Commits for kent

v309_preview to v309_preview2 (2014-11-10 to 2014-11-17) v309

• Draft Django data models from Ben Passarelli.
  • src/hg/cirm/quakeLab/djangoModels/cellcapturemodels.py - lines changed 266, context: html, text, full: html, text
  • src/hg/cirm/quakeLab/djangoModels/quantifymodels.py - lines changed 45, context: html, text, full: html, text
  • src/hg/cirm/quakeLab/djangoModels/sequencemodels.py - lines changed 144, context: html, text, full: html, text
• Cut of something to convert the django models from Quake lab to .as files.
  • src/hg/cirm/quakeLab/djangoModelToAs/djangoModelToAs.c - lines changed 132, context: html, text, full: html, text
• Adding synQueuePutUnprotected, a minor optimization.
  • src/inc/synQueue.h - lines changed 4, context: html, text, full: html, text
  • src/lib/synQueue.c - lines changed 7, context: html, text, full: html, text
• Simplifying logic
  • src/lib/pthreadDoList.c - lines changed 37, context: html, text, full: html, text
• Testing pthreadDoList example usage code.
  • src/hg/oneShot/freen/freen.c - lines changed 56, context: html, text, full: html, text
• Removing old function that would be considered one shot these days.
  • src/hg/genoPheno/gpShuffleData/gpShuffleData.c - lines changed 159, context: html, text, full: html, text
  • src/hg/genoPheno/gpShuffleData/makefile - lines changed 14, context: html, text, full: html, text
• Removing more unused old cruft.
  • src/hg/genoPheno/fakeData/smallGeno.tab - lines changed 556, context: html, text, full: html, text
  • src/hg/genoPheno/gpFakeData/gpFakeData.c - lines changed 419, context: html, text, full: html, text
  • src/hg/genoPheno/gpFakeData/makefile - lines changed 14, context: html, text, full: html, text
• Removing more unused old cruft.
  • src/parasol/broadHub/broadHub.c - lines changed 750, context: html, text, full: html, text
  • src/parasol/broadHub/makefile - lines changed 14, context: html, text, full: html, text
  • src/parasol/broadNode/broadNode.c - lines changed 473, context: html, text, full: html, text
  • src/parasol/broadNode/makefile - lines changed 14, context: html, text, full: html, text
  • src/parasol/broadNodeStart/broadNodeStart.c - lines changed 54, context: html, text, full: html, text
  • src/parasol/broadNodeStart/makefile - lines changed 14, context: html, text, full: html, text
• Replaced md5hash function with equivalent call to md5ForFile library function.
  • src/hg/hgTables/genomeSpace.c - lines changed 21, context: html, text, full: html, text
• Fixing up sort order and adding treatment subgroup.
  • src/hg/makeDb/outside/uwDnaseTrackHub/uwDnaseTrackHub.c - lines changed 36, context: html, text, full: html, text
• Deleting out of place binary file
  • src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/sorted.bb - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• Adding new pipelineClose() function that combines pipelineWait and pipelineFree and applying it where it makes sense, in some cases fixing non-symptomatic bugs from missing pipelineWaits
  • src/hg/hgc/hgdpClick.c - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/hgFind.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadPsl/hgLoadPsl.c - lines changed 8, context: html, text, full: html, text
  • src/hg/pslPartition/pslPartition.c - lines changed 2, context: html, text, full: html, text
  • src/inc/pipeline.h - lines changed 8, context: html, text, full: html, text
  • src/lib/mailViaPipe.c - lines changed 4, context: html, text, full: html, text
  • src/lib/pipeline.c - lines changed 14, context: html, text, full: html, text
  • src/lib/textOut.c - lines changed 2, context: html, text, full: html, text
• Adding new pipelineClose() function that combines pipelineWait and pipelineFree and applying it where it makes sense, in some cases fixing non-symptomatic bugs from missing pipelineWaits
  • src/lib/linefile.c - lines changed 2, context: html, text, full: html, text
• Replacing old md5 module with one that follows same interface (except for some things noone used) but that is implemented by calling the md5sum program in a pipe. For large files this is about 40% faster, and for small things it just adds a couple of milliseconds. Also this gets rid of the only piece of GPL licensed code in the tree, which makes the intellecual property easier to manage.
  • src/hg/oneShot/freen/freen.c - lines changed 39, context: html, text, full: html, text
  • src/inc/md5.h - lines changed 24, context: html, text, full: html, text
  • src/lib/md5.c - lines changed 338, context: html, text, full: html, text
• Second cut, this time all in one file.
  • src/hg/cirm/quakeLab/djangoModels/cellcapturemodels.py - lines changed 266, context: html, text, full: html, text
  • src/hg/cirm/quakeLab/djangoModels/quantifymodels.py - lines changed 45, context: html, text, full: html, text
  • src/hg/cirm/quakeLab/djangoModels/sequencemodels.py - lines changed 144, context: html, text, full: html, text
  • src/hg/cirm/quakeLab/djangoModels/take1/cellcapturemodels.py - lines changed 266, context: html, text, full: html, text
  • src/hg/cirm/quakeLab/djangoModels/take1/quantifymodels.py - lines changed 45, context: html, text, full: html, text
  • src/hg/cirm/quakeLab/djangoModels/take1/sequencemodels.py - lines changed 144, context: html, text, full: html, text
  • src/hg/cirm/quakeLab/djangoModels/take2/models.py - lines changed 324, context: html, text, full: html, text
• Fixing misplaced newline.
  • src/hg/cirm/quakeLab/djangoModels/take2/models.py - lines changed 2, context: html, text, full: html, text
• Merging with root.
• Getting latest updates.
• Adding trixSearchCmp function to header file and fixed documentation.
  • src/inc/trix.h - lines changed 3, context: html, text, full: html, text
  • src/lib/trix.c - lines changed 1, context: html, text, full: html, text