Commits for ceisenhart

v330_preview to v330_preview2.1 (2016-03-07 to 2016-03-14) v330

• Some minor changes, cleaning up the code a bit and adding in more comments where needed. Refs #16341
  
  • src/hg/js/d3.dendrograms.js - lines changed 329, context: html, text, full: html, text
• Updating the /kent/src/hg/js makefile to include d3.dendrograms.js refs #16341
  
  • src/hg/js/makefile - lines changed 1, context: html, text, full: html, text
• Adding in a sibling comparison function to the multi threaded function, refs #16216
  
  • src/inc/hacTree.h - lines changed 5, context: html, text, full: html, text
• Adding in a sibling comparison function to the multi threaded function, refs #16216
  
  • src/lib/hacTree.c - lines changed 24, context: html, text, full: html, text
• Changing the test directory makefile a bit. Still looking for an easy way to implement changes suggested by Angie, refs #16216
  
  • src/hg/expMatrixToJson/tests/makefile - lines changed 3, context: html, text, full: html, text
• Modified the clustering algorithm, added in a sibling comparison function that decides the first born child. Refs #16216
  
  • src/hg/expMatrixToJson/expMatrixToJson.c - lines changed 160, context: html, text, full: html, text
• Changed the underlying library file and had to update this program. The program will run the same, now it passes an extra NULL into one of the library functions.
  
  • src/utils/bigWigCluster/bigWigCluster.c - lines changed 1, context: html, text, full: html, text
• Changing variable names, refs #16216
  
  • src/hg/expMatrixToJson/expMatrixToJson.c - lines changed 10, context: html, text, full: html, text
• Fixing the meta data file so it only reads one line as suggested by Jim in #16789, refs #16182
  
  • src/hg/cirm/cdw/wrangle/addMetaDataToJson/addMetaDataToJson - lines changed 15, context: html, text, full: html, text
• Changing the program name as suggested by Jim in #16789, refs #16182
  
  • src/hg/expMatrixClustersForDendrogram/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/expMatrixToJson/expMatrixClustersForDendrogram.c - lines changed 636, context: html, text, full: html, text
  • src/hg/expMatrixToJson/expMatrixToJson.c - lines changed 636, context: html, text, full: html, text
• Made the dependency files depend on an environment varialbe CIRM as suggested by Max, refs #16244
  
  • src/hg/cirm/cdw/wrangle/condenseMatrix/condenseMatrix - lines changed 49, context: html, text, full: html, text
  • src/hg/cirm/cdw/wrangle/condenseMatrix/makefile - lines changed 3, context: html, text, full: html, text
• Commenting the code a bunch, refs #16341
  
  • src/hg/js/d3.dendrograms.js - lines changed 521, context: html, text, full: html, text