Scripts/Flag_placer.py
def issameorientation(read):
    """ The issameorientation function returns a bool returning true if a pair of reads have the same orientation and
    the mate is on the same chromosome. It will return false if this is not the case

    :param read: Pysam object containing data of a read.
    :return bool: A boolean returning True if the reads of a pair have the same orientation.
    """
    if (read.is_paired and not read.mate_is_unmapped and read.is_reverse == read.mate_is_reverse and
        read.reference_name == read.next_reference_name):
        return True

    return False
 The issameorientation function returns a bool returning true if a pair of reads have the same orientation and
    the mate is on the same chromosome. It will return false if this is not the case

    :param read: Pysam object containing data of a read.
    :return bool: A boolean returning True if the reads of a pair have the same orientation.
    
The issameorientation function returns a bool returning true if a pair of reads have the same orientation and
the mate is on the same chromosome. It will return false if this is not the case
The issameorientation function returns a bool returning true if a pair of reads have the same orientation and the mate is on the same chromosome . It will return false if this is not the case
def issameorientation(read):
    if (read.is_paired and not read.mate_is_unmapped and read.is_reverse == read.mate_is_reverse and
        read.reference_name == read.next_reference_name):
        return True
    return False
def issameorientation ( read ) : if ( read . is_paired and not read . mate_is_unmapped and read . is_reverse == read . mate_is_reverse and read . reference_name == read . next_reference_name ) : return True return False
The issameorientation function returns a bool returning true if a pair of reads have the same orientation and
the mate is on the same chromosome.
The issameorientation function returns a bool returning true if a pair of reads have the same orientation and the mate is on the same chromosome .
""" The issameorientation function returns a bool returning true if a pair of reads have the same orientation and
    the mate is on the same chromosome. It will return false if this is not the case

    :param read: Pysam object containing data of a read.
    :return bool: A boolean returning True if the reads of a pair have the same orientation.
    """
A boolean returning True if the reads of a pair have the same orientation.
A boolean returning True if the reads of a pair have the same orientation .
bool
read
Pysam object containing data of a read.
Pysam object containing data of a read .