Commits for angie

v285_preview to v285_preview2 (2013-06-04 to 2013-06-11) v285

• Generating sequence names as <db>_<track>_<itemName> works great exceptfor bed3 tracks that have NULL names. Use an incrementing count to
  generate distinct names instead. fixes #10995
  
  • src/hg/lib/hgSeq.c - lines changed 5, context: html, text, full: html, text
• Valuable feedback from code review -- thanks Tim! refs 10977
  • src/hg/hgVai/libifyMe.c - lines changed 10, context: html, text, full: html, text
  • src/hg/hgVai/libifyMe.h - lines changed 1, context: html, text, full: html, text
  • src/hg/inc/hubConnect.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/hubConnect.c - lines changed 1, context: html, text, full: html, text
• Revert "Added support for multi-view composites of type pgSnp. There are no config options for pgSnp, so disable the config pop-up in configurableByAjax. refs #683"This reverts commit 275a4e6b9d4eef6b3408e29198d94883b0e809ca.
  -- Tim pointed out in code review that there is a much better way to avoid the warnBox at the end of cfgTypeFromTdb. refs #10977 #683
  
  • src/hg/inc/trackDb.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c - lines changed 4, context: html, text, full: html, text
• Avoid warnBox at the end of cfgTypeFromTdb for pgSnp tracks with views. Thanks Tim! refs #10977 #683
  • src/hg/lib/trackDbCustom.c - lines changed 2, context: html, text, full: html, text
• Added support for remaining dbNSFP sources; added longLabels to VEP output header lines. refs #6152
  • src/hg/hgVai/hgVai.c - lines changed 465, context: html, text, full: html, text
  • src/hg/hgVai/libifyMe.c - lines changed 29, context: html, text, full: html, text
  • src/hg/hgVai/libifyMe.h - lines changed 5, context: html, text, full: html, text
  • src/hg/inc/annoFormatVep.h - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/annoFormatVep.c - lines changed 304, context: html, text, full: html, text
  • src/hg/lib/tests/annoGratorTester.c - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/tests/expected/annoGrator/gpFx.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/lib/tests/expected/annoGrator/vepOut.txt - lines changed 3, context: html, text, full: html, text
  • src/lib/annoStreamBigWig.c - lines changed 6, context: html, text, full: html, text
• Oops, hgVarAnnogrator is catching up with 2b5eb866 -- since it's notin top-level build, it's too easy to overlook things that break it.
  I intend to replace it with a less variant-centric CGI when hgVai is stable.
  
  • src/hg/hgVarAnnogrator/hgVarAnnogrator.c - lines changed 2, context: html, text, full: html, text
• Added a chunked-query mode to annoStreamDb, similar to that of annoStreamBigBed,so that we can quickly drain sqlResults from smaller queries instead of keeping
  a genome-wide sqlResult open for the whole time we're processing -- that was
  making mysql have mysterious hangs on hgwdev. (http://bugs.mysql.com/bug.php?id=50399)
  
  • src/hg/lib/annoStreamDb.c - lines changed 280, context: html, text, full: html, text
  • src/hg/lib/tests/annoGratorTester.c - lines changed 29, context: html, text, full: html, text
  • src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt - lines changed 39, context: html, text, full: html, text
  • src/hg/lib/tests/input/annoGrator/pgForTestingGpFx.pgSnp.tab - lines changed 10, context: html, text, full: html, text
  • src/inc/annoAssembly.h - lines changed 4, context: html, text, full: html, text
  • src/lib/annoAssembly.c - lines changed 10, context: html, text, full: html, text
  • src/lib/annoGrator.c - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/lib/annoStreamBigBed.c - lines changed 5, context: html, text, full: html, text