How to use the pysam.qualities_to_qualitystring function in pysam

assert alns[0].cigarstring == "21M"
    assert alns[0].reference_start == 30
    assert alns[0].reference_end == 51
    assert alns[0].is_reverse

    qs = "<<<<<<<:<9/,&,22;;<<<"
    read.query_qualities = pysam.qualitystring_to_array(qs)
    alns = genome_source.align(Alignment(read))

    import warnings
    with warnings.catch_warnings():
        # this is a python 2/3 incompatibility I think, where the warning
        # indicates array.tostring() is deprecated but array.tobytes()
        # only exists in py3
        warnings.simplefilter("ignore")
        assert pysam.qualities_to_qualitystring(alns[0].query_qualities) == qs[::-1]

mdtag=None,
        name="dummy",
        mapq=10,
        baseq=30,
        reference_start=0,
        reference_id=0):
    read = pysam.AlignedSegment()
    read.seq = seq
    read.cigarstring = cigar
    if mdtag:
        read.set_tag("MD", mdtag)
    read.qname = name
    read.mapq = mapq
    read.reference_start = reference_start
    read.reference_id = reference_id
    qualities_string = pysam.qualities_to_qualitystring([baseq] * len(seq))
    read.qual = qualities_string.encode("ascii")
    return read

mdtag=None,
        name="dummy",
        mapq=10,
        baseq=30,
        reference_start=0,
        reference_id=0):
    read = pysam.AlignedSegment()
    read.seq = seq
    read.cigarstring = cigar
    if mdtag:
        read.set_tag("MD", mdtag)
    read.qname = name
    read.mapq = mapq
    read.reference_start = reference_start
    read.reference_id = reference_id
    qualities_string = pysam.qualities_to_qualitystring([baseq] * len(seq))
    read.qual = qualities_string.encode("ascii")
    return read

firstseq = r1.query_sequence
	secondseq = r2.query_sequence

	# Check if sequences match : # they won't match if there are soft clips
	if firstseq == secondseq : 

		if ForwardRead and PairedRead : del forwardcache[d] # assume that if sequences are same, reads are same too (mapper should treat them in a similar way)
		elif ForwardRead : del forwardsingle[d]
		elif not ForwardRead and PairedRead : del reversecache[d], positioncache[d]
		else : del reversesingle[d], positionsingle[d]

		return 

	newqual = pysam.qualities_to_qualitystring(r1.query_qualities)
	secondqual = pysam.qualities_to_qualitystring(r2.query_qualities)

	if not ForwardRead : # reverse seq and qual
	
		firstseq = firstseq[::-1]
		secondseq = secondseq[::-1]
		newqual = newqual[::-1]
		secondqual = secondqual[::-1]
	# Check that the MD tag actually exists
	try:
		r1_MD = r1.get_tag('MD')
		r2_MD = r2.get_tag('MD')
	except KeyError:
		sys.stderr.write("Error: MD tag doesn't exist in input file\n")
		sys.exit(1)

	# Turn seq and qual into a list

r2 = reversesingle[d]

	firstseq = r1.query_sequence
	secondseq = r2.query_sequence

	# Check if sequences match : # they won't match if there are soft clips
	if firstseq == secondseq : 

		if ForwardRead and PairedRead : del forwardcache[d] # assume that if sequences are same, reads are same too (mapper should treat them in a similar way)
		elif ForwardRead : del forwardsingle[d]
		elif not ForwardRead and PairedRead : del reversecache[d], positioncache[d]
		else : del reversesingle[d], positionsingle[d]

		return 

	newqual = pysam.qualities_to_qualitystring(r1.query_qualities)
	secondqual = pysam.qualities_to_qualitystring(r2.query_qualities)

	if not ForwardRead : # reverse seq and qual
	
		firstseq = firstseq[::-1]
		secondseq = secondseq[::-1]
		newqual = newqual[::-1]
		secondqual = secondqual[::-1]
	# Check that the MD tag actually exists
	try:
		r1_MD = r1.get_tag('MD')
		r2_MD = r2.get_tag('MD')
	except KeyError:
		sys.stderr.write("Error: MD tag doesn't exist in input file\n")
		sys.exit(1)

if cigarlist[-1] != 4 :
					MinFlankStart = 0

	# Check if the MD tag actually exists
	try:
		row_MD = row.get_tag('MD')
	except KeyError:
		sys.stderr.write("Error: MD tag doesn't exist in input file\n")
		sys.exit(1)

	mincut, maxcut = FindCutoffIndices(newcigar, MinFlankEnd, MinFlankStart, ForwardRead)

	# If read does not need to be split, just copy previous read object to new list
	if splits == 0 and newcigar == row.cigar :

		newqual = DiscardVariants(pysam.qualities_to_qualitystring(row.query_qualities), row_MD, newcigar, mincut, maxcut)
		newrow = CreateReadObject(row, row.query_sequence, newqual, newcigar, row.reference_start)
		yield newrow 

	elif splits == 0 : # cigar, seq, qual have been trimmed

		newseq = row.query_sequence[start:end]
		newqual = pysam.qualities_to_qualitystring(row.query_qualities)[start:end]

		newqual = DiscardVariants(newqual, row_MD, newcigar, mincut, maxcut)
		newrow = CreateReadObject(row, newseq, newqual, newcigar, row.reference_start)
		yield newrow 
		
	else :
		if newcigar != row.cigar : 
			row.cigar = newcigar
			q = pysam.qualities_to_qualitystring(row.query_qualities)[start:end]

# ===== Write consensus bam =====
                        if tag_dict[tag] == 2:
                            doubletons += 1
                            doubleton_bam.write(SSCS_read)
                        else:
                            SSCS_bam.write(SSCS_read)    
                            SSCS_reads += 1
                        
                        # ===== write as fastq file =====                        
                        #if SSCS_read.is_reverse and SSCS_read.is_read1:
                        #fastq_seq = SSCS_read.query_sequence.decode("utf-8") 
                        fastq_seq = SSCS[0] 
                        
                        if 'rev' in tag:
                            fastq_seq = reverse_seq(fastq_seq)
                            fastq_qual = pysam.qualities_to_qualitystring(reversed(SSCS[1]))
                        else:
                            fastq_qual = pysam.qualities_to_qualitystring(SSCS[1])
                        
                        if tag_dict[tag] == 2:
                            if 'R1' in tag:
                                doubleton_fastqFile1.write('@{}\n{}\n+\n{}\n'.format(SSCS_read.query_name, fastq_seq, fastq_qual))
                            else:
                                doubleton_fastqFile2.write('@{}\n{}\n+\n{}\n'.format(SSCS_read.query_name, fastq_seq, fastq_qual))                            
                        else:
                            if 'R1' in tag:
                                fastqFile1.write('@{}\n{}\n+\n{}\n'.format(SSCS_read.query_name, fastq_seq, fastq_qual))
                            else:
                                fastqFile2.write('@{}\n{}\n+\n{}\n'.format(SSCS_read.query_name, fastq_seq, fastq_qual))
                        
                    # Remove read from dictionary after writing
                    del bam_dict[tag]

def quality_array_to_string(quality_list):
    """Convert list of phred quality values to string.

    :param quality_list: List of phred quality scores.
    :returns: Quality string.
    :rtype: str
    """
    return pysam.qualities_to_qualitystring(quality_list)

def CreateSplitRead(row, position, k, i) :

	startread = position
	newcigar = []
	newstring = ''
	oldseq = row.query_sequence
	oldqual = pysam.qualities_to_qualitystring(row.query_qualities)
	newqual = ''

	while k < len(row.cigar) :
	
		cigartype, cigarlength = row.cigar[k]
						
		# cigartype 1 stands for insertion
		# in this case, position should be kept as it is
		if cigartype == 1 :
			newstring +=  oldseq[i:(cigarlength+i)]
			newqual += oldqual[i:(cigarlength+i)]
			i += cigarlength
			newcigar.append((cigartype, cigarlength))	
			k += 1	

		# cigartype 2 stands for deletion