Scripts/softclip_graph.py
def true_start(cigar, matchstart):
    """ The true_start function receives the cigar string and the starting position of the first match in a read. It
    returns the start position of the read including unmapped parts.

    :param cigar: a list containing tuples representing the cigar string.
    :param matchstart: an integer representing the start of the first mapped base of a read.
    """
    overshoot = 0

    for element in cigar:
        if element[0] != 0:
            overshoot += element[1]
        else:
            break

    read_start = matchstart - overshoot

    return read_start
 The true_start function receives the cigar string and the starting position of the first match in a read. It
    returns the start position of the read including unmapped parts.

    :param cigar: a list containing tuples representing the cigar string.
    :param matchstart: an integer representing the start of the first mapped base of a read.
    
The true_start function receives the cigar string and the starting position of the first match in a read. It
returns the start position of the read including unmapped parts.
The true_start function receives the cigar string and the starting position of the first match in a read . It returns the start position of the read including unmapped parts .
def true_start(cigar, matchstart):
    overshoot = 0
    for element in cigar:
        if element[0] != 0:
            overshoot += element[1]
        else:
            break
    read_start = matchstart - overshoot
    return read_start
def true_start ( cigar , matchstart ) : overshoot = 0 for element in cigar : if element [ 0 ] != 0 : overshoot += element [ 1 ] else : break read_start = matchstart - overshoot return read_start
The true_start function receives the cigar string and the starting position of the first match in a read.
The true_start function receives the cigar string and the starting position of the first match in a read .
""" The true_start function receives the cigar string and the starting position of the first match in a read. It
    returns the start position of the read including unmapped parts.

    :param cigar: a list containing tuples representing the cigar string.
    :param matchstart: an integer representing the start of the first mapped base of a read.
    """
cigar
a list containing tuples representing the cigar string.
a list containing tuples representing the cigar string .
matchstart
an integer representing the start of the first mapped base of a read.
an integer representing the start of the first mapped base of a read .