-sep list in tab-sep output.
    refs #14579
    
• src/hg/lib/trackHubCheck.c
  • lines changed 494, context: html, text, full: html, text
    1. Add -test option to use genome-test spec file. 2. Remove unneeded errCatch (from code review). 3. Simplify code org (delibify unshared code); bye to lib/trackHubCheck.c. refs #10015
    
• src/hg/lib/web.c
  • lines changed 2, context: html, text, full: html, text
    Don't restrict hgIntegrator to private hosts anymore -- we're going to release it!
    refs #14579
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added micMur2 - Mouse lemur refs #15292
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    fixup bisBis1 config refs #15388
    
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    Added micMur2 - Mouse lemur refs #15292
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    ignore augustusGene table nothing to check refs #13088
    
• src/hg/makeDb/trackDb/human/chainNetMicMur1.ra
  • lines changed 15, context: html, text, full: html, text
    turn of micMur2 chainNet for alpha target leave micMur1 as beta public refs #15292
    
• src/hg/makeDb/trackDb/human/chainNetMicMur2.ra
  • lines changed 15, context: html, text, full: html, text
    turn of micMur2 chainNet for alpha target leave micMur1 as beta public refs #15292
    
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
  • lines changed 15, context: html, text, full: html, text
    turn of micMur2 chainNet for alpha target leave micMur1 as beta public refs #15292
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    turn of micMur2 chainNet for alpha target leave micMur1 as beta public refs #15292
    
• src/hg/makeDb/trackDb/human/hg38/hg38Patch3.html
  • lines changed 3, context: html, text, full: html, text
    Made slight modification to description page; modified release tags for Patch 2 & 3; refs #15143
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Made slight modification to description page; modified release tags for Patch 2 & 3; refs #15143
    
  • lines changed 2, context: html, text, full: html, text
    Edited release tags for Patch 2 & 3; refs #15143
    
• src/hg/makeDb/trackDb/loadTracks
  • lines changed 1, context: html, text, full: html, text
    fixed undefined variable when -local is not specified
    
• src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Change based on CR, refs #15403
    
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 51, context: html, text, full: html, text
    turn of micMur2 chainNet for alpha target leave micMur1 as beta public refs #15292
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    add search rule for augustusGene track refs #13088
    
• src/hg/utils/automation/doAugustus.pl
  • lines changed 14, context: html, text, full: html, text
    auto detect UTR option and manage no partBundles correctly refs #13088
    
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 1, context: html, text, full: html, text
    correct symlink for synNet downloads refs #14560
    
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 562, context: html, text, full: html, text
    1. Add -test option to use genome-test spec file. 2. Remove unneeded errCatch (from code review). 3. Simplify code org (delibify unshared code); bye to lib/trackHubCheck.c. refs #10015
    
  • lines changed 97, context: html, text, full: html, text
    1. Get version from doc. 2. Fix err messages. refs #10015
    
  • lines changed 9, context: html, text, full: html, text
    Fix to handling of deprecated settings. refs #10015
    
• src/lib/annoFormatTab.c
  • lines changed 18, context: html, text, full: html, text
    In order to make it more clear that wiggle values are averaged now,
    print out wiggle's value column as "valueAverage" in the header.
    refs #14579 note 61
    
• src/utils/bedToBigBed/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    fixup expected failing command so its failure code will not bother make refs #15417
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v317 final build
    

• lines changed: 2959
• files changed: 58