File Changes for kent

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

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