Fuc

-------------------

* :issue:`23`: Deprecate methods :meth:`pyvcf.VcfFrame.markmiss_ad/af/dp` and add new method :meth:`pyvcf.VcfFrame.markmiss`.
* Add new command :command:`vcf_filter`.
* Update methods :meth:`pycov.CovFrame.slice/plot_region`.
* :issue:`24`: Add new method :meth:`pyvcf.VcfFrame.drop_duplicates`.
* Update :meth:`pymaf.MafFrame.plot_snvcls` method to support various plotting modes.
* Rename ``horizontal`` argument of :meth:`pymaf.MafFrame.plot_varsum` method to ``flip``.

-------------------

* Add new method :meth:`pymaf.MafFrame.to_vcf`.
* :issue:`21`: Add new command :command:`maf_maf2vcf`.
* Add new method :meth:`pyvcf.VcfFrame.rename`.
* Add new command :command:`vcf_rename`.
* Add new method :meth:`pymaf.MafFrame.plot_vaf`.
* Update :meth:`pyvcf.VcfFrame.slice` method.
* Update :command:`vcf_slice` command.

-------------------

* Add new method :meth:`pyvcf.VcfFrame.add_af`.
* Add new method :meth:`pyvcf.VcfFrame.extract`.
* Deprecate methods :meth:`pyvep.filter_af/biotype/nothas/impact`.
* Add new method :meth:`pyvep.filter_query`.
* :issue:`19`: Add new command :command:`vcf_vep`.
* Rename :meth:`pyvcf.VcfFrame.plot_histplot` to :meth:`pyvcf.VcfFrame.plot_tmb`.
* Add ``scipy`` package as dependency for performing statistical analysis.
* Add new method :meth:`pyvcf.VcfFrame.plot_hist`.

-------------------

* :issue:`16`: Add new method :meth:`pyvcf.VcfFrame.cfilter_empty`.
* Add new methods :meth:`pyvep.filter_af/lof`.
* Add ``matplotlib-venn`` package as dependency for plotting Venn diagrams.
* Add new methods :meth:`pyvcf.plot_comparison/regplot/histplot`.
* :issue:`17`: Add new method :meth:`pyvep.filter_biotype`.
* Add new class :class:`pyvcf.AnnFrame`.

-------------------

* Add new methods :meth:`pymaf.plot_summary/varsum`.
* Add new command :command:`maf_sumplt`.
* Add new method :meth:`pymaf.MafFrame.to_string`.
* Update :command:`maf_oncoplt` command.
* Add new method :meth:`pyvcf.VcfFrame.filter_qual`.
* Deprecate method :meth:`pymaf.plot_legend` and add :meth:`pymaf.legend_handles` method.
* Add new methods :meth:`pymaf.AnnFrame.legend_handles/plot_annot`.
* Add new method :meth:`pyvcf.VcfFrame.expand`.
* Rename methods :meth:`pyvcf.gt_missing/haspolyp` to :meth:`pyvcf.gt_miss/polyp`.
* Add new method :meth:`pybed.BedFrame.from_frame`.
* :issue:`14`: Add new method :meth:`pyvcf.VcfFrame.to_bed` and new command :command:`vcf_vcf2bed`.

------------------

* Add new submodule ``pymaf``.
* Deprecate method :meth:`pyvcf.read_file` and add :meth:`pyvcf.VcfFrame.from_file` method.
* Deprecate method :meth:`pybed.read_file` and add :meth:`pybed.BedFrame.from_file` method.
* Deprecate method :meth:`pyfq.read_file` and add :meth:`pyfq.FqFrame.from_file` method.
* Deprecate method :meth:`pycov.read_file` and add :meth:`pycov.CovFrame.from_file` method.
* Add new method :meth:`common.parse_region`.
* Add new commands :command:`maf_oncoplt/vcf2maf`.