trapes.py 文件源码

def findCountsInRegion(bamF, start, end, tcr):
    readsArr = []
    mappedFile = pysam.AlignmentFile(bamF,"rb")
    readsIter = mappedFile.fetch(tcr, start, end)
    for read in readsIter:
        if read.is_read1 :
            newName =  read.query_name + '_1'
        else:
            newName = read.query_name + '_2'
        if newName not in readsArr:
            readsArr.append(newName)
    mappedFile.close()
    counts = len(readsArr)
    return counts