Fuc

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* Update :meth:`pyvcf.has_chr_prefix` method to ignore the HLA contigs for GRCh38.
* :issue:`71`: Deprecate :meth:`common.plot_cytobands` method.

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* :issue:`67`: Fix bug in :meth:`pymaf.MafFrame.plot_waterfall` method where ``count=1`` was causing color mismatch.
* Add new submodule ``pychip``.
* Add new method :meth:`common.reverse_complement`.
* Fix bug in :meth:`common.extract_sequence` method where a long DNA sequence output was truncated.
* :issue:`68`: Refresh the variant consequences database from Ensembl VEP. The database's latest update was on May 31, 2021.

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* ``fuc`` now has a citation! Please refer to the publication “`ClinPharmSeq: A targeted sequencing panel for clinical pharmacogenetics implementation <https://doi.org/10.1371/journal.pone.0272129>`__” by Lee et al., 2022 (Steven is the first author). Fore more details, see the Citation section in README.
* Update ``pyvcf`` submodule to accept "sites-only" VCF.
* Add new method :meth:`pyvcf.VcfFrame.filter_gsa`.
* Add new method :meth:`pyvcf.VcfFrame.duplicated`.
* Add new optional argument ``to_csv`` to :meth:`pymaf.MafFrame.plot_regplot_tmb` method.
* Add new optional argument ``count`` to :meth:`pymaf.MafFrame.plot_mutated_matched` method.

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* Fix bug in :meth:`pyvcf.VcfFrame.pseudophase` method.
* Add new methods :meth:`pyvcf.VcfFrame.diploidize` and :meth:`pyvcf.gt_diploidize`.
* Update :meth:`pyvcf.VcfFrame.get_af` method to handle situations where there are multiple records with the same ``REF`` allele.
* Add new method :meth:`pymaf.MafFrame.plot_regplot_tmb`.
* Rename :meth:`pyvcf.VcfFrame.plot_regplot` method to :meth:`pyvcf.VcfFrame.plot_regplot_tmb` and :meth:`pymaf.MafFrame.plot_regplot` method to :meth:`pymaf.MafFrame.plot_regplot_gene`.

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* Add new optional argument ``--stranded`` to :command:`ngs-quant` command.
* Add new method :meth:`pycov.CovFrame.merge`.
* Add new method :meth:`pycov.merge`.
* :issue:`61`: Update :meth:`pymaf.MafFrame.from_vcf` method to automatically detect CSQ field in INFO column (thanks `lbeltrame <https://github.com/lbeltrame>`__).
* :issue:`63`: Update :meth:`pyvcf.VcfFrame.sort` method to handle contigs that are not pre-defined.

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* Add new method :meth:`pybam.index` which simply wraps :meth:`pysam.index` method.
* Update :command:`bam-index` command to use :meth:`pybam.index` method.
* Add new method :meth:`pybam.slice`.
* Update :command:`bam-slice` command to use :meth:`pybam.slice` method.
* Update :command:`ngs-bam2fq` and :command:`ngs-fq2bam` commands to allow users to run in local environment.
* Update :command:`ngs-fq2bam` command to handle cases where input FASTQ does not have information on flowcell and barcode.
* Update :meth:`pyvcf.call` method to run more efficiently.