File Changes for kent

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

• src/hg/cirm/quakeLab/djangoModelToAs/djangoModelToAs.c
  • lines changed 132, context: html, text, full: html, text
    Cut of something to convert the django models from Quake lab to .as files.
• src/hg/cirm/quakeLab/djangoModels/cellcapturemodels.py
  • lines changed 266, context: html, text, full: html, text
    Draft Django data models from Ben Passarelli.
  • lines changed 266, context: html, text, full: html, text
    Second cut, this time all in one file.
• src/hg/cirm/quakeLab/djangoModels/quantifymodels.py
  • lines changed 45, context: html, text, full: html, text
    Draft Django data models from Ben Passarelli.
  • lines changed 45, context: html, text, full: html, text
    Second cut, this time all in one file.
• src/hg/cirm/quakeLab/djangoModels/sequencemodels.py
  • lines changed 144, context: html, text, full: html, text
    Draft Django data models from Ben Passarelli.
  • lines changed 144, context: html, text, full: html, text
    Second cut, this time all in one file.
• src/hg/cirm/quakeLab/djangoModels/take1/cellcapturemodels.py
  • lines changed 266, context: html, text, full: html, text
    Second cut, this time all in one file.
• src/hg/cirm/quakeLab/djangoModels/take1/quantifymodels.py
  • lines changed 45, context: html, text, full: html, text
    Second cut, this time all in one file.
• src/hg/cirm/quakeLab/djangoModels/take1/sequencemodels.py
  • lines changed 144, context: html, text, full: html, text
    Second cut, this time all in one file.
• src/hg/cirm/quakeLab/djangoModels/take2/models.py
  • lines changed 324, context: html, text, full: html, text
    Second cut, this time all in one file.
  • lines changed 2, context: html, text, full: html, text
    Fixing misplaced newline.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/sorted.bb
  • lines changed 0, context: html, text, full: html, text
    Deleting out of place binary file
• src/hg/genoPheno/fakeData/smallGeno.tab
  • lines changed 556, context: html, text, full: html, text
    Removing more unused old cruft.
• src/hg/genoPheno/gpFakeData/gpFakeData.c
  • lines changed 419, context: html, text, full: html, text
    Removing more unused old cruft.
• src/hg/genoPheno/gpFakeData/makefile
  • lines changed 14, context: html, text, full: html, text
    Removing more unused old cruft.
• src/hg/genoPheno/gpShuffleData/gpShuffleData.c
  • lines changed 159, context: html, text, full: html, text
    Removing old function that would be considered one shot these days.
• src/hg/genoPheno/gpShuffleData/makefile
  • lines changed 14, context: html, text, full: html, text
    Removing old function that would be considered one shot these days.
• src/hg/hgTables/genomeSpace.c
  • lines changed 21, context: html, text, full: html, text
    Replaced md5hash function with equivalent call to md5ForFile library function.
• src/hg/hgc/hgdpClick.c
  • lines changed 6, 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/hg/lib/hgFind.c
  • lines changed 1, 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/hg/makeDb/hgLoadPsl/hgLoadPsl.c
  • lines changed 8, 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/hg/makeDb/outside/uwDnaseTrackHub/uwDnaseTrackHub.c
  • lines changed 36, context: html, text, full: html, text
    Fixing up sort order and adding treatment subgroup.
• src/hg/oneShot/freen/freen.c
  • lines changed 56, context: html, text, full: html, text
    Testing pthreadDoList example usage code.
  • lines changed 39, 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/pslPartition/pslPartition.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/inc/md5.h
  • lines changed 24, 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/inc/pipeline.h
  • lines changed 8, 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/inc/synQueue.h
  • lines changed 4, context: html, text, full: html, text
    Adding synQueuePutUnprotected, a minor optimization.
• src/inc/trix.h
  • lines changed 3, context: html, text, full: html, text
    Adding trixSearchCmp function to header file and fixed documentation.
• src/lib/linefile.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/mailViaPipe.c
  • lines changed 4, 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/md5.c
  • lines changed 338, 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/lib/pipeline.c
  • lines changed 14, 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/pthreadDoList.c
  • lines changed 37, context: html, text, full: html, text
    Simplifying logic
• src/lib/synQueue.c
  • lines changed 7, context: html, text, full: html, text
    Adding synQueuePutUnprotected, a minor optimization.
• 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/trix.c
  • lines changed 1, context: html, text, full: html, text
    Adding trixSearchCmp function to header file and fixed documentation.
• src/parasol/broadHub/broadHub.c
  • lines changed 750, context: html, text, full: html, text
    Removing more unused old cruft.
• src/parasol/broadHub/makefile
  • lines changed 14, context: html, text, full: html, text
    Removing more unused old cruft.
• src/parasol/broadNode/broadNode.c
  • lines changed 473, context: html, text, full: html, text
    Removing more unused old cruft.
• src/parasol/broadNode/makefile
  • lines changed 14, context: html, text, full: html, text
    Removing more unused old cruft.
• src/parasol/broadNodeStart/broadNodeStart.c
  • lines changed 54, context: html, text, full: html, text
    Removing more unused old cruft.
• src/parasol/broadNodeStart/makefile
  • lines changed 14, context: html, text, full: html, text
    Removing more unused old cruft.