Fuc

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

* Add new method :meth:`pymaf.MafFrame.matrix_waterfall_matched`.
* Add new method :meth:`pymaf.MafFrame.plot_waterfall_matched`.
* Add new method :meth:`pymaf.MafFrame.plot_tmb_matched`.
* Add new method :meth:`pymaf.MafFrame.plot_mutated_matched`.
* Add new method :meth:`pymaf.MafFrame.plot_oncoplot_matched`.
* Deprecate method :meth:`pymaf.MafFrame.legend_handles`.
* Add new method :meth:`common.legend_handles`.
* Deprecate classes :class:`pyvcf.AnnFrame` and :class:`pymaf.AnnFrame`. Add new class :class:`common.AnnFrame`.
* Rename :meth:`common.file2list` method to :meth:`convert_file2list`.
* Add new method :meth:`common.convert_num2cat`.
* Add new command :command:`fuc-undetm`.
* Add new method :meth:`common.plot_annot_matched`.
* Add new argument ``sheet`` to :command:`fuc-demux` command.
* Add new class :class:`common.Variant`.
* Add new method :meth:`pyvcf.rescue_filtered_variants`.
* Add new arguments ``a_size`` and ``b_size`` to :meth:`pymaf.MafFrame.plot_regplot` method.
* Rename ``hue`` and ``hue_order`` arguments in plotting methods to ``group_col`` and ``group_order``, respectively.

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

* Fix bug in :meth:`pymaf.MafFrame.plot_mutated` when using the ``hue`` option.
* Add new argument ``sort`` to :meth:`pymaf.MafFrame.plot_vaf` method.
* Add new method :meth:`pymaf.MafFrame.plot_matrixs`.
* Add new method :meth:`pymaf.MafFrame.plot_matrixg`.
* Add new method :meth:`pymaf.MafFrame.compute_clonality`.
* Add new method :meth:`pymaf.MafFrame.plot_clonality`.
* Fix bug in :meth:`pymaf.MafFrame.plot_evolution` when there are no variants to display for the specified samples.
* :issue:`34`: Add new method :meth:`pymaf.MafFrame.plot_genepair`.
* :issue:`34`: Add new method :meth:`pymaf.MafFrame.plot_interactions`.
* Update the :command:`fuc-demux` command to output a better figure.
* Add new method :meth:`common.plot_cytobands`.
* Add new method :meth:`pycov.CovFrame.plot_uniformity`.
* Add new method :meth:`pycov.CovFrame.plot_distribution`.
* Rename :meth:`pycov.CovFrame.from_file` method to :meth:`pycov.CovFrame.from_bam`.
* Add new method :meth:`pycov.CovFrame.from_file`.
* Add new command :command:`fuc-depth`.
* Add new method :meth:`common.file2list`.
* Add new method :meth:`pyvcf.VcfFrame.chr_prefix`.
* Fix bug in :meth:`pyvcf.gt_unphase` when '.|.' is provided.
* Update :meth:`pyvcf.VcfFrame.compare` method to only consider biallelic sites.
* Update :meth:`pyvcf.VcfFrame.compare` method to support comparison of SNVs only and INDELs only.
* Update :meth:`pymaf.MafFrame.from_vcf` method so that ``names`` argument is no longer required when ``keys`` argument is used.

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

* Update :command:`fq-count` command to run significantly faster.
* Update :command:`fuc-find` command to support pattern matching that is more robust than just file extension.
* Update :meth:`pyvcf.VcfFrame.subset` method to take string as input in addition to list.
* Fix bug in :meth:`pymaf.MafFrame.plot_snvclss` method when certain SNV classes are entirely missing.
* Add new package ``statsmodels`` as dependency for performing statistical analysis.
* Update :meth:`pymaf.MafFrame.plot_regplot` method to calculate and print summary statistics as well.
* Update :meth:`pyvcf.VcfFrame.plot_regplot` method to calculate and print summary statistics as well.
* :issue:`32`: Add :meth:`pyvcf.VcfFrame.miss2ref` method.
* Update :meth:`pymaf.MafFrame.plot_tmb` method to draw empty bars with warning when specified samples do not exist.
* Update :meth:`pymaf.MafFrame.plot_waterfall` method to draw empty bars with warning when specified samples do not exist.
* Add ``flip`` argument to :meth:`pymaf.MafFrame.plot_genes` method.
* Add new method :meth:`pymaf.MafFrame.plot_mutated`.

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

* Add new method :meth:`pymaf.MafFrame.plot_lollipop`.
* :issue:`30`: Add :meth:`pymaf.MafFrame.plot_rainfall` method.
* :issue:`30`: Add :meth:`pyvcf.VcfFrame.plot_rainfall` method.
* Update :meth:`pymaf.MafFrame.to_vcf` method to output sorted VCF.
* Add new method :meth:`pymaf.MafFrame.matrix_prevalence`.
* Add new method :meth:`pymaf.MafFrame.plot_regplot`.
* Add new argument ``samples`` to :meth:`pymaf.MafFrame.plot_snvclss` method.
* Add new method :meth:`pymaf.MafFrame.plot_evolution`.
* Add new submodule ``pygff``.

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

* Rename the commands (e.g. :command:`vcf_merge` to :command:`vcf-merge`).
* Add new argument ``flip`` to :meth:`pymaf.MafFrame.plot_vaf` method.
* Update :meth:`pymaf.MafFrame.plot_vaf` method to support creation of a grouped bar plot.
* Factor out ``count`` mode of :meth:`pymaf.MafFrame.plot_snvcls` method to new method :meth:`pymaf.MafFrame.plot_snvclsc`.
* Factor out ``proportion`` mode of :meth:`pymaf.MafFrame.plot_snvcls` method to new method :meth:`pymaf.MafFrame.plot_snvclsp`.
* Factor out ``samples`` mode of :meth:`pymaf.MafFrame.plot_snvcls` method to new method :meth:`pymaf.MafFrame.plot_snvclss`.
* Factor out ``titv`` mode of :meth:`pymaf.MafFrame.plot_snvcls` method to new method :meth:`pymaf.MafFrame.plot_titv`.
* Deprecate method :meth:`pymaf.MafFrame.plot_snvcls`.
* Add new argument ``hue_order`` to :meth:`pyvcf.VcfFrame.plot_hist` method.
* Update aesthetic aspect of :meth:`pymaf.MafFrame.plot_oncoplot` method.
* Add new argument ``width`` to :meth:`pymaf.MafFrame.plot_tmb` method.
* Add new arguments ``palette`` and ``flip`` to :meth:`pymaf.MafFrame.plot_vartype` method.
* Update :meth:`pymaf.MafFrame.plot_snvclsc` method to support creation of a grouped bar plot.
* Update :meth:`pymaf.MafFrame.plot_snvclsp` method to support creation of a grouped box plot.
* Add new method :meth:`pyvcf.VcfFrame.plot_snvclsc` (simply wraps :meth:`pymaf.MafFrame.plot_snvclsc` method).
* Add new method :meth:`pyvcf.VcfFrame.plot_snvclsp` (simply wraps :meth:`pymaf.MafFrame.plot_snvclsp` method).
* Add new method :meth:`pyvcf.VcfFrame.plot_snvclss` (simply wraps :meth:`pymaf.MafFrame.plot_snvclss` method).
* Add new method :meth:`pyvcf.VcfFrame.plot_titv` (simply wraps :meth:`pymaf.MafFrame.plot_titv` method).
* :issue:`28`: Update :meth:`pymaf.MafFrame.from_vcf` method to handle unannotated VCF data.

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

* Update :command:`vcf_filter` command.
* Update :command:`tbl_sum` command.
* Add ``samples`` and ``shape`` attributes to :class:`pymaf.AnnFrame` class.
* Rename :meth:`pymaf.MafFrame.compute_genes/tmb/waterfall` methods to :meth:`pymaf.MafFrame.matrix_genes/tmb/waterfall`.
* Add ``keep_empty`` argument to :meth:`pymaf.MafFrame.matrix_waterfall/plot_oncoplot/plot_waterfall` methods.
* Add :meth:`pymaf.MafFrame.filter_annot` method.
* Add :meth:`pymaf.AnnFrame.sorted_samples` method.
* Fix bug in :meth:`pymaf.MafFrame.to_frame` method.
* Deprecate methods :meth:`pyvep.filter_lof/clinsig`.
* Update :meth:`pymaf.MafFrame.from_vcf` method to extract genotype keys (e.g. DP, AD, AF).
* Update :command:`bam_slice` and :command:`bam_rename` commands.
* Deprecate method :meth:`pybam.rename`.