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Fix README flags #4

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@schorlton schorlton commented Nov 15, 2020

The new flags in the README are incorrect. I've simply updated them to match:

main_group.add_argument('--barcode_stats_csv', action='store_true',
help='Option to output a csv file with start/ end/ middle barcode names '
'and percentage identities for each given read. ')
main_group.add_argument('--format', choices=['auto', 'fasta', 'fastq', 'fasta.gz', 'fastq.gz'],
default='auto',
help='Output format for the reads - if auto, the '
'format will be chosen based on the output filename or the input '
'read format')
main_group.add_argument('-v', '--verbosity', type=int, default=1,
help='Level of progress information: 0 = none, 1 = some, 2 = lots, '
'3 = full - output will go to stdout if reads are saved to '
'a file and stderr if reads are printed to stdout')
main_group.add_argument('-t', '--threads', type=int, default=default_threads,
help='Number of threads to use for adapter alignment')
barcode_group = parser.add_argument_group('Barcode binning settings',
'Control the binning of reads based on barcodes '
'(i.e. barcode demultiplexing)')
barcode_group.add_argument('-b', '--barcode_dir',
help='Reads will be binned based on their barcode and saved to '
'separate files in this directory (incompatible with '
'--output)')
barcode_group.add_argument('--barcode_labels', action='store_true',
help='Reads will have a label added to their header with their barcode')
barcode_group.add_argument('--extended_labels', action='store_true',

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