All File Changes

v317_base to v318_preview (2015-06-01 to 2015-06-08) v318

• src/hg/das/das.c
  • lines changed 18, context: html, text, full: html, text
    Add support for ctgPos table type (like bed w/swizzled columns and 'contig' for name)
    and possibly other swizzled-bed types if we still have any of those.
    refs #15432
    
• src/hg/hgMirror/hgMirror
  • lines changed 10, context: html, text, full: html, text
    fixing gbib species sort order, refs #15473
    
  • lines changed 12, context: html, text, full: html, text
    checking if db is valid on hgdownload in hgMirror, refs #15473
    
  • lines changed 2, context: html, text, full: html, text
    fix missing db arg in hgMirror show subtracks, refs #15471
    
• src/hg/hgTablesTest/hgTablesTest.c
  • lines changed 2, context: html, text, full: html, text
    Fix for hgTablesTest checking of commas in join results: it's the
    second column, not the first, that should be checked for commas.
    refs #15237
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 21, context: html, text, full: html, text
    changes to get NCBI RefSeq track to use the trackVersion table, and to
    grab Genbank information when available. #13673
    
  • lines changed 8, context: html, text, full: html, text
    Revert "support setting transMap track default item labeling in trackDb (#15440)"
    
    This reverts commit ec6300a5b8e9b70968f7657becefb23ef9b23021.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    removing dropbox-hosted files from parallel downloading. refs #12728
    
  • lines changed 1, context: html, text, full: html, text
    removing a debug printf statement
    
• src/hg/hgTracks/menu.c
  • lines changed 6, context: html, text, full: html, text
    changes to get NCBI RefSeq track to use the trackVersion table, and to
    grab Genbank information when available. #13673
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 22, context: html, text, full: html, text
    changes to get NCBI RefSeq track to use the trackVersion table, and to
    grab Genbank information when available. #13673
    
• src/hg/hgTracks/snakeTrack.c
  • lines changed 8, context: html, text, full: html, text
    add left label for snakes in pack and dense modes (no redmine)
    
• src/hg/hgTracks/transMapTracks.c
  • lines changed 37, context: html, text, full: html, text
    Revert "support setting transMap track default item labeling in trackDb (#15440)"
    
    This reverts commit ec6300a5b8e9b70968f7657becefb23ef9b23021.
    
• src/hg/hgTracks/wigTrack.c
  • lines changed 5, context: html, text, full: html, text
    fixing a bug where a wig file would open a new file for every span on gbib (thanks Angie!)
    
• src/hg/hgVai/hgVai.c
  • lines changed 12, context: html, text, full: html, text
    Added support for bigGenePred to anno* libs for hgVai and hgIntegrator.
    While updating annoFormatVep.c to use column indices from autoSql instead of
    hardcoding genePred indices, I found that I had been using an incorrect index
    for strand anyway -- so I removed 3 lines of no-op code.
    refs #15439
    
• src/hg/hgc/hgc.c
  • lines changed 165, context: html, text, full: html, text
    changes to get NCBI RefSeq track to use the trackVersion table, and to
    grab Genbank information when available. #13673
    
• src/hg/htdocs/cite.html
  • lines changed 12, context: html, text, full: html, text
    Updated annotation data reference to 2015 update paper
    
• src/hg/htdocs/goldenPath/help/hgIntegratorHelp.html
  • lines changed 130, context: html, text, full: html, text
    First pass at editing hgIntergrator help doc, refs #14579
    
  • lines changed 33, context: html, text, full: html, text
    Fleshed out the introduction. Changed file mode bits (chmod a+x) so
    that the topbar would be included.
    refs #14579
    
  • lines changed 171, context: html, text, full: html, text
    Another round of edits to hgIntegrator help page. Adding images for help page. refs #14579
    
  • lines changed 94, context: html, text, full: html, text
    Added an explanation of how we handle multiple overlapping items in
    multiple secondary tables. Made an editorial pass over the whole doc
    and substituted DNase Clusters for SNPs because I think of genes+snps
    as hgVai's domain.
    refs #14579
    
• src/hg/htdocs/goldenPath/help/trackDb/makefile
  • lines changed 14, context: html, text, full: html, text
    Changes after GBPT review. Rename 'core' support level to 'base'. Add 'required' level. refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.css
  • lines changed 2, context: html, text, full: html, text
    Changes after GBPT review. Rename 'core' support level to 'base'. Add 'required' level. refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js
  • lines changed 3, context: html, text, full: html, text
    Changes after GBPT review. Rename 'core' support level to 'base'. Add 'required' level. refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 785, context: html, text, full: html, text
    Changes after GBPT review. Rename 'core' support level to 'base'. Add 'required' level. refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v0.html
  • lines changed 23, context: html, text, full: html, text
    Add description of setting levels. Add link support to makefile. refs #10015
    
  • lines changed 58, context: html, text, full: html, text
    Changes after GBPT review. Rename 'core' support level to 'base'. Add 'required' level. refs #10015
    
  • lines changed 1, context: html, text, full: html, text
    Remove priority from proposed V0 base level
    
  • lines changed 4, context: html, text, full: html, text
    Switch a few proposed level settings (base/full) after viewing Dalliance and discussions with WashU. Getting ready to send out to external sites for comment. refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 24, context: html, text, full: html, text
    Changes after GBPT review. Rename 'core' support level to 'base'. Add 'required' level. refs #10015
    
• src/hg/htdocs/images/hgIntegratorAddTrack.png
  • lines changed 0, context: html, text, full: html, text
    Another round of edits to hgIntegrator help page. Adding images for help page. refs #14579
    
• src/hg/htdocs/images/hgIntegratorDataSourceConfig.png
  • lines changed 0, context: html, text, full: html, text
    Another round of edits to hgIntegrator help page. Adding images for help page. refs #14579
    
  • lines changed 0, context: html, text, full: html, text
    Added an explanation of how we handle multiple overlapping items in
    multiple secondary tables. Made an editorial pass over the whole doc
    and substituted DNase Clusters for SNPs because I think of genes+snps
    as hgVai's domain.
    refs #14579
    
• src/hg/htdocs/images/hgIntegratorFieldsConfig.png
  • lines changed 0, context: html, text, full: html, text
    Another round of edits to hgIntegrator help page. Adding images for help page. refs #14579
    
  • lines changed 0, context: html, text, full: html, text
    Added an explanation of how we handle multiple overlapping items in
    multiple secondary tables. Made an editorial pass over the whole doc
    and substituted DNase Clusters for SNPs because I think of genes+snps
    as hgVai's domain.
    refs #14579
    
• src/hg/htdocs/images/hgIntegratorHgTracksExample.png
  • lines changed 0, context: html, text, full: html, text
    Another round of edits to hgIntegrator help page. Adding images for help page. refs #14579
    
  • lines changed 0, context: html, text, full: html, text
    Added an explanation of how we handle multiple overlapping items in
    multiple secondary tables. Made an editorial pass over the whole doc
    and substituted DNase Clusters for SNPs because I think of genes+snps
    as hgVai's domain.
    refs #14579
    
• src/hg/htdocs/images/hgIntegratorHgTracksExample2.png
  • lines changed 0, context: html, text, full: html, text
    Added an explanation of how we handle multiple overlapping items in
    multiple secondary tables. Made an editorial pass over the whole doc
    and substituted DNase Clusters for SNPs because I think of genes+snps
    as hgVai's domain.
    refs #14579
    
• src/hg/htdocs/training/index.html
  • lines changed 24, context: html, text, full: html, text
    added Brazil meeting and dropped those in the past
    
  • lines changed 1, context: html, text, full: html, text
    added back WIDTH for first column
    
• src/hg/inc/bigGenePred.h
  • lines changed 4, context: html, text, full: html, text
    Added support for bigGenePred to anno* libs for hgVai and hgIntegrator.
    While updating annoFormatVep.c to use column indices from autoSql instead of
    hardcoding genePred indices, I found that I had been using an incorrect index
    for strand anyway -- so I removed 3 lines of no-op code.
    refs #15439
    
• src/hg/inc/genePred.h
  • lines changed 4, context: html, text, full: html, text
    Added support for bigGenePred to anno* libs for hgVai and hgIntegrator.
    While updating annoFormatVep.c to use column indices from autoSql instead of
    hardcoding genePred indices, I found that I had been using an incorrect index
    for strand anyway -- so I removed 3 lines of no-op code.
    refs #15439
    
• src/hg/inc/transMapStuff.h
  • lines changed 10, context: html, text, full: html, text
    Revert "support setting transMap track default item labeling in trackDb (#15440)"
    
    This reverts commit ec6300a5b8e9b70968f7657becefb23ef9b23021.
    
• src/hg/js/model/hgIntegrator/hgIntegratorModel.js
  • lines changed 13, context: html, text, full: html, text
    hgIntegratorModel: schemaUrlFromTrackPath can't assume that mutState
    already has db, because it's possible for the groupedTrackDb to
    arrive from the server *before* the other query's results with
    cladeOrgDb etc. Use the db embedded in groupedTrackDb in that
    case.
    refs #14579
    
• src/hg/lib/annoFormatVep.c
  • lines changed 15, context: html, text, full: html, text
    Added support for bigGenePred to anno* libs for hgVai and hgIntegrator.
    While updating annoFormatVep.c to use column indices from autoSql instead of
    hardcoding genePred indices, I found that I had been using an incorrect index
    for strand anyway -- so I removed 3 lines of no-op code.
    refs #15439
    
• src/hg/lib/annoGratorGpVar.c
  • lines changed 9, context: html, text, full: html, text
    Added support for bigGenePred to anno* libs for hgVai and hgIntegrator.
    While updating annoFormatVep.c to use column indices from autoSql instead of
    hardcoding genePred indices, I found that I had been using an incorrect index
    for strand anyway -- so I removed 3 lines of no-op code.
    refs #15439
    
• src/hg/lib/annoStreamWig.c
  • lines changed 17, context: html, text, full: html, text
    For GBiB support, we can't simply assume that wib files are on local disk;
    we must use hReplaceGbdb and UDC in case they are remote. Following suit
    with Max's changes to wigTrack.c wigLoadPreDraw (225c0d55).
    refs #14579 note 106
    
• src/hg/lib/bigGenePred.c
  • lines changed 33, context: html, text, full: html, text
    Added support for bigGenePred to anno* libs for hgVai and hgIntegrator.
    While updating annoFormatVep.c to use column indices from autoSql instead of
    hardcoding genePred indices, I found that I had been using an incorrect index
    for strand anyway -- so I removed 3 lines of no-op code.
    refs #15439
    
• src/hg/lib/ensFace.c
  • lines changed 26, context: html, text, full: html, text
    changes to get NCBI RefSeq track to use the trackVersion table, and to
    grab Genbank information when available. #13673
    
• src/hg/lib/genePred.c
  • lines changed 45, context: html, text, full: html, text
    Added support for bigGenePred to anno* libs for hgVai and hgIntegrator.
    While updating annoFormatVep.c to use column indices from autoSql instead of
    hardcoding genePred indices, I found that I had been using an incorrect index
    for strand anyway -- so I removed 3 lines of no-op code.
    refs #15439
    
• src/hg/lib/hAnno.c
  • lines changed 3, context: html, text, full: html, text
    Recognize bigGenePred type and provide better error message for
    unrecognized type from hub track (instead of trying to fall back on
    getting sql table info which of course fails for a hub).
    refs #14579
    
  • lines changed 2, context: html, text, full: html, text
    Found a couple more places in hAnno.c that also need to recognize bigGenePred.
    refs #14579
    
  • lines changed 15, context: html, text, full: html, text
    Added support for bigGenePred to anno* libs for hgVai and hgIntegrator.
    While updating annoFormatVep.c to use column indices from autoSql instead of
    hardcoding genePred indices, I found that I had been using an incorrect index
    for strand anyway -- so I removed 3 lines of no-op code.
    refs #15439
    
• src/hg/lib/hdb.c
  • lines changed 5, context: html, text, full: html, text
    make tracks that have no little table, only bigDataUrl entries in
    trackDb, show up on gbib, refs #15466
    
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    fixing a hgTracks bug that I introduced recently,
    currently affects only hgwdev, refs #15480
    
• src/hg/lib/tests/expected/annoGrator/snpBigWigToTabOut.txt
  • lines changed 1, context: html, text, full: html, text
    Updating test files for changing wiggle column "value" to "valueAverage"
    in the tab-sep output since we're now printing out average values.
    refs #14579
    
• src/hg/lib/tests/expected/annoGrator/snpConsDbToTabOutShort.txt
  • lines changed 1, context: html, text, full: html, text
    Updating test files for changing wiggle column "value" to "valueAverage"
    in the tab-sep output since we're now printing out average values.
    refs #14579
    
• src/hg/lib/trackVersion.c
  • lines changed 1, context: html, text, full: html, text
    changes to get NCBI RefSeq track to use the trackVersion table, and to
    grab Genbank information when available. #13673
    
• src/hg/makeDb/doc/hg38/hg19MassiveLift.txt
  • lines changed 25, context: html, text, full: html, text
    Documentation for hg19 to hg38 lifted tracks
    
• src/hg/makeDb/doc/mm10.txt
  • lines changed 52, context: html, text, full: html, text
    ucsc genes wrap-up #15145
    
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes15.csh
  • lines changed 8, context: html, text, full: html, text
    ucsc genes wrap-up #15145
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added bisBis1 - Bison bison bison refs #15388
    
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added bisBis1 - Bison bison bison refs #15388
    
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
  • lines changed 21, context: html, text, full: html, text
    more changes to gff3ToGenePred to support NCBI RefSeq. #13673
    
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 67, context: html, text, full: html, text
    Changes after GBPT review. Rename 'core' support level to 'base'. Add 'required' level. refs #10015
    
  • lines changed 1, context: html, text, full: html, text
    Fix level test after rework. refs #10015
    
• src/inc/gff3.h
  • lines changed 2, context: html, text, full: html, text
    more changes to gff3ToGenePred to support NCBI RefSeq. #13673
    
• src/lib/gff3.c
  • lines changed 2, context: html, text, full: html, text
    more changes to gff3ToGenePred to support NCBI RefSeq. #13673
    
• src/lib/udc.c
  • lines changed 12, context: html, text, full: html, text
    allowing a single redirect in udc info requests, refs #12728
    
• src/tagStorm/jsonToTagStorm/tests/errCheck.sh
  • lines changed 41, context: html, text, full: html, text
    A makefile, shell script and some dummy files for error testing
    
• src/tagStorm/jsonToTagStorm/tests/error.json
  • lines changed 1, context: html, text, full: html, text
    A makefile, shell script and some dummy files for error testing
    
• src/tagStorm/jsonToTagStorm/tests/error2.json
  • lines changed 1, context: html, text, full: html, text
    A different error that needs to be checked
    
• src/tagStorm/jsonToTagStorm/tests/expError.txt
  • lines changed 2, context: html, text, full: html, text
    A makefile, shell script and some dummy files for error testing
    
• src/tagStorm/jsonToTagStorm/tests/expError2.txt
  • lines changed 1, context: html, text, full: html, text
    A different error that needs to be checked
    
• src/tagStorm/jsonToTagStorm/tests/makefile
  • lines changed 3, context: html, text, full: html, text
    A makefile, shell script and some dummy files for error testing
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v317 preview1 refs #15483
    
• src/utils/qa/weeklybld/doHgNearTestRobot.csh
  • lines changed 1, context: html, text, full: html, text
    Telling hgNearTest to take its test data from beta when testing beta.
    

• lines changed: 2161
• files changed: 77