Fuc

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

* Add new optional argument ``filter_off`` to :class:`pykallisto.KallistoFrame` constructor, which is useful for generating a simple count or tpm matrix.
* Add new optional argument ``--dir-path`` to :command:`vcf-call` command for storing intermediate files.
* Add new optional argument ``--gap_frac`` to :command:`vcf-call` command so that users can control indel calling sensitivity.
* Add new optional argument ``--group-samples`` to :command:`vcf-call` command so that users can group samples into populations and apply the HWE assumption within but not across the populations.
* Fix minor bug in :meth:`pyvcf.call` method when ``pybed.BedFrame`` object is given as ``regions``.

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

* Fix bug in :meth:`pykallisto.KallistoFrame.compute_fold_change` method.
* Add new method :meth:`pyvcf.call` and new command :command:`vcf-call`.
* Combine optional arguments ``bam`` and ``fn`` into single positional argument ``bams`` for :meth:`pycov.CovFrame.from_bam` method. The same goes for :command:`bam-depth` command (combine ``--bam`` and ``--fn`` into ``bams``).
* Combine optional arguments ``bed`` and ``region`` into single optional argument ``regions`` for :meth:`pycov.CovFrame.from_bam` method. The same goes for :command:`bam-depth` command (combine ``--bed`` and ``--region`` into ``--regions``).
* Update :meth:`pycov.CovFrame.from_bam` method and :command:`bam-depth` command to automatically handle the 'chr' string.
* Rename :meth:`pyvcf.VcfFrame.variants` method to :meth:`pyvcf.VcfFrame.to_variants`.
* Add new optional arguments ``force`` and ``missing`` to :meth:`pyvcf.row_updateinfo` method.
* Add new method :meth:`pyvcf.gt_ploidy`.
* Update :meth:`pyvcf.gt_polyp` method to use :meth:`pyvcf.gt_ploidy` method internally.
* :issue:`53`: Add new methods to compute AC/AN/AF in the INFO column: :meth:`pyvcf.row_computeinfo` and :meth:`pyvcf.VcfFrame.compute_info`.
* :issue:`54`: Update :meth:`pyvcf.VcfFrame.cfilter_empty` method so that users can control missingness threshold for filtering samples.
* Rename :meth:`pyvcf.VcfFrame.cfilter_empty` method to :meth:`pyvcf.VcfFrame.empty_samples`.
* Update :meth:`common.sort_regions` method to support regions containing an ALT contig (e.g. chr16_KI270854v1_alt).

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

* Update :command:`fuc-find` command to allow users to control whether to use recursive retrieving.
* Add new command :command:`ngs-trim`.
* Add new command :command:`ngs-quant`.
* Add new submodule ``pykallisto``.
* Update :meth:`pycov.CovFrame.from_bam` method to use filename as sample name when the SM tag is missing.
* Add new method :meth:`pyvcf.row_phased`. From now on, it's used to get the ``pyvcf.VcfFrame.phased`` property.
* Add new method :meth:`pyvcf.split` and :command:`vcf-split` command for splitting VCF by individual.
* Update :meth:`pyvcf.merge` method, :meth:`pyvcf.VcfFrame.merge` method, and :command:`vcf-merge` command to automatically handle the 'chr' string.

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

* Add new property ``pyvcf.VcfFrame.phased``.
* Update :meth:`pyvcf.VcfFrame.slice` method to automatically handle the 'chr' string.
* Add new argument ``--thread`` to :command:`ngs-hc` command. This argument will be used to set ``--native-pair-hmm-threads`` for GATK's :command:`HaplotypeCaller` command, ``--reader-threads`` for GATK's :command:`GenomicsDBImport` command, and ``-XX:ParallelGCThreads`` and ``-XX:ConcGCThreads`` for Java.
* Add new argument ``--batch`` to :command:`ngs-hc` command. This argument will be used to set ``--batch-size`` for GATK's :command:`GenomicsDBImport` command.
* Update :command:`ngs-bam2fq` command to fix the SGE issue that outputs an error like ``Unable to run job: denied: "XXXXX" is not a valid object name (cannot start with a digit)``.
* Update :command:`ngs-hc` command so that when ``--posix`` is set, it will use ``--genomicsdb-shared-posixfs-optimizations`` argument from GATK's :command:`GenomicsDBImport` command in addition to exporting relevant shell variable (i.e. ``export TILEDB_DISABLE_FILE_LOCKING=1``).
* Add new argument ``--job`` to :command:`ngs-fq2bam` command.
* Update :command:`ngs-fq2bam` command so that BAM creation step and BAM processing step are now in one step.
* Update :command:`ngs-fq2bam` command so that ``--thread`` is now also used to set ``-XX:ParallelGCThreads`` and ``-XX:ConcGCThreads`` for Java.
* Add new method :meth:`common.parse_list_or_file`.

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

* Update :meth:`pyvcf.VcfFrame.filter_empty` method so that users can choose a varying number of missing genotypes as threshold.
* Add new method :meth:`pyvcf.plot_af_correlation`.
* Update :command:`bam-slice` command to support BED file as input for specifying regions. Additionally, from now on, the command will automatically handle the annoying 'chr' prefix.
* Add new method :meth:`pycov.CovFrame.matrix_uniformity`.
* Fix bug in :meth:`pyvcf.slice` method when the input region is missing start or end.
* Add new command :command:`ngs-bam2fq`.
* Add new command :command:`fa-filter`.
* Update :meth:`pycov.CovFrame.plot_region` and :meth:`pyvcf.VcfFrame.plot_region` methods to raise an error if the CovFrame/VcfFrame is empty.
* Update :meth:`pyvcf.VcfFrame.filter_*` methods so that they don't raise an error when the VcfFrame is empty (i.e. will return the empty VcfFrame).
* Update :meth:`common.plot_exons` method to not italicize text by default (use ``name='$text$'`` to italicize).
* Add new argument ``--posix`` to :command:`ngs-hc` command.
* Add new method :meth:`common.AnnFrame.subset`.
* Update :meth:`common.AnnFrame.plot_annot` method to raise an error if user provides an invalid group in ``group_order``.
* Add new method :meth:`pymaf.MafFrame.get_gene_concordance`.

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

* Rename ``file`` argument to ``vcf`` for :command:`vcf-slice` command.
* Add new command :command:`vcf-index`.
* Add new method :meth:`pyvcf.has_chr_prefix`.
* Add new command :meth:`common.update_chr_prefix`.
* Update :meth:`pyvcf.slice` method to automatically handle the 'chr' prefix.
* Fix bug caused by a typo in :meth:`pyvcf.VcfFrame.filter_sampany` method.