File Changes for tdreszer

v259_base to v260_preview (2011-11-07 to 2011-11-15) v260

• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 14, context: html, text, full: html, text
    When document link setting in cv.ra contains 'missing' then then rpint that. For redmine 1012
  • lines changed 14, context: html, text, full: html, text
    Extended 'missing' support to individual validation documents.
• src/hg/hgTables/asObj.c
  • lines changed 111, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/hgTables/bam.c
  • lines changed 11, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/hgTables/bigBed.c
  • lines changed 37, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/hgTables/bigWig.c
  • lines changed 14, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/hgTables/filterFields.c
  • lines changed 35, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/hgTables/hgTables.h
  • lines changed 28, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/hgTables/makefile
  • lines changed 1, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/hgTables/schema.c
  • lines changed 47, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
  • lines changed 2, context: html, text, full: html, text
    Fixed mrna schema bug 5990.
• src/hg/hgTables/vcf.c
  • lines changed 26, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/hgTracks/hgTracks.c
  • lines changed 15, context: html, text, full: html, text
    Subtracks need groups if there will be sorting later.
  • lines changed 15, context: html, text, full: html, text
    Redmine 5992. Backing out previous fix in order to make a targeted fix for patching. At this checkin, code should be back to 6f7dabcd1d87152560c0b66bb126bce0a0582415.
  • lines changed 3, context: html, text, full: html, text
    Redmine 5992. This is the targetted conservative fix to hgTracks.c. Please make a patch from the difference between this and the previos hgTracks.c check-in
• src/hg/hgTracks/imageV2.c
  • lines changed 1, context: html, text, full: html, text
    Thanks Larry for finding this obscure bug. Handing off pointer instead of pointer to pointer to a routine that takes a void pointer.
  • lines changed 52, context: html, text, full: html, text
    Remove old code that was ifdef'd out.
• src/hg/hgc/bigBedClick.c
  • lines changed 47, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/hgc/hgc.c
  • lines changed 72, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
  • lines changed 55, context: html, text, full: html, text
    Get DNA color feature: added support for composites and limited to currently visible tracks. This is for redmine 685.
• src/hg/hgc/hgc.h
  • lines changed 5, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/inc/bedDetail.h
  • lines changed 4, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/inc/hui.h
  • lines changed 15, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/inc/makeItemsItem.h
  • lines changed 3, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/inc/pgSnp.h
  • lines changed 3, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/inc/samAlignment.h
  • lines changed 6, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/inc/trackDb.h
  • lines changed 30, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/lib/bedDetail.c
  • lines changed 7, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/lib/hui.c
  • lines changed 189, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
  • lines changed 3, context: html, text, full: html, text
    Fixed newly introduced filterBy bug.
• src/hg/lib/makeItemsItem.c
  • lines changed 7, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/lib/pgSnp.c
  • lines changed 7, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/lib/samAlignment.c
  • lines changed 8, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/lib/trackDbCustom.c
  • lines changed 12, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/makeDb/trackDb/README
  • lines changed 81, context: html, text, full: html, text
    Updated README as per redmine 5963. Documented filterComposite which was a major oversight and viewLimitsMax which has existed since the reign of dinosaurs. Also removed mention of 'metadata' lines, 'hierarchy' and 'dividers' which are no longer supported.
• src/inc/bigBed.h
  • lines changed 8, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/inc/vcf.h
  • lines changed 4, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/lib/bigBed.c
  • lines changed 22, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/lib/vcf.c
  • lines changed 22, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582