R/sequenceInfoInPartition.R

In strandCheckR: Calculate strandness information of a bam file

# #' @title calculate the first/last base/read of each sequence within the part
# #' @param seqInfo a data frame contains information of sequence
# #' @winStep the step of sliding windows

sequenceInfoInPartition <- function(seqInfo, winWidth, winStep) 
{
    reqNames <- c("Sequence", "Length", "NbReads")
    stopifnot(all(reqNames %in% names(seqInfo)))
    lengthInPart <- pmax(seqInfo$Length,winWidth)
    lengthOfPart <- 
        winStep * ceiling(c(0, cumsum(as.numeric(lengthInPart)))/winStep)
    nbReadsOfPart <- c(0, cumsum(seqInfo$NbReads))
    # update seqInfo
    seqInfo$FirstBaseInPart <- lengthOfPart[-length(lengthOfPart)] + 1
    seqInfo$LastBaseInPart <- lengthOfPart[-1]
    seqInfo$FirstReadInPart <- nbReadsOfPart[-length(nbReadsOfPart)] + 1
    seqInfo$LastReadInPart <- nbReadsOfPart[-1]
    return(seqInfo)
}