File Changes for angie

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/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/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/htdocs/goldenPath/help/hgIntegratorHelp.html
  • 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 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/images/hgIntegratorDataSourceConfig.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/images/hgIntegratorFieldsConfig.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/images/hgIntegratorHgTracksExample.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/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/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/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/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/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