Opossum.py 文件源码

def CreateReadObject(read, newseq, newqual, newcigar, startread, basetag=[]) :

    a = pysam.AlignedSegment()
    a.query_name = read.query_name
    a.query_sequence = newseq
    a.query_qualities = pysam.qualitystring_to_array(newqual)
    a.cigar = newcigar
    a.reference_start = startread

    # If (Star) mapper has assigned a value of 255 to mapping quality,
    # change it to 50
    mapqual = read.mapping_quality 
    if mapqual == 255 :
        a.mapping_quality = 50
    else :
        a.mapping_quality = mapqual

    a.reference_id = read.reference_id

    # If read has RG read group tag, keep it
    try :
        r_RG = read.get_tag('RG')
        a.tags = ()
        a.set_tag('RG', r_RG)
    except :
        a.tags = ()

    a.next_reference_id = -1
    a.next_reference_start = -1
    a.template_length = 0
    a.flag = UpdateFlag(read.flag)

    return a


# Goes through the given cigar list and reports how many times cigarType is equal to 3
# Optional field is finalpos, which is cutoff position for counting the splits (relative to start pos)
# Default value for finalpos is something very large