Commits for kent

v273_preview2 to v273_base (2012-09-11 to 2012-09-18) v273

• Tighting up spacing between button rows.
  • src/hg/hgTracks/hgTracks.c - lines changed 1, context: html, text, full: html, text
• Adding a bunch of debugging code. Preventing higher level counts on output from follang below the children's counts. Thinking about (but not yet implementing) change so ends of input lines are not put in a 2-mers and 1-mers when lines are 3 or more long.
  • src/kehayden/alphaChain/alphaChain.c - lines changed 72, context: html, text, full: html, text
• Converting some debugging code into verbose logging statements.
  • src/kehayden/alphaChain/alphaChain.c - lines changed 13, context: html, text, full: html, text
• Reworking command line and refactoring to add monomer classification info. Not yet implemented, just refactoring.
  • src/kehayden/alphaChain/alphaChain.c - lines changed 95, context: html, text, full: html, text
• Loading in monomer order file.
  • src/kehayden/alphaChain/alphaChain.c - lines changed 58, context: html, text, full: html, text
• Some refactoring. Making it so saves entire generated chain in memory so that can go back further than just last 3.
  • src/kehayden/alphaChain/alphaChain.c - lines changed 46, context: html, text, full: html, text
• Refactoring - working towards making predictNext more general.
  • src/kehayden/alphaChain/alphaChain.c - lines changed 37, context: html, text, full: html, text
• Adding a flag to prevent init from happening twice in dnaUtilOpen.
  • src/lib/dnautil.c - lines changed 1, context: html, text, full: html, text
• Making program look at the monomer order file to help it's predictions in case where it has nothing it can use in the markov chains.
  • src/kehayden/alphaChain/alphaChain.c - lines changed 122, context: html, text, full: html, text
• Adding inputs to alphaChain from Y chromosome as a test set.
  • src/kehayden/alphaChain/DYZ3.pairRdData.txt - lines changed 834, context: html, text, full: html, text
  • src/kehayden/alphaChain/DYZ3_alphaChain_monOrder.txt - lines changed 34, context: html, text, full: html, text
• Removing pairFile command line parameter since not yet using it. Improving usage message.
  • src/kehayden/alphaChain/alphaChain.c - lines changed 7, context: html, text, full: html, text
  • src/kehayden/alphaChain/doIt - lines changed 2, context: html, text, full: html, text