YulongNiu

samtools view -b Example_Condition1.sam -o Example_Condition1.bam
samtools view -b Example_Condition2.sam -o Example_Condition2.bam

## reverse
samtools view -h -f 16 Example_Condition1.bam -o Example_Condition1_rev.bam
## forward
samtools view -h -F 16 Example_Condition1.bam -o Example_Condition1_forw.bam

## reverse
samtools view -h -f 16 Example_Condition2.bam -o Example_Condition2_rev.bam

YulongNiu

SSIndex <- function(i, len, wise = 5) {

  min <- i - wise
  min <- ifelse(min < 1, 1, min)

  max <- i + wise
  max <- ifelse(max > len, len, max)

  return(seq(min, max))
}

YulongNiu

##~~~~~~~~~~~~~~~~~~~~~~~~~define class~~~~~~~~~~~~~~~~~~~~~~~~~
## new class
setClass(Class = 'trick',
         slots = c(id = 'character', time = 'matrix'),
         validity = function(object) {
           if (length(object@id) != nrow(object@time)) {
             warns <- paste('length of id is', length(object@id), 'is not equal to row number of time', nrow(object@time))
             return(warns)
           } else {
             return(TRUE)