Dms-tools

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* Print versions of all external packages (some were overlooked before)

* Make ``dms_merge`` handle the ``*mutdiffsel.txt`` files created by ``dms_diffselection``.

* Added ``translate_codon_to_aa`` and ``return_as_df`` options to dms_tools.file_io.ReadDMSCounts().

* Added ``dms_tools.utils.ParseNSMutFreqBySite()``.

* Make ``dms_correlate`` handle the ``mutdiffsel.txt`` and ``sitediffsel.txt`` files created by ``dms_diffselection``.

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* Added ``--mincounts`` option to ``dms_diffselection``, and make ``dms_logoplot`` properly plot differential selection with missing values.

* Added test (``./tests/test_diffselection.py``) for ``dms_diffselection``

* ``dms_barcodedsubamplicons`` now gives exactly reproducible output regardless of order of input reads.

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* In ``dms_diffselection``, the pseudocounts are now scaled by the **smaller** depth library at each site.

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* Added ``dms_diffselection`` program.

* Added ``--colormap`` and ``--overlay3`` options to ``dms_logoplot``

* Make ``dms_merge`` remove sites indicated as *None* when in *renumber* mode, added ``--skipfirstline`` option, and made commas an allowable separator.

* Increased number of colors allowed by *PlotMutCountFracs* (used by ``dms_summarizealignments``)

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* Moved repository and docs from https://github.com/jbloom/dms_tools and http://jbloom.github.io/dms_tools to https://github.com/jbloomlab/dms_tools and http://jbloomlab.github.io/dms_tools

* Catch problems with ``dms_merge`` if multiple input files of the same name.

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* Added option to sum count files in ``dms_merge``, with or without normalization of counts at each site.

* Updated *dms_tools.file_io.IteratePairedFASTQ* to permit parsing of FASTQ files generated by ``fastq-dump``.