Scripts/Flag_placer.py
def calculate_overshoot(cigar):
    """ The calculate overshoot function calculates the number of basepairs that have not been mapped but are part of
    the read.

    :param cigar: a list containing tuples representing the cigar string.
    :return overshoot: an integer indicating the number of basepairs in the read before it is mapped.
    """
    overshoot = 0
    for element in cigar:
        if element[0]:
            overshoot += element[1]
        else:
            break

    return overshoot
 The calculate overshoot function calculates the number of basepairs that have not been mapped but are part of
    the read.

    :param cigar: a list containing tuples representing the cigar string.
    :return overshoot: an integer indicating the number of basepairs in the read before it is mapped.
    
The calculate overshoot function calculates the number of basepairs that have not been mapped but are part of
the read.
The calculate overshoot function calculates the number of basepairs that have not been mapped but are part of the read .
def calculate_overshoot(cigar):
    overshoot = 0
    for element in cigar:
        if element[0]:
            overshoot += element[1]
        else:
            break
    return overshoot
def calculate_overshoot ( cigar ) : overshoot = 0 for element in cigar : if element [ 0 ] : overshoot += element [ 1 ] else : break return overshoot
The calculate overshoot function calculates the number of basepairs that have not been mapped but are part of
the read.
The calculate overshoot function calculates the number of basepairs that have not been mapped but are part of the read .
""" The calculate overshoot function calculates the number of basepairs that have not been mapped but are part of
    the read.

    :param cigar: a list containing tuples representing the cigar string.
    :return overshoot: an integer indicating the number of basepairs in the read before it is mapped.
    """
an integer indicating the number of basepairs in the read before it is mapped.
an integer indicating the number of basepairs in the read before it is mapped .
overshoot
cigar
a list containing tuples representing the cigar string.
a list containing tuples representing the cigar string .