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Made `filter-fasta.py` print an error message when the `--checkResultCount`
check fails even if `--quiet` was used.

Add `rotate` method to `Read` class, plus tests.

Added `--rotate` option to `filter-fasta.py`.

Added `--upper`, `--lower`, `--upperId`, and `--lowerId` options to `filter-fasta.py`.

Removed `required` flag from `--out` option of `bin/plot-windowed-identity.py`.

Added `bin/plot-windowed-identity.py` along with `WindowedIdentity` class and tests.

Has known vulnerabilities

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