How to use the pysam.view function in pysam

custom_print( "[ Reading readdb file ]" )
	region_fast5_files = dict()
	with open (o_readdb, "r") as file:
		for line in file:
			l = line.split("\t")
			read_id = l.pop(0)
			if read_id in region_read_ids:
				fast5_file = l.pop(0)
				region_fast5_files[str(read_id)] = fast5_file.rstrip()

	# --------------------------------------------------------
	# PART 5:   Make a region BAM and BAI file
	# --------------------------------------------------------
	new_bam = "reads.bam"
	custom_print( "[ Writing to a new BAM file ] \t" + new_bam )
	region_reads = pysam.view("-b", o_bam, draft_ga_coords, "-o", new_bam, catch_stdout=False)
	
	new_bam_index = new_bam + ".bai"
	custom_print( "[ Writing to a new BAI file ] \t" + new_bam_index )
	pysam.index(new_bam, new_bam_index)

	# --------------------------------------------------------
	# PART 6: 	With user input ref coords, extract all 
	#		aligned	reads within these coordinates 
	#		and make new FASTA file
	# --------------------------------------------------------
	# detect type of sequences file then handle accordingly
	file_type = detect_fa_filetype(o_fa)
	new_fa = "reads.fasta"
	custom_print( "[ Writing to a new fasta file ]\t" +  new_fa )
	with open (new_fa, "w") as fout:
		if ".gz" in file_type:

if not os.path.exists(bam_ngmlr_file):
        if stats_trigger in ['y', 'yes']:
            log.debug('[Alignment][ngmlral] - ngmlr -t %s -r %s -q %s -x ont' % (th, ref, fast_Q_file))
            ngmlrline = subprocess.Popen(['ngmlr', '-t', str(th), '-r', str(ref), '-q', str(fast_Q_file), '-x ont'],
                                         stdout=subprocess.PIPE)
            PairDict = sam_parser(ngmlrline, ngmlr_ext_dir)
        else:
            sam_nglmr_file = os.path.join(ngmlr_ext_dir, (prefix + '.sam'))
            log.debug(
                '[Alignment][ngmlral] - ngmlr -t %s -r %s -q %s -o %s -x ont' % (th, ref, fast_Q_file, sam_ngmlr_file))
            ngmlrline = subprocess.Popen(
                ['ngmlr', '-t', str(th), '-r', str(ref), '-q', str(fast_Q_file), '-o', str(sam_ngmlr_file), '-x ont'],
                stdout=subprocess.PIPE).wait()
            outputfilebam = os.path.join(ngmlr_ext_dir, (prefix + '.tmp.bam'))
            log.debug('[Alignment][ngmlral] - samtools view -Sb -@ %s %s -o %s' % (th, sam_nglmr_file, outputfilebam))
            pysam.view("-Sb", "-@%s" % str(th), sam_nglmr_file, "-o%s" % outputfilebam, catch_stdout=False)
            os.remove(sam_nglmr_file)
            pysam.sort(outputfilebam, "-o%s" % bam_ngmlr_file, catch_stdout=False)
            log.debug('[Alignment][ngmlral] - samtools index %s -@%s' % (bam_ngmlr_file, str(th)))
            pysam.index(bam_ngmlr_file, "-@%s" % str(th), catch_stdout=False)
            os.remove(outputfilebam)
    else:
        log.warning('[Alignment][ngmlral] - file %s already exists!' % bam_ngmlr_file)
    try:
        shutil.move(ngmlr_ext_dir, os.path.join(work_dir, out_dir))
    except shutil.Error:
        log.error("Unable to move %s" % ngmlr_ext_dir)

def _get_sort_order(in_bam, config):
    for line in pysam.view("-H", in_bam).split("\r\n"):
        if line.startswith("@HD"):
            for keyval in line.split()[1:]:
                key, val = keyval.split(":")
                if key == "SO":
                    return val

aligned_sam_path = 'aligned.sam'

command_pattern = "/minimap2-2.17_x64-linux/minimap2 -ax sr {REFERENCE_PATH} {SRC_FILES} -R '@RG\tID:RSP11055\tPL:ILLUMINA\tPU:NONE\tSM:RSP11055' > {ALIGNED_SAM_PATH}"

command = command_pattern.format(REFERENCE_PATH=reference_path, SRC_FILES=" ".join(files), ALIGNED_SAM_PATH=aligned_sam_path)

start = datetime.now()
logging.info("Command start: {}".format(command))
subprocess.call(command, shell=True)
delta = datetime.now() - start
logging.info("Command finish in {}: {}".format(delta, command))

aligned_sam = pysam.AlignmentFile(aligned_sam_path, "rb")
aligned_bam_path = 'aligned.bam'
aligned_sorted_bam_path = 'aligned.sorted.bam'
bam_content = pysam.view('-bh', aligned_sam_path)

with open(aligned_bam_path, 'wb') as file:
    file.write(bam_content)

pysam.sort('-o', aligned_sorted_bam_path, aligned_bam_path)

def get_sam_data(bam_file, regions=None):
    args = [bam_file]
    if regions:
        args.extend(regions)
    return pysam.view(*args)

command = command_pattern.format(REFERENCE_PATH=reference_path, SRC_FILES=" ".join(files),
                                         ALIGNED_SAM_PATH=aligned_sam_path)

        start = datetime.now()
        logging.info("Alignment start: {}".format(command))
        subprocess.call(command, shell=True)
        delta = datetime.now() - start
        logging.info("Alignment finish in {}: {}".format(delta, command))

        aligned_bam_path = file_prefix + '.bam'
        aligned_sorted_bam_path = file_prefix + '.sorted.bam'

        start = datetime.now()
        logging.info("Convert to BAM start: {}".format(aligned_sam_path))
        bam_content = pysam.view('-bh', aligned_sam_path)

        with open(aligned_bam_path, 'wb') as file:
            file.write(bam_content)
        delta = datetime.now() - start
        logging.info("Convert to BAM finish in {}: {}".format(delta, aligned_sam_path))

        start = datetime.now()
        logging.info("Sort start: {}".format(aligned_bam_path))
        pysam.sort('-o', aligned_sorted_bam_path, aligned_bam_path)
        delta = datetime.now() - start
        logging.info("Sort finish in {}: {}".format(aligned_bam_path, delta))

        gcs_uri = gcs_utils.upload_file(client, aligned_sorted_bam_path,
                                        RESULT_SORTED_DIR_NAME + '/' + get_file_name_from_uri(aligned_sorted_bam_path),
                                        "text/plain", 'cannabis-3k-results')
        remove_local_dir(files_dir)

ext = ".uniq{0}".format(ext)

    if opts.unmapped:
        uopts = [x for x in mopts]
        uoutfile = samfile.replace(oext, ".unmapped{0}".format(ext))
        uopts.extend(["-f4", samfile, "-o{0}".format(uoutfile)])
        view_opts.append(uopts)

    outfile = samfile.replace(oext, ".mapped{0}".format(ext))
    mopts.extend(["-F4", samfile, "-o{0}".format(outfile)])
    view_opts.append(mopts)

    for vo in view_opts:
        logging.debug('samtools view {0}'.format(" ".join(vo)))

    jobs = Jobs(pysam.view, [(z for z in x) for x in view_opts])
    jobs.run()

def execute(self, inBam, exclude, readList, outBam, picardOptions=None, JVMmemory=None):    # pylint: disable=W0221
        picardOptions = picardOptions or []

        if tools.samtools.SamtoolsTool().isEmpty(inBam):
            # Picard FilterSamReads cannot deal with an empty input BAM file
            shutil.copyfile(inBam, outBam)
        elif os.path.getsize(readList) == 0:
            # Picard FilterSamReads cannot deal with an empty READ_LIST_FILE
            if exclude:
                shutil.copyfile(inBam, outBam)
            else:
                tmpf = util.file.mkstempfname('.sam')
                if inBam.endswith('.sam'):
                    # output format (sam/bam) is inferred by samtools based on file extension
                    header = pysam.view('-o', tmpf, '-H', '-S', inBam, catch_stdout=False)
                else:
                    header = pysam.view('-o', tmpf, '-H', inBam, catch_stdout=False)
                # pysam.AlignmentFile cannot write an empty file
                # samtools cannot convert SAM -> BAM on an empty file
                # but Picard SamFormatConverter can deal with empty files
                opts = ['INPUT=' + tmpf, 'OUTPUT=' + outBam, 'VERBOSITY=ERROR']
                PicardTools.execute(self, 'SamFormatConverter', opts, JVMmemory='50m')
        else:
            opts = [
                'INPUT=' + inBam, 'OUTPUT=' + outBam, 'READ_LIST_FILE=' + readList,
                'FILTER=' + (exclude and 'excludeReadList' or 'includeReadList'), 'WRITE_READS_FILES=false'
            ]
            PicardTools.execute(self, self.subtoolName, opts + picardOptions, JVMmemory)

picardOptions = picardOptions or []

        if tools.samtools.SamtoolsTool().isEmpty(inBam):
            # Picard FilterSamReads cannot deal with an empty input BAM file
            shutil.copyfile(inBam, outBam)
        elif os.path.getsize(readList) == 0:
            # Picard FilterSamReads cannot deal with an empty READ_LIST_FILE
            if exclude:
                shutil.copyfile(inBam, outBam)
            else:
                tmpf = util.file.mkstempfname('.sam')
                if inBam.endswith('.sam'):
                    # output format (sam/bam) is inferred by samtools based on file extension
                    header = pysam.view('-o', tmpf, '-H', '-S', inBam, catch_stdout=False)
                else:
                    header = pysam.view('-o', tmpf, '-H', inBam, catch_stdout=False)
                # pysam.AlignmentFile cannot write an empty file
                # samtools cannot convert SAM -> BAM on an empty file
                # but Picard SamFormatConverter can deal with empty files
                opts = ['INPUT=' + tmpf, 'OUTPUT=' + outBam, 'VERBOSITY=ERROR']
                PicardTools.execute(self, 'SamFormatConverter', opts, JVMmemory='50m')
        else:
            opts = [
                'INPUT=' + inBam, 'OUTPUT=' + outBam, 'READ_LIST_FILE=' + readList,
                'FILTER=' + (exclude and 'excludeReadList' or 'includeReadList'), 'WRITE_READS_FILES=false'
            ]
            PicardTools.execute(self, self.subtoolName, opts + picardOptions, JVMmemory)

picardOptions = picardOptions or []

        if tools.samtools.SamtoolsTool().isEmpty(inBam):
            # Picard FilterSamReads cannot deal with an empty input BAM file
            shutil.copyfile(inBam, outBam)
        elif os.path.getsize(readList) == 0:
            # Picard FilterSamReads cannot deal with an empty READ_LIST_FILE
            if exclude:
                shutil.copyfile(inBam, outBam)
            else:
                tmpf = util.file.mkstempfname('.sam')
                if inBam.endswith('.sam'):
                    # output format (sam/bam) is inferred by samtools based on file extension
                    header = pysam.view('-o', tmpf, '-H', '-S', inBam, catch_stdout=False)
                else:
                    header = pysam.view('-o', tmpf, '-H', inBam, catch_stdout=False)
                # pysam.AlignmentFile cannot write an empty file
                # samtools cannot convert SAM -> BAM on an empty file
                # but Picard SamFormatConverter can deal with empty files
                opts = ['INPUT=' + tmpf, 'OUTPUT=' + outBam, 'VERBOSITY=ERROR']
                PicardTools.execute(self, 'SamFormatConverter', opts, JVMmemory='50m')
        else:
            opts = [
                'INPUT=' + inBam, 'OUTPUT=' + outBam, 'READ_LIST_FILE=' + readList,
                'FILTER=' + (exclude and 'excludeReadList' or 'includeReadList'), 'WRITE_READS_FILES=false'
            ]
            PicardTools.execute(self, self.subtoolName, opts + picardOptions, JVMmemory)