Seqmagick

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* Fix bug in ``--squeeze``
* More informative messages in ``seqmagick primer-trim``
* Added ``--alphabet`` flag to allow writing NEXUS (GH-23)
* Exiting without error on SIGPIPE in extract-ids, info (GH-17)
* Ambiguities are translated as 'X' in --translate (GH-16)
* Allowing '.' or '-' as gap character (GH-18)
* ``--name-prefix`` and ``--name-suffix`` no longer create a mangled description (GH-19)
* Files owned by another user can be mogrified, as long as they are group writeable (GH-14)
* Add ``backtrans-align`` subcommand, which maps unaligned nucleotides onto a
protein alignment (GH-20)
* Allow FASTQ as input to quality-filter
* Significantly expand functionality of quality-filter: identify and trim
barcodes/primers; report detailed failure information.
* Cleanup, additional tests
* Add ``--drop`` filter to convert and mogrify (GH-24)
* Apply current umask when creating files (GH-26)
* Support stdin in ``seqmagick info`` (GH-27)
* Support translating ambiguous nucleotides, if codon translation is unambiguous

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* Fix bug in ``quality-filter`` MinLengthFilter
* Case consistency in seqmagick

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* Internal reorganization - transformations are converted to partial functions,
then applied.
* Argument order now affects order of tranformation application.
* Change default output format to 'align' for TTYs in seqmagick info
* Add BioPython as dependency (closes GH-7)
* Add ``primer-trim`` subcommand
* Add option to apply custom function(s) to sequences
* Add new filtering options: ``--squeeze-threshold``, ``--min-ungapped-length``
``--include-from-file`` ``--exclude-from-file``
* Removed seqmagick muscle
* Added new subcommand ``quality-filter``
* Added new subcommand ``extract-ids`` (closes GH-13)
* Allow use of '-' to indicate stdin / stdout (closes GH-11)
* Add mapping from .phyx to ``phylip-relaxed`` (targeted for BioPython 1.58)

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* Refactoring
* Added hyphenation to multi-word command line options (e.g.
``--deduplicatetaxa`` -> ``--deduplicate-taxa``)
* Add support for ``.needle``, ``.sff`` formats
* Close GH-4

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Initial release