Commits for larrym

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

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