Fuc

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

* Add new method :meth:`pybam.count_allelic_depth`.
* Update :meth:`common.parse_variant` method to handle position-only strings as input (e.g. '22-42127941-G-A' vs. '22-42127941').
* Add new command :command:`bam-aldepth`.
* Rename :meth:`pybam.has_chr` method to :meth:`pybam.has_chr_prefix`.
* Rename :meth:`pybed.BedFrame.chr_prefix`, :meth:`pycov.CovFrame.chr_prefix`, :meth:`pyvcf.VcfFrame.chr_prefix` methods to :meth:`pybed.BedFrame.update_chr_prefix`, :meth:`pycov.CovFrame.update_chr_prefix`, :meth:`pyvcf.VcfFrame.update_chr_prefix`.
* Add new properties ``pybed.BedFrame.has_chr_prefix``, ``pycov.CovFrame.has_chr_prefix``, ``pyvcf.VcfFrame.has_chr_prefix``.
* Add new method :meth:`pyvcf.slice`.
* Add new method :meth:`pyvcf.VcfFrame.from_string`.
* Remove ``nrows`` argument from :meth:`pyvcf.VcfFrame.from_file` method.
* Add new argument ``regions`` to :meth:`pyvcf.VcfFrame.from_file` method.
* Add new property ``pybed.BedFrame.shape``.
* Add new method :meth:`pybed.BedFrame.to_regions`.
* Add new method :meth:`pybed.BedFrame.from_regions`.
* Update :meth:`pyvcf.VcfFrame.from_file` method to accept BED data to specify regions of interest.
* Update :command:`vcf-slice` command to run significantly faster by allowing random access.
* Add new method :meth:`common.sort_regions`.
* Fix minor bug in :meth:`pyvcf.VcfFrame.get_af` method when the variant of interest does not exist in VcfFrame.

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

* Add new method :meth:`common.sort_variants`.
* Add new method :meth:`pyvcf.VcfFrame.variants`.
* Add new method :meth:`pymaf.MafFrame.variants`.
* Add new method :meth:`pymaf.MafFrame.subset`.
* Add new method :meth:`pymaf.MafFrame.calculate_concordance`.
* Add new method :meth:`pymaf.MafFrame.copy`.
* Add new method :meth:`pymaf.MafFrame.filter_indel`.
* Add new method :meth:`pymaf.MafFrame.plot_comparison`.

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

* Add new command :command:`fuc-bgzip`.
* Add new command :command:`tabix-index`.
* Fix bug in :meth:`pyvcf.VcfFrame.from_file` method when ``meta_only`` is ``True``.
* Update :meth:`pyvcf.VcfFrame.from_file` method to extract VCF headers as well when ``meta_only`` is ``True``.
* Add new command :command:`tabix-slice`.
* Update :meth:`pyvcf.VcfFrame.chr_prefix`, :meth:`pybed.BedFrame.chr_prefix`, and :meth:`pycov.CovFrame.chr_prefix` methods to skip lines that already have ``chr`` string when ``mode='add'``.
* Add new methods :meth:`common.rename` and :meth:`pycov.CovFrame.rename`.
* Add new command :command:`cov-rename`.
* Add new method :meth:`pyvcf.gt_het`.
* Add new method :meth:`pyvcf.gt_pseudophase`.

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

* Update :class:`pycov.CovFrame` class to ensure that the ``Chromosome`` column is always string.
* Update :meth:`pycov.CovFrame.from_file` method to accept file-like object as input as well.
* Add new argument ``metadata`` to :meth:`pyvcf.VcfFrame.strip` method.
* Update :meth:`pyvcf.VcfFrame.from_file` method to accept file-like object as input as well.
* Add new method :meth:`pycov.CovFrame.mask_bed`.
* Add new method :meth:`pycov.CovFrame.chr_prefix`.
* Add new property ``contigs`` to :class:`pybed.BedFrame` class.
* Add new method :meth:`pybed.BedFrame.chr_prefix`.
* Add new methods :meth:`pybed.BedFrame.copy_meta` and :meth:`pybed.BedFrame.sort`.
* Add new method :meth:`pybed.BedFrame.merge`.
* Add new property ``empty`` to :class:`pyvcf.VcfFrame` class.
* Fix minor bug in :meth:`pyvcf.VcfFrame.strip` method when sample genotypes don't have the same number of fields as FORMAT.
* Add new method :meth:`pycov.CovFrame.subset` method.
* Add new method :meth:`common.color_print`.
* Add new method :meth:`pycov.concat`.
* Add new command :command:`cov-concat`.
* Update :class:`pyvcf.VcfFrame` to enforce the dtypes.
* Update :meth:`pyvcf.VcfFrame.add_af` method to output allele fraction for each ALT allele.
* Fix bug in :meth:`pyvcf.VcfFrame.add_af` method when the sum of allelic depths is 0.
* Add new method :meth:`pyvcf.VcfFrame.get_af`.

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

* Update :meth:`pyvcf.VcfFrame.from_file` method to be more memory efficient by pre-specifying data type for each VCF column.
* Update :meth:`pyvcf.VcfFrame.from_file` method to raise error if one or more VCF columns are missing, except for the FORMAT column (i.e. "sites-only" VCFs).
* Add new property ``sites_only`` to :class:`pyvcf.VcfFrame`.
* Update :meth:`pyvcf.VcfFrame.merge` method to handle sites-only VCFs.
* Add new method :meth:`pyvcf.VcfFrame.filter_vcf`.
* Add new arguments ``--bed`` and ``--vcf`` to :command:`vcf-slice` command.
* Update :meth:`common.parse_region` method to output ``NaN`` instead of 0.
* Add new method :meth:`common.parse_variant`.
* Update :meth:`pycov.CovFrame.from_file` method to be more memory efficient by pre-specifying data type for each of the columns in the input text file.
* Update :meth:`pycov.CovFrame.from_file` method to raise error if 'Chromosome' or 'Position' column is missing.
* Add new method :meth:`pyvcf.VcfFrame.fetch`.
* Update :meth:`pyvcf.VcfFrame.strip` method to handle cases where one or more specified FORMAT keys are missing in a row.
* Add new method :meth:`pyvcf.VcfFrame.pseudophase`.
* Update :meth:`pyvcf.VcfFrame.filter_vcf` method to also use REF and ALT (previously it only used CHROM and POS).
* Add new argument ``--zero`` to :command:`bam-depth` command.
* Update :meth:`pycov.CovFrame.plot_region` method: 1) New argument ``label`` has been added. 2) Argument ``names`` has been deprecated. 3) New argument ``sample`` has been added. 4) From now on, by default the method will plot profile for single sample specified by ``sample`` as opposed to all samples at once. 5) From now on, argument ``region`` can be omitted if there is only one contig.
* Add new property ``contigs`` to :class:`pyvcf.CovFrame`.
* Add new methods :meth:`pyvcf.CovFrame.copy` and :meth:`pyvcf.CovFrame.copy_df`.
* Update :meth:`pyvcf.CovFrame.from_file` method to accept GZIP compressed files. Also add new argument ``compression``.
* Add new methods :meth:`pyvcf.CovFrame.to_string` and :meth:`pyvcf.CovFrame.to_file`.

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

* Rename :meth:`pyvcf.VcfFrame.compare` method to :meth:`pyvcf.VcfFrame.calculate_concordance`.
* Add new method :meth:`pyvcf.VcfFrame.compare`.
* Add new property ``contigs`` to :class:`pyvcf.VcfFrame`.
* Add new method :meth:`pyvcf.VcfFrame.plot_region`.
* Add special genotype keys to :meth:`pyvcf.VcfFrame.extract` method.
* :issue:`39`: Update :meth:`pyvcf.VcfFrame.extract` method to ignore rows where the genotype key of interest is not present.
* Rename :meth:`pyvcf.VcfFrame.extract` method to :meth:`pyvcf.VcfFrame.extract_format`.
* Rename :meth:`pyvcf.VcfFrame.plot_hist` method to :meth:`pyvcf.VcfFrame.plot_hist_format`.
* Add new method :meth:`pyvcf.VcfFrame.extract_info`.
* Add new method :meth:`pyvcf.VcfFrame.plot_hist_info`.
* Add new method :meth:`common.plot_exons`.
* Update :meth:`pycov.CovFrame.plot_uniformity` method to accept a list of x positions.
* Add new command :command:`ngs-fq2bam`.
* Add new command :command:`ngs-hc`.
* Add new command :command:`ngs-pon`.
* Add new command :command:`ngs-m2`.
* Add new method :meth:`common.conda_env`.
* Add new argument ``meta_only`` to :meth:`pyvcf.VcfFrame.from_file` method.
* Add new argument ``nrows`` to :meth:`pyvcf.VcfFrame.from_file` method.
* Deprecate :meth:`pybam.header` method.
* Add new method :meth:`pybam.has_chr`.