Changelog
0.37.0 (2023-09-09)
#67: Fix bug in
pymaf.MafFrame.plot_waterfall()
method wherecount=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
topymaf.MafFrame.plot_regplot_tmb()
method.Add new optional argument
count
topymaf.MafFrame.plot_mutated_matched()
method.
0.35.0 (2022-07-12)
Fix bug in
pyvcf.VcfFrame.pseudophase()
method.Add new methods
pyvcf.VcfFrame.diploidize()
andpyvcf.gt_diploidize()
.Update
pyvcf.VcfFrame.get_af()
method to handle situations where there are multiple records with the sameREF
allele.Add new method
pymaf.MafFrame.plot_regplot_tmb()
.Rename
pyvcf.VcfFrame.plot_regplot()
method topyvcf.VcfFrame.plot_regplot_tmb()
andpymaf.MafFrame.plot_regplot()
method topymaf.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 wrapspysam.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
topykallisto.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 whenpybed.BedFrame
object is given asregions
.
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
andfn
into single positional argumentbams
forpycov.CovFrame.from_bam()
method. The same goes for bam-depth command (combine--bam
and--fn
intobams
).Combine optional arguments
bed
andregion
into single optional argumentregions
forpycov.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 topyvcf.VcfFrame.to_variants()
.Add new optional arguments
force
andmissing
topyvcf.row_updateinfo()
method.Add new method
pyvcf.gt_ploidy()
.Update
pyvcf.gt_polyp()
method to usepyvcf.gt_ploidy()
method internally.#53: Add new methods to compute AC/AN/AF in the INFO column:
pyvcf.row_computeinfo()
andpyvcf.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 topyvcf.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 thepyvcf.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()
andpyvcf.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 (usename='$text$'
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 ingroup_order
.Add new method
pymaf.MafFrame.get_gene_concordance()
.
0.27.0 (2021-11-20)
Rename
file
argument tovcf
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 topybam.has_chr_prefix()
.Rename
pybed.BedFrame.chr_prefix()
,pycov.CovFrame.chr_prefix()
,pyvcf.VcfFrame.chr_prefix()
methods topybed.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 frompyvcf.VcfFrame.from_file()
method.Add new argument
regions
topyvcf.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 whenmeta_only
isTrue
.Update
pyvcf.VcfFrame.from_file()
method to extract VCF headers as well whenmeta_only
isTrue
.Add new command tabix-slice.
Update
pyvcf.VcfFrame.chr_prefix()
,pybed.BedFrame.chr_prefix()
, andpycov.CovFrame.chr_prefix()
methods to skip lines that already havechr
string whenmode='add'
.Add new methods
common.rename()
andpycov.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 theChromosome
column is always string.Update
pycov.CovFrame.from_file()
method to accept file-like object as input as well.Add new argument
metadata
topyvcf.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
topybed.BedFrame
class.Add new method
pybed.BedFrame.chr_prefix()
.Add new methods
pybed.BedFrame.copy_meta()
andpybed.BedFrame.sort()
.Add new method
pybed.BedFrame.merge()
.Add new property
empty
topyvcf.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
topyvcf.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 outputNaN
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 argumentlabel
has been added. 2) Argumentnames
has been deprecated. 3) New argumentsample
has been added. 4) From now on, by default the method will plot profile for single sample specified bysample
as opposed to all samples at once. 5) From now on, argumentregion
can be omitted if there is only one contig.Add new property
contigs
topyvcf.CovFrame
.Add new methods
pyvcf.CovFrame.copy()
andpyvcf.CovFrame.copy_df()
.Update
pyvcf.CovFrame.from_file()
method to accept GZIP compressed files. Also add new argumentcompression
.Add new methods
pyvcf.CovFrame.to_string()
andpyvcf.CovFrame.to_file()
.
0.21.0 (2021-08-16)
Rename
pyvcf.VcfFrame.compare()
method topyvcf.VcfFrame.calculate_concordance()
.Add new method
pyvcf.VcfFrame.compare()
.Add new property
contigs
topyvcf.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 topyvcf.VcfFrame.extract_format()
.Rename
pyvcf.VcfFrame.plot_hist()
method topyvcf.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
topyvcf.VcfFrame.from_file()
method.Add new argument
nrows
topyvcf.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
andpymaf.AnnFrame
. Add new classcommon.AnnFrame
.Rename
common.file2list()
method toconvert_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
andb_size
topymaf.MafFrame.plot_regplot()
method.Rename
hue
andhue_order
arguments in plotting methods togroup_col
andgroup_order
, respectively.
0.19.0 (2021-07-31)
Fix bug in
pymaf.MafFrame.plot_mutated()
when using thehue
option.Add new argument
sort
topymaf.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 topycov.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 thatnames
argument is no longer required whenkeys
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 topymaf.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
topymaf.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
topymaf.MafFrame.plot_vaf()
method.Update
pymaf.MafFrame.plot_vaf()
method to support creation of a grouped bar plot.Factor out
count
mode ofpymaf.MafFrame.plot_snvcls()
method to new methodpymaf.MafFrame.plot_snvclsc()
.Factor out
proportion
mode ofpymaf.MafFrame.plot_snvcls()
method to new methodpymaf.MafFrame.plot_snvclsp()
.Factor out
samples
mode ofpymaf.MafFrame.plot_snvcls()
method to new methodpymaf.MafFrame.plot_snvclss()
.Factor out
titv
mode ofpymaf.MafFrame.plot_snvcls()
method to new methodpymaf.MafFrame.plot_titv()
.Deprecate method
pymaf.MafFrame.plot_snvcls()
.Add new argument
hue_order
topyvcf.VcfFrame.plot_hist()
method.Update aesthetic aspect of
pymaf.MafFrame.plot_oncoplot()
method.Add new argument
width
topymaf.MafFrame.plot_tmb()
method.Add new arguments
palette
andflip
topymaf.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 wrapspymaf.MafFrame.plot_snvclsc()
method).Add new method
pyvcf.VcfFrame.plot_snvclsp()
(simply wrapspymaf.MafFrame.plot_snvclsp()
method).Add new method
pyvcf.VcfFrame.plot_snvclss()
(simply wrapspymaf.MafFrame.plot_snvclss()
method).Add new method
pyvcf.VcfFrame.plot_titv()
(simply wrapspymaf.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
andshape
attributes topymaf.AnnFrame
class.Rename
pymaf.MafFrame.compute_genes/tmb/waterfall()
methods topymaf.MafFrame.matrix_genes/tmb/waterfall()
.Add
keep_empty
argument topymaf.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 methodpyvcf.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 ofpymaf.MafFrame.plot_varsum()
method toflip
.
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()
topyvcf.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)
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 addpymaf.legend_handles()
method.Add new methods
pymaf.AnnFrame.legend_handles/plot_annot()
.Add new method
pyvcf.VcfFrame.expand()
.Rename methods
pyvcf.gt_missing/haspolyp()
topyvcf.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 addpyvcf.VcfFrame.from_file()
method.Deprecate method
pybed.read_file()
and addpybed.BedFrame.from_file()
method.Deprecate method
pyfq.read_file()
and addpyfq.FqFrame.from_file()
method.Deprecate method
pycov.read_file()
and addpycov.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
andpycov
.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
andseaborn
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 topyvcf.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 topyvcf.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 andpyvcf.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 topysnpeff
.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
, andVcfFrame
topybed
,pyfq
, andpyvcf
, 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.