Merge pull request #42 from sbslee/0.23.0-dev

0.23.0 dev
sbslee · Sep 21, 2021 · 480a563 · 480a563
2 parents 43a08b8 + e6d8400
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,6 +1,30 @@
 Changelog
 *********
 
+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)
 -------------------
 

diff --git a/README.rst b/README.rst
@@ -114,17 +114,18 @@ For getting help on the fuc CLI:
        bam-depth    Compute read depth from SAM/BAM/CRAM files.
        bam-head     Print the header of a SAM/BAM/CRAM file.
        bam-index    Index a SAM/BAM/CRAM file.
-       bam-rename   Rename the samples in a SAM/BAM/CRAM file.
+       bam-rename   Rename the sample in a SAM/BAM/CRAM file.
        bam-slice    Slice a SAM/BAM/CRAM file.
        bed-intxn    Find the intersection of two or more BED files.
        bed-sum      Summarize a BED file.
+       cov-concat   Concatenate TSV files containing depth of coverage data.
        fq-count     Count sequence reads in FASTQ files.
        fq-sum       Summarize a FASTQ file.
-       fuc-undetm   Compute top unknown barcodes using undertermined FASTQ from bcl2fastq.
        fuc-compf    Compare the contents of two files.
        fuc-demux    Parse the Reports directory from bcl2fastq.
        fuc-exist    Check whether certain files exist.
        fuc-find     Find all filenames matching a specified pattern recursively.
+       fuc-undetm   Compute top unknown barcodes using undertermined FASTQ from bcl2fastq.
        maf-maf2vcf  Convert a MAF file to a VCF file.
        maf-oncoplt  Create an oncoplot with a MAF file.
        maf-sumplt   Create a summary plot with a MAF file.
@@ -138,7 +139,7 @@ For getting help on the fuc CLI:
        vcf-filter   Filter a VCF file.
        vcf-merge    Merge two or more VCF files.
        vcf-rename   Rename the samples in a VCF file.
-       vcf-slice    Slice a VCF file for one or more specified regions.
+       vcf-slice    Slice a VCF file for specified regions.
        vcf-vcf2bed  Convert a VCF file to a BED file.
        vcf-vep      Filter a VCF file annotated by Ensembl VEP.