Scripts/Flag_placer.py
def true_position(read):
    """ The true_position function receives a read and determines the start of the read as presented in igv by including
    unmapped basepairs.

    :param read: pysam object containing data of a read.
    :return start: an integer indicating the true start of a read.
    :return end: an integer idicating the true end of a read.
    """
    cigar = read.cigar
    start = read.positions[0] - calculate_overshoot(cigar)
    end = read.positions[-1] + calculate_overshoot(cigar[::-1])

    return start, end
 The true_position function receives a read and determines the start of the read as presented in igv by including
    unmapped basepairs.

    :param read: pysam object containing data of a read.
    :return start: an integer indicating the true start of a read.
    :return end: an integer idicating the true end of a read.
    
The true_position function receives a read and determines the start of the read as presented in igv by including
unmapped basepairs.
The true_position function receives a read and determines the start of the read as presented in igv by including unmapped basepairs .
def true_position(read):
    cigar = read.cigar
    start = read.positions[0] - calculate_overshoot(cigar)
    end = read.positions[-1] + calculate_overshoot(cigar[::-1])
    return start, end
def true_position ( read ) : cigar = read . cigar start = read . positions [ 0 ] - calculate_overshoot ( cigar ) end = read . positions [ - 1 ] + calculate_overshoot ( cigar [ : : - 1 ] ) return start , end
The true_position function receives a read and determines the start of the read as presented in igv by including
unmapped basepairs.
The true_position function receives a read and determines the start of the read as presented in igv by including unmapped basepairs .
""" The true_position function receives a read and determines the start of the read as presented in igv by including
    unmapped basepairs.

    :param read: pysam object containing data of a read.
    :return start: an integer indicating the true start of a read.
    :return end: an integer idicating the true end of a read.
    """
an integer indicating the true start of a read.
an integer indicating the true start of a read .
start
an integer idicating the true end of a read.
an integer idicating the true end of a read .
end
read
pysam object containing data of a read.
pysam object containing data of a read .