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README.md
@@ -80,6 +80,7 @@ An observed barcode matches an expected barcode if all the following are true:
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mismatches (see `--max-mismatches`).
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2. The difference between number of mismatches in the best and second best barcodes is greater
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than or equal to the minimum mismatch delta (`--min-mismatch-delta`).
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+
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The expected barcode sequence may contains Ns, which are not counted as mismatches regardless
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of the observed base (e.g. the expected barcode `AAN` will have zero mismatches relative to
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both the observed barcodes `AAA` and `AAN`).
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