Changelog

0.38.0 (2024-06-16)

  • Update pyvcf.has_chr_prefix() method to ignore the HLA contigs for GRCh38.

  • #71: Deprecate common.plot_cytobands() method.

0.37.0 (2023-09-09)

  • #67: Fix bug in pymaf.MafFrame.plot_waterfall() method where count=1 was causing color mismatch.

  • Add new submodule pychip.

  • Add new method common.reverse_complement().

  • Fix bug in common.extract_sequence() method where a long DNA sequence output was truncated.

  • #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 pyvcf.VcfFrame.filter_gsa().

  • Add new method pyvcf.VcfFrame.duplicated().

  • Add new optional argument to_csv to pymaf.MafFrame.plot_regplot_tmb() method.

  • Add new optional argument count to pymaf.MafFrame.plot_mutated_matched() method.

0.35.0 (2022-07-12)

  • Fix bug in pyvcf.VcfFrame.pseudophase() method.

  • Add new methods pyvcf.VcfFrame.diploidize() and pyvcf.gt_diploidize().

  • Update pyvcf.VcfFrame.get_af() method to handle situations where there are multiple records with the same REF allele.

  • Add new method pymaf.MafFrame.plot_regplot_tmb().

  • Rename pyvcf.VcfFrame.plot_regplot() method to pyvcf.VcfFrame.plot_regplot_tmb() and pymaf.MafFrame.plot_regplot() method to pymaf.MafFrame.plot_regplot_gene().

0.34.0 (2022-06-08)

  • Add new optional argument --stranded to ngs-quant command.

  • Add new method pycov.CovFrame.merge().

  • Add new method pycov.merge().

  • #61: Update pymaf.MafFrame.from_vcf() method to automatically detect CSQ field in INFO column (thanks @lbeltrame).

  • #63: Update pyvcf.VcfFrame.sort() method to handle contigs that are not pre-defined.

0.33.1 (2022-05-03)

  • Add new method pybam.index() which simply wraps pysam.index() method.

  • Update bam-index command to use pybam.index() method.

  • Add new method pybam.slice().

  • Update bam-slice command to use pybam.slice() method.

  • Update ngs-bam2fq and ngs-fq2bam commands to allow users to run in local environment.

  • Update ngs-fq2bam command to handle cases where input FASTQ does not have information on flowcell and barcode.

  • Update pyvcf.call() method to run more efficiently.

0.32.0 (2022-04-02)

  • Add new optional argument filter_off to pykallisto.KallistoFrame constructor, which is useful for generating a simple count or tpm matrix.

  • Add new optional argument --dir-path to vcf-call command for storing intermediate files.

  • Add new optional argument --gap_frac to vcf-call command so that users can control indel calling sensitivity.

  • Add new optional argument --group-samples to 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 pyvcf.call() method when pybed.BedFrame object is given as regions.

0.31.0 (2022-03-01)

  • Fix bug in pykallisto.KallistoFrame.compute_fold_change() method.

  • Add new method pyvcf.call() and new command vcf-call.

  • Combine optional arguments bam and fn into single positional argument bams for pycov.CovFrame.from_bam() method. The same goes for bam-depth command (combine --bam and --fn into bams).

  • Combine optional arguments bed and region into single optional argument regions for pycov.CovFrame.from_bam() method. The same goes for bam-depth command (combine --bed and --region into --regions).

  • Update pycov.CovFrame.from_bam() method and bam-depth command to automatically handle the ‘chr’ string.

  • Rename pyvcf.VcfFrame.variants() method to pyvcf.VcfFrame.to_variants().

  • Add new optional arguments force and missing to pyvcf.row_updateinfo() method.

  • Add new method pyvcf.gt_ploidy().

  • Update pyvcf.gt_polyp() method to use pyvcf.gt_ploidy() method internally.

  • #53: Add new methods to compute AC/AN/AF in the INFO column: pyvcf.row_computeinfo() and pyvcf.VcfFrame.compute_info().

  • #54: Update pyvcf.VcfFrame.cfilter_empty() method so that users can control missingness threshold for filtering samples.

  • Rename pyvcf.VcfFrame.cfilter_empty() method to pyvcf.VcfFrame.empty_samples().

  • Update common.sort_regions() method to support regions containing an ALT contig (e.g. chr16_KI270854v1_alt).

0.30.0 (2022-02-05)

  • Update fuc-find command to allow users to control whether to use recursive retrieving.

  • Add new command ngs-trim.

  • Add new command ngs-quant.

  • Add new submodule pykallisto.

  • Update pycov.CovFrame.from_bam() method to use filename as sample name when the SM tag is missing.

  • Add new method pyvcf.row_phased(). From now on, it’s used to get the pyvcf.VcfFrame.phased property.

  • Add new method pyvcf.split() and vcf-split command for splitting VCF by individual.

  • Update pyvcf.merge() method, pyvcf.VcfFrame.merge() method, and vcf-merge command to automatically handle the ‘chr’ string.

0.29.0 (2021-12-19)

  • Add new property pyvcf.VcfFrame.phased.

  • Update pyvcf.VcfFrame.slice() method to automatically handle the ‘chr’ string.

  • Add new argument --thread to ngs-hc command. This argument will be used to set --native-pair-hmm-threads for GATK’s HaplotypeCaller command, --reader-threads for GATK’s GenomicsDBImport command, and -XX:ParallelGCThreads and -XX:ConcGCThreads for Java.

  • Add new argument --batch to ngs-hc command. This argument will be used to set --batch-size for GATK’s GenomicsDBImport command.

  • Update 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 ngs-hc command so that when --posix is set, it will use --genomicsdb-shared-posixfs-optimizations argument from GATK’s GenomicsDBImport command in addition to exporting relevant shell variable (i.e. export TILEDB_DISABLE_FILE_LOCKING=1).

  • Add new argument --job to ngs-fq2bam command.

  • Update ngs-fq2bam command so that BAM creation step and BAM processing step are now in one step.

  • Update ngs-fq2bam command so that --thread is now also used to set -XX:ParallelGCThreads and -XX:ConcGCThreads for Java.

  • Add new method common.parse_list_or_file().

0.28.0 (2021-12-05)

  • Update pyvcf.VcfFrame.filter_empty() method so that users can choose a varying number of missing genotypes as threshold.

  • Add new method pyvcf.plot_af_correlation().

  • Update 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 pycov.CovFrame.matrix_uniformity().

  • Fix bug in pyvcf.slice() method when the input region is missing start or end.

  • Add new command ngs-bam2fq.

  • Add new command fa-filter.

  • Update pycov.CovFrame.plot_region() and pyvcf.VcfFrame.plot_region() methods to raise an error if the CovFrame/VcfFrame is empty.

  • Update 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 common.plot_exons() method to not italicize text by default (use name='$text$' to italicize).

  • Add new argument --posix to ngs-hc command.

  • Add new method common.AnnFrame.subset().

  • Update common.AnnFrame.plot_annot() method to raise an error if user provides an invalid group in group_order.

  • Add new method pymaf.MafFrame.get_gene_concordance().

0.27.0 (2021-11-20)

  • Rename file argument to vcf for vcf-slice command.

  • Add new command vcf-index.

  • Add new method pyvcf.has_chr_prefix().

  • Add new command common.update_chr_prefix().

  • Update pyvcf.slice() method to automatically handle the ‘chr’ prefix.

  • Fix bug caused by a typo in pyvcf.VcfFrame.filter_sampany() method.

0.26.0 (2021-10-24)

  • Add new method pybam.count_allelic_depth().

  • Update common.parse_variant() method to handle position-only strings as input (e.g. ‘22-42127941-G-A’ vs. ‘22-42127941’).

  • Add new command bam-aldepth.

  • Rename pybam.has_chr() method to pybam.has_chr_prefix().

  • Rename pybed.BedFrame.chr_prefix(), pycov.CovFrame.chr_prefix(), pyvcf.VcfFrame.chr_prefix() methods to pybed.BedFrame.update_chr_prefix(), pycov.CovFrame.update_chr_prefix(), 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 pyvcf.slice().

  • Add new method pyvcf.VcfFrame.from_string().

  • Remove nrows argument from pyvcf.VcfFrame.from_file() method.

  • Add new argument regions to pyvcf.VcfFrame.from_file() method.

  • Add new property pybed.BedFrame.shape.

  • Add new method pybed.BedFrame.to_regions().

  • Add new method pybed.BedFrame.from_regions().

  • Update pyvcf.VcfFrame.from_file() method to accept BED data to specify regions of interest.

  • Update vcf-slice command to run significantly faster by allowing random access.

  • Add new method common.sort_regions().

  • Fix minor bug in pyvcf.VcfFrame.get_af() method when the variant of interest does not exist in VcfFrame.

0.25.0 (2021-10-09)

  • Add new method common.sort_variants().

  • Add new method pyvcf.VcfFrame.variants().

  • Add new method pymaf.MafFrame.variants().

  • Add new method pymaf.MafFrame.subset().

  • Add new method pymaf.MafFrame.calculate_concordance().

  • Add new method pymaf.MafFrame.copy().

  • Add new method pymaf.MafFrame.filter_indel().

  • Add new method pymaf.MafFrame.plot_comparison().

0.24.0 (2021-10-02)

  • Add new command fuc-bgzip.

  • Add new command tabix-index.

  • Fix bug in pyvcf.VcfFrame.from_file() method when meta_only is True.

  • Update pyvcf.VcfFrame.from_file() method to extract VCF headers as well when meta_only is True.

  • Add new command tabix-slice.

  • Update pyvcf.VcfFrame.chr_prefix(), pybed.BedFrame.chr_prefix(), and pycov.CovFrame.chr_prefix() methods to skip lines that already have chr string when mode='add'.

  • Add new methods common.rename() and pycov.CovFrame.rename().

  • Add new command cov-rename.

  • Add new method pyvcf.gt_het().

  • Add new method pyvcf.gt_pseudophase().

0.23.0 (2021-09-21)

  • Update pycov.CovFrame class to ensure that the Chromosome column is always string.

  • Update pycov.CovFrame.from_file() method to accept file-like object as input as well.

  • Add new argument metadata to pyvcf.VcfFrame.strip() method.

  • Update pyvcf.VcfFrame.from_file() method to accept file-like object as input as well.

  • Add new method pycov.CovFrame.mask_bed().

  • Add new method pycov.CovFrame.chr_prefix().

  • Add new property contigs to pybed.BedFrame class.

  • Add new method pybed.BedFrame.chr_prefix().

  • Add new methods pybed.BedFrame.copy_meta() and pybed.BedFrame.sort().

  • Add new method pybed.BedFrame.merge().

  • Add new property empty to pyvcf.VcfFrame class.

  • Fix minor bug in pyvcf.VcfFrame.strip() method when sample genotypes don’t have the same number of fields as FORMAT.

  • Add new method pycov.CovFrame.subset() method.

  • Add new method common.color_print().

  • Add new method pycov.concat().

  • Add new command cov-concat.

  • Update pyvcf.VcfFrame to enforce the dtypes.

  • Update pyvcf.VcfFrame.add_af() method to output allele fraction for each ALT allele.

  • Fix bug in pyvcf.VcfFrame.add_af() method when the sum of allelic depths is 0.

  • Add new method pyvcf.VcfFrame.get_af().

0.22.0 (2021-09-04)

  • Update pyvcf.VcfFrame.from_file() method to be more memory efficient by pre-specifying data type for each VCF column.

  • Update 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 pyvcf.VcfFrame.

  • Update pyvcf.VcfFrame.merge() method to handle sites-only VCFs.

  • Add new method pyvcf.VcfFrame.filter_vcf().

  • Add new arguments --bed and --vcf to vcf-slice command.

  • Update common.parse_region() method to output NaN instead of 0.

  • Add new method common.parse_variant().

  • Update 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 pycov.CovFrame.from_file() method to raise error if ‘Chromosome’ or ‘Position’ column is missing.

  • Add new method pyvcf.VcfFrame.fetch().

  • Update pyvcf.VcfFrame.strip() method to handle cases where one or more specified FORMAT keys are missing in a row.

  • Add new method pyvcf.VcfFrame.pseudophase().

  • Update pyvcf.VcfFrame.filter_vcf() method to also use REF and ALT (previously it only used CHROM and POS).

  • Add new argument --zero to bam-depth command.

  • Update 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 pyvcf.CovFrame.

  • Add new methods pyvcf.CovFrame.copy() and pyvcf.CovFrame.copy_df().

  • Update pyvcf.CovFrame.from_file() method to accept GZIP compressed files. Also add new argument compression.

  • Add new methods pyvcf.CovFrame.to_string() and pyvcf.CovFrame.to_file().

0.21.0 (2021-08-16)

  • Rename pyvcf.VcfFrame.compare() method to pyvcf.VcfFrame.calculate_concordance().

  • Add new method pyvcf.VcfFrame.compare().

  • Add new property contigs to pyvcf.VcfFrame.

  • Add new method pyvcf.VcfFrame.plot_region().

  • Add special genotype keys to pyvcf.VcfFrame.extract() method.

  • #39: Update pyvcf.VcfFrame.extract() method to ignore rows where the genotype key of interest is not present.

  • Rename pyvcf.VcfFrame.extract() method to pyvcf.VcfFrame.extract_format().

  • Rename pyvcf.VcfFrame.plot_hist() method to pyvcf.VcfFrame.plot_hist_format().

  • Add new method pyvcf.VcfFrame.extract_info().

  • Add new method pyvcf.VcfFrame.plot_hist_info().

  • Add new method common.plot_exons().

  • Update pycov.CovFrame.plot_uniformity() method to accept a list of x positions.

  • Add new command ngs-fq2bam.

  • Add new command ngs-hc.

  • Add new command ngs-pon.

  • Add new command ngs-m2.

  • Add new method common.conda_env().

  • Add new argument meta_only to pyvcf.VcfFrame.from_file() method.

  • Add new argument nrows to pyvcf.VcfFrame.from_file() method.

  • Deprecate pybam.header() method.

  • Add new method pybam.has_chr().

0.20.0 (2021-08-07)

  • Add new method pymaf.MafFrame.matrix_waterfall_matched().

  • Add new method pymaf.MafFrame.plot_waterfall_matched().

  • Add new method pymaf.MafFrame.plot_tmb_matched().

  • Add new method pymaf.MafFrame.plot_mutated_matched().

  • Add new method pymaf.MafFrame.plot_oncoplot_matched().

  • Deprecate method pymaf.MafFrame.legend_handles().

  • Add new method common.legend_handles().

  • Deprecate classes pyvcf.AnnFrame and pymaf.AnnFrame. Add new class common.AnnFrame.

  • Rename common.file2list() method to convert_file2list().

  • Add new method common.convert_num2cat().

  • Add new command fuc-undetm.

  • Add new method common.plot_annot_matched().

  • Add new argument sheet to fuc-demux command.

  • Add new class common.Variant.

  • Add new method pyvcf.rescue_filtered_variants().

  • Add new arguments a_size and b_size to 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 pymaf.MafFrame.plot_mutated() when using the hue option.

  • Add new argument sort to pymaf.MafFrame.plot_vaf() method.

  • Add new method pymaf.MafFrame.plot_matrixs().

  • Add new method pymaf.MafFrame.plot_matrixg().

  • Add new method pymaf.MafFrame.compute_clonality().

  • Add new method pymaf.MafFrame.plot_clonality().

  • Fix bug in pymaf.MafFrame.plot_evolution() when there are no variants to display for the specified samples.

  • #34: Add new method pymaf.MafFrame.plot_genepair().

  • #34: Add new method pymaf.MafFrame.plot_interactions().

  • Update the fuc-demux command to output a better figure.

  • Add new method common.plot_cytobands().

  • Add new method pycov.CovFrame.plot_uniformity().

  • Add new method pycov.CovFrame.plot_distribution().

  • Rename pycov.CovFrame.from_file() method to pycov.CovFrame.from_bam().

  • Add new method pycov.CovFrame.from_file().

  • Add new command fuc-depth.

  • Add new method common.file2list().

  • Add new method pyvcf.VcfFrame.chr_prefix().

  • Fix bug in pyvcf.gt_unphase() when ‘.|.’ is provided.

  • Update pyvcf.VcfFrame.compare() method to only consider biallelic sites.

  • Update pyvcf.VcfFrame.compare() method to support comparison of SNVs only and INDELs only.

  • Update 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 fq-count command to run significantly faster.

  • Update fuc-find command to support pattern matching that is more robust than just file extension.

  • Update pyvcf.VcfFrame.subset() method to take string as input in addition to list.

  • Fix bug in pymaf.MafFrame.plot_snvclss() method when certain SNV classes are entirely missing.

  • Add new package statsmodels as dependency for performing statistical analysis.

  • Update pymaf.MafFrame.plot_regplot() method to calculate and print summary statistics as well.

  • Update pyvcf.VcfFrame.plot_regplot() method to calculate and print summary statistics as well.

  • #32: Add pyvcf.VcfFrame.miss2ref() method.

  • Update pymaf.MafFrame.plot_tmb() method to draw empty bars with warning when specified samples do not exist.

  • Update pymaf.MafFrame.plot_waterfall() method to draw empty bars with warning when specified samples do not exist.

  • Add flip argument to pymaf.MafFrame.plot_genes() method.

  • Add new method pymaf.MafFrame.plot_mutated().

0.17.0 (2021-07-08)

  • Add new method pymaf.MafFrame.plot_lollipop().

  • #30: Add pymaf.MafFrame.plot_rainfall() method.

  • #30: Add pyvcf.VcfFrame.plot_rainfall() method.

  • Update pymaf.MafFrame.to_vcf() method to output sorted VCF.

  • Add new method pymaf.MafFrame.matrix_prevalence().

  • Add new method pymaf.MafFrame.plot_regplot().

  • Add new argument samples to pymaf.MafFrame.plot_snvclss() method.

  • Add new method pymaf.MafFrame.plot_evolution().

  • Add new submodule pygff.

0.16.0 (2021-07-02)

  • Rename the commands (e.g. vcf_merge to vcf-merge).

  • Add new argument flip to pymaf.MafFrame.plot_vaf() method.

  • Update pymaf.MafFrame.plot_vaf() method to support creation of a grouped bar plot.

  • Factor out count mode of pymaf.MafFrame.plot_snvcls() method to new method pymaf.MafFrame.plot_snvclsc().

  • Factor out proportion mode of pymaf.MafFrame.plot_snvcls() method to new method pymaf.MafFrame.plot_snvclsp().

  • Factor out samples mode of pymaf.MafFrame.plot_snvcls() method to new method pymaf.MafFrame.plot_snvclss().

  • Factor out titv mode of pymaf.MafFrame.plot_snvcls() method to new method pymaf.MafFrame.plot_titv().

  • Deprecate method pymaf.MafFrame.plot_snvcls().

  • Add new argument hue_order to pyvcf.VcfFrame.plot_hist() method.

  • Update aesthetic aspect of pymaf.MafFrame.plot_oncoplot() method.

  • Add new argument width to pymaf.MafFrame.plot_tmb() method.

  • Add new arguments palette and flip to pymaf.MafFrame.plot_vartype() method.

  • Update pymaf.MafFrame.plot_snvclsc() method to support creation of a grouped bar plot.

  • Update pymaf.MafFrame.plot_snvclsp() method to support creation of a grouped box plot.

  • Add new method pyvcf.VcfFrame.plot_snvclsc() (simply wraps pymaf.MafFrame.plot_snvclsc() method).

  • Add new method pyvcf.VcfFrame.plot_snvclsp() (simply wraps pymaf.MafFrame.plot_snvclsp() method).

  • Add new method pyvcf.VcfFrame.plot_snvclss() (simply wraps pymaf.MafFrame.plot_snvclss() method).

  • Add new method pyvcf.VcfFrame.plot_titv() (simply wraps pymaf.MafFrame.plot_titv() method).

  • #28: Update pymaf.MafFrame.from_vcf() method to handle unannotated VCF data.

0.15.0 (2021-06-24)

  • Update vcf_filter command.

  • Update tbl_sum command.

  • Add samples and shape attributes to pymaf.AnnFrame class.

  • Rename pymaf.MafFrame.compute_genes/tmb/waterfall() methods to pymaf.MafFrame.matrix_genes/tmb/waterfall().

  • Add keep_empty argument to pymaf.MafFrame.matrix_waterfall/plot_oncoplot/plot_waterfall() methods.

  • Add pymaf.MafFrame.filter_annot() method.

  • Add pymaf.AnnFrame.sorted_samples() method.

  • Fix bug in pymaf.MafFrame.to_frame() method.

  • Deprecate methods pyvep.filter_lof/clinsig().

  • Update pymaf.MafFrame.from_vcf() method to extract genotype keys (e.g. DP, AD, AF).

  • Update bam_slice and bam_rename commands.

  • Deprecate method pybam.rename().

0.14.0 (2021-06-20)

  • #23: Deprecate methods pyvcf.VcfFrame.markmiss_ad/af/dp() and add new method pyvcf.VcfFrame.markmiss().

  • Add new command vcf_filter.

  • Update methods pycov.CovFrame.slice/plot_region().

  • #24: Add new method pyvcf.VcfFrame.drop_duplicates().

  • Update pymaf.MafFrame.plot_snvcls() method to support various plotting modes.

  • Rename horizontal argument of pymaf.MafFrame.plot_varsum() method to flip.

0.13.0 (2021-06-16)

  • Add new method pymaf.MafFrame.to_vcf().

  • #21: Add new command maf_maf2vcf.

  • Add new method pyvcf.VcfFrame.rename().

  • Add new command vcf_rename.

  • Add new method pymaf.MafFrame.plot_vaf().

  • Update pyvcf.VcfFrame.slice() method.

  • Update vcf_slice command.

0.12.0 (2021-06-12)

  • Add new method pyvcf.VcfFrame.add_af().

  • Add new method pyvcf.VcfFrame.extract().

  • Deprecate methods pyvep.filter_af/biotype/nothas/impact().

  • Add new method pyvep.filter_query().

  • #19: Add new command vcf_vep.

  • Rename pyvcf.VcfFrame.plot_histplot() to pyvcf.VcfFrame.plot_tmb().

  • Add scipy package as dependency for performing statistical analysis.

  • Add new method pyvcf.VcfFrame.plot_hist().

0.11.0 (2021-06-10)

  • #16: Add new method pyvcf.VcfFrame.cfilter_empty().

  • Add new methods pyvep.filter_af/lof().

  • Add matplotlib-venn package as dependency for plotting Venn diagrams.

  • Add new methods pyvcf.plot_comparison/regplot/histplot().

  • #17: Add new method pyvep.filter_biotype().

  • Add new class pyvcf.AnnFrame.

0.10.0 (2021-06-03)

  • Add new methods pymaf.plot_summary/varsum().

  • Add new command maf_sumplt.

  • Add new method pymaf.MafFrame.to_string().

  • Update maf_oncoplt command.

  • Add new method pyvcf.VcfFrame.filter_qual().

  • Deprecate method pymaf.plot_legend() and add pymaf.legend_handles() method.

  • Add new methods pymaf.AnnFrame.legend_handles/plot_annot().

  • Add new method pyvcf.VcfFrame.expand().

  • Rename methods pyvcf.gt_missing/haspolyp() to pyvcf.gt_miss/polyp().

  • Add new method pybed.BedFrame.from_frame().

  • #14: Add new method pyvcf.VcfFrame.to_bed() and new command vcf_vcf2bed.

0.9.0 (2021-06-01)

  • Add new submodule pymaf.

  • Deprecate method pyvcf.read_file() and add pyvcf.VcfFrame.from_file() method.

  • Deprecate method pybed.read_file() and add pybed.BedFrame.from_file() method.

  • Deprecate method pyfq.read_file() and add pyfq.FqFrame.from_file() method.

  • Deprecate method pycov.read_file() and add pycov.CovFrame.from_file() method.

  • Add new method common.parse_region().

  • Add new commands 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. vfmerge to vcf_merge).

  • #11: Add new command bam_slice.

  • Add new commands 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 fucdemux.

  • Add new method pyvcf.VcfFrame.filter_phased().

  • Add new method pyvcf.VcfFrame.meta_keys().

  • Update pyvep.filter_clinsig() method.

  • Update pyvep.filter_impact() method.

  • Add as_nan argument to pyvcf.VcfFrame.markmiss_ad/af/dp() methods.

  • Deprecate method pyvcf.update().

  • Add new methods 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 pyvcf.VcfFrame.markmiss_ad().

  • Add full argument to pyvcf.VcfFrame.markmiss_ad/af/dp() methods.

  • Add new command fucfind.

  • Update dfsum command.

0.5.0 (2021-05-06)

  • Add biopython package as dependency for working with BGZF compressed files.

  • Update pyvcf.read_file() method and pyvcf.VcfFrame.to_file() method to support BGZF compressed files.

  • Update Read the Docs.

  • Add new method pyvcf.VcfFrame.slice().

  • Add new command vfslice.

0.4.1 (2021-05-03)

  • Update Read the Docs.

  • Add new methods to pyvcf.VcfFrame class.

  • #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 pyvcf.VcfFrame class.

  • Add new extension autodocsumm to Read the Docs.

  • Add contents to Read the Docs.

0.2.0 (2021-04-26)

  • #2: Fix Read the Docs automodule not working properly.

  • #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 pyvcf.VcfFrame class.

  • Add new submodule snpeff.

0.1.4 (2021-04-21)

  • Initial release.