alignAdjust=function(inputfile, outDir="",twoBitFile,athresh=1,adjustsize=0){
if(!file.exists(inputfile)){
stop(paste("Input file not found,",inputfile,sep=" "))
}
if(!file.exists(twoBitFile)){
stop(paste("twoBit file not found,",twoBitFile,sep=" "))
}
.C("alignAdjust",as.character(inputfile),as.character(outDir),as.character(twoBitFile),as.integer(athresh),as.integer(adjustsize),PACKAGE="zinba")
gc()
}
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