Commits for kent

v275_preview2 to v275_base (2012-10-23 to 2012-10-30) v275

• Renaming and otherwise refactoring alphaChain program into alphaAsm. Making it hold reads in a list for multiple passes.
  • src/kehayden/alphaAsm/alphaAsm.c - lines changed 887, context: html, text, full: html, text
  • src/kehayden/alphaAsm/doIt - lines changed 2, context: html, text, full: html, text
  • src/kehayden/alphaAsm/makefile - lines changed 18, context: html, text, full: html, text
• Starting to do orphan beginning/end processing.
  • src/kehayden/alphaAsm/alphaAsm.c - lines changed 107, context: html, text, full: html, text
• Adding missing types based on reads.
  • src/kehayden/alphaAsm/alphaAsm.c - lines changed 183, context: html, text, full: html, text
• Integrating orphans (things that are only at beginning or end of any read) by adding fake reads.
  • src/kehayden/alphaAsm/alphaAsm.c - lines changed 147, context: html, text, full: html, text
• Rearranging order so integrateOrphans gets called before markovChains are made.
  • src/kehayden/alphaAsm/alphaAsm.c - lines changed 4, context: html, text, full: html, text
• Making it use lower order model once higher order model has reached outTarget. Improving top level comment.
  • src/kehayden/alphaAsm/alphaAsm.c - lines changed 89, context: html, text, full: html, text
• Adding pseudoCount.
  • src/kehayden/alphaAsm/alphaAsm.c - lines changed 33, context: html, text, full: html, text
• Polishing code and comments without changing meaning at all.
  • src/kehayden/alphaAsm/alphaAsm.c - lines changed 32, context: html, text, full: html, text
• Updating comment to reflect how code actually works these days.
  • src/parasol/paraHub/paraHub.c - lines changed 23, context: html, text, full: html, text
• Removing old unused one line script.
  • src/kehayden/alphaChain/sampleIt - lines changed 1, context: html, text, full: html, text
• Making testing framework fit usual conventions more.
  • src/kehayden/alphaChain/doIt - lines changed 2, context: html, text, full: html, text
  • src/kehayden/alphaChain/makefile - lines changed 3, context: html, text, full: html, text
• Making testing framework fit usual conventions more.
  • src/kehayden/alphaAsm/doIt - lines changed 2, context: html, text, full: html, text
  • src/kehayden/alphaAsm/makefile - lines changed 4, context: html, text, full: html, text
  • src/kehayden/alphaAsm/yReads.txt - lines changed 966, context: html, text, full: html, text
  • src/kehayden/alphaAsm/yTypeOrder.txt - lines changed 34, context: html, text, full: html, text
• Improving readability.
  • src/kehayden/alphaAsm/alphaAsm.c - lines changed 7, context: html, text, full: html, text
• Improving output and adding command line option.
  • src/hg/oneShot/testSearch/testSearch.c - lines changed 23, context: html, text, full: html, text
• Moving testSearch out of oneShot and renaming it to trixSearch to be more specific.
  • src/hg/oneShot/testSearch/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/oneShot/testSearch/testSearch.c - lines changed 76, context: html, text, full: html, text
  • src/index/trixSearch/makefile - lines changed 14, context: html, text, full: html, text
  • src/index/trixSearch/trixSearch.c - lines changed 76, context: html, text, full: html, text
• Bumping blat version.
  • src/blat/version.doc - lines changed 1, context: html, text, full: html, text
  • src/inc/genoFind.h - lines changed 1, context: html, text, full: html, text
• Resolving conflicts in blat version bump.
  • src/blat/version.doc - lines changed 2, context: html, text, full: html, text