CHANGELOG.rst

Changelog

0.38.0 (2024-06-16)

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

0.37.0 (2023-09-09)

• :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.

0.36.0 (2022-08-12)

• fuc now has a citation! Please refer to the publication “ClinPharmSeq: A targeted sequencing panel for clinical pharmacogenetics implementation” 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.

0.35.0 (2022-07-12)

• 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`.

0.34.0 (2022-06-08)

• 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).
• :issue:`63`: Update :meth:`pyvcf.VcfFrame.sort` method to handle contigs that are not pre-defined.

0.33.1 (2022-05-03)

• 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.

0.32.0 (2022-04-02)

• 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.

0.31.0 (2022-03-01)

• 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).

0.30.0 (2022-02-05)

• 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.

0.29.0 (2021-12-19)

• 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`.

0.28.0 (2021-12-05)

• 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`.

0.27.0 (2021-11-20)

• 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.

0.26.0 (2021-10-24)

• 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.

0.25.0 (2021-10-09)

• 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`.

0.24.0 (2021-10-02)

• 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`.

0.23.0 (2021-09-21)

• 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`.

0.22.0 (2021-09-04)

• 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`.

0.21.0 (2021-08-16)

• 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`.

0.20.0 (2021-08-07)

• 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.

0.19.0 (2021-07-31)

• 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.

0.18.0 (2021-07-20)

• 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`.

0.17.0 (2021-07-08)

• 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.

0.16.0 (2021-07-02)

• 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.

0.15.0 (2021-06-24)

• 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`.

0.14.0 (2021-06-20)

• :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.

0.13.0 (2021-06-16)

• 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.

0.12.0 (2021-06-12)

• 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`.

0.11.0 (2021-06-10)

• :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`.

0.10.0 (2021-06-03)

• 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`.

0.9.0 (2021-06-01)

• 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`.

0.8.0 (2021-05-27)

• Add pysam package as dependency for working with SAM/BAM/CRAM files.
• Add new submodules pybam and pycov.
• Rename the commands (e.g. :command:`vfmerge` to :command:`vcf_merge`).
• :issue:`11`: Add new command :command:`bam_slice`.
• Add new commands :command:`bam_head/index/rename`.

0.7.0 (2021-05-23)

• Add lxml package as dependency for parsing HTML files.
• Add matplotlib and seaborn packages as dependency for creating figures.
• Add new command :command:`fucdemux`.
• Add new method :meth:`pyvcf.VcfFrame.filter_phased`.
• Add new method :meth:`pyvcf.VcfFrame.meta_keys`.
• Update :meth:`pyvep.filter_clinsig` method.
• Update :meth:`pyvep.filter_impact` method.
• Add as_nan argument to :meth:`pyvcf.VcfFrame.markmiss_ad/af/dp` methods.
• Deprecate method :meth:`pyvcf.update`.
• Add new methods :meth:`pyvcf.row_updateinfo/parseinfo`.
• The fuc package is now available on Bioconda.

0.6.0 (2021-05-16)

• Update Read the Docs.
• Add new method :meth:`pyvcf.VcfFrame.markmiss_ad`.
• Add full argument to :meth:`pyvcf.VcfFrame.markmiss_ad/af/dp` methods.
• Add new command :command:`fucfind`.
• Update :command:`dfsum` command.

0.5.0 (2021-05-06)

• Add biopython package as dependency for working with BGZF compressed files.
• Update :meth:`pyvcf.read_file` method and :meth:`pyvcf.VcfFrame.to_file` method to support BGZF compressed files.
• Update Read the Docs.
• Add new method :meth:`pyvcf.VcfFrame.slice`.
• Add new command :command:`vfslice`.

0.4.1 (2021-05-03)

• Update Read the Docs.
• Add new methods to :class:`pyvcf.VcfFrame` class.
• :issue:`6`: Add new extension sphinx.ext.linkcode to Read the Docs.

0.3.2 (2021-04-30)

• Rename snpeff submodule to pysnpeff.
• Add new submodule pyvep.
• Update :class:`pyvcf.VcfFrame` class.
• Add new extension autodocsumm to Read the Docs.
• Add contents to Read the Docs.

0.2.0 (2021-04-26)

• :issue:`2`: Fix Read the Docs automodule not working properly.
• :issue:`3`: Add new extension sphinx-issues to Read the Docs.
• Rename submodules BedFrame, FastqFrame, and VcfFrame to pybed, pyfq, and pyvcf, respectively.
• Add new methods to pyvcf submodule.
• Add new methods to :class:`pyvcf.VcfFrame` class.
• Add new submodule snpeff.

0.1.4 (2021-04-21)

• Initial release.