File Changes for larrym

v235_base to v236_preview (2010-07-06 to 2010-07-13) v236

• src/hg/inc/dnaMarkovSql.h
  • lines changed 13, context: html, text, full: html, text
    add dnaMarkSql
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    fix 'trackDbJson' is undefined' message reported by mary
• src/hg/lib/dnaMarkovSql.c
  • lines changed 25, context: html, text, full: html, text
    add dnaMarkSql
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    add dnaMarkovSql.o
• src/hg/utils/automation/HgDb.pm
  • lines changed 19, context: html, text, full: html, text
    add update and insert methods
• src/hg/utils/motifFinder/motifFinder.c
  • lines changed 16, context: html, text, full: html, text
    change 'multiple hits in a peak' algo to use exponential backoff of the prior
  • lines changed 41, context: html, text, full: html, text
    start adding code to look for multiple binding sites in the same peak
  • lines changed 155, context: html, text, full: html, text
    find largest scoring motif(s) in bed items
• src/hg/utils/mutationClassifier/mutationClassifier.c
  • lines changed 27, context: html, text, full: html, text
    replace mysql order by with in memory sort to get a big speedup
  • lines changed 12, context: html, text, full: html, text
    add pos w/n motif and distance to nearest gene to output
  • lines changed 5, context: html, text, full: html, text
    code cleanup
  • lines changed 5, context: html, text, full: html, text
    fprintf => verbose
  • lines changed 12, context: html, text, full: html, text
    refactor code into loadMark2
  • lines changed 18, context: html, text, full: html, text
    look for regulatory mutations w/n introns
  • lines changed 78, context: html, text, full: html, text
    add skipGeneModel option; support 2nd-order markov background model
  • lines changed 2, context: html, text, full: html, text
    free seq after use
  • lines changed 10, context: html, text, full: html, text
    scoreDelta -> minDelta
  • lines changed 80, context: html, text, full: html, text
    print out nearest gene for regulatory mutations
  • lines changed 26, context: html, text, full: html, text
    add scoreDelta option
  • lines changed 15, context: html, text, full: html, text
    fix bug in handling of multiple files caused by failing to re-initialize lists
• src/hg/utils/mutationClassifier/test/test.bed
  • lines changed 17, context: html, text, full: html, text
    make SNPs zero length
• src/inc/dnaMarkov.h
  • lines changed 9, context: html, text, full: html, text
    add dnaMotifBitScoreWithMarkovBg
• src/inc/dnaMotif.h
  • lines changed 7, context: html, text, full: html, text
    add dnaMotifBitScoreWithMarkovBg
• src/lib/dnaMarkov.c
  • lines changed 63, context: html, text, full: html, text
    add dnaMotifBitScoreWithMarkovBg
• src/lib/dnaMotif.c
  • lines changed 1, context: html, text, full: html, text
    code cleanup
  • lines changed 72, context: html, text, full: html, text
    add dnaMotifBitScoreWithMarkovBg