]0;/data/images/proton/DKlab/mr/parclip/shrimpreczko@max:/data/images/proton/DKlab/mr/parclip/shrimp$ for i in *md.bam
> do
> samtools sort $i $i.srt
> samtools index $i.srt.bam
> echo $i
> done

require(wavClusteR)
 b=readSortedBam("2hrep2-15mMm.bam.md.bam.srt.bam")
 countTable <- getAllSub( b, minCov = 10 )
head( countTable )
plotSubstitutions( countTable, highlight = "TC" )
  model <- fitMixtureModel(countTable, substitution = "TC")
  (support <- getExpInterval( model, bayes = TRUE ) )
plotSubstitutions( countTable, highlight = "TC", model )
highConfSub <- getHighConfSub( countTable, 
                               support = support, 
                               substitution = "TC" )
coverage <- coverage( b )