Atri Bhattacharya
650b23c155
Too many changes to list, for details see included NEWS file or https://github.com/samtools/bcftools/releases/tag/1.21 - Update to version 1.20: Too many changes to list, for details see included NEWS file or https://github.com/samtools/bcftools/releases/tag/1.20 OBS-URL: https://build.opensuse.org/package/show/science/bcftools?expand=0&rev=21
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-------------------------------------------------------------------
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Fri Mar 28 10:56:23 UTC 2025 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
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- Update to version 1.21:
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Too many changes to list, for details see included NEWS file or
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https://github.com/samtools/bcftools/releases/tag/1.21
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- Update to version 1.20:
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Too many changes to list, for details see included NEWS file or
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https://github.com/samtools/bcftools/releases/tag/1.20
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-------------------------------------------------------------------
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Wed Jan 3 01:50:42 UTC 2024 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
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- Update to version 1.19
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Too many changes to list, for details see
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https://github.com/samtools/bcftools/releases/tag/1.19
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- Update to version 1.18
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Too many changes to list, for details see
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https://github.com/samtools/bcftools/releases/tag/1.18
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- Update to version 1.17
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Too many changes to list, for details see
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https://github.com/samtools/bcftools/releases/tag/1.17
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-------------------------------------------------------------------
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Fri Aug 26 22:11:10 UTC 2022 - Jan Engelhardt <jengelh@inai.de>
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- Update to release 1.16
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* New plugin `bcftools +variant-distance` to annotate records
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with distance to the nearest variant.
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* The -i/-e filtering expression gained support for multiple
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filters, e.g. `-i FILTER="A;B"`.
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- Resolve "file packaged twice" rpmlint warnings
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-------------------------------------------------------------------
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Thu Apr 21 15:34:00 UTC 2022 - Ferdinand Thiessen <rpm@fthiessen.de>
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- Update to version 1.15.1
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* bcftools annotate: New -H, --header-line convenience option to
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pass a header line on command line
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* bcftools csq: A list of consequence types supported by bcftools
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csq has been added to the manual page.
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* bcftools +fill-tags:
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* Extend generalized functions so that FORMAT tags can be filled
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as well
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* Allow multiple custom functions in a single run.
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* bcftools norm:
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* Fix an assertion failure triggered when a faulty VCF file with
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a '-' character in the REF allele was used with bcftools
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norm --atomize.
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* Fix the loss of phasing in half-missing genotypes in variant
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atomization
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* bcftools roh: Fix a bug that could result in an endless loop or
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incorrect AF estimate when missing genotypes are present and
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the --estimate-AF - option was used
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* bcftools +split-vep: VEP fields with characters disallowed in
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VCF tag names by the specification couldn't be queried.
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- Update to version 1.15
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* New bcftools head subcommand for conveniently displaying the
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headers of a VCF or BCF file.
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* The -T, --targets-file option had the following bug originating
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in HTSlib code
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* bcftools annotate:
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* In addition to --rename-annots, which requires a file with
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name mappings, it is now possible to do the same on the
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command line -c NEW_TAG:=OLD_TAG
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* Add new option --min-overlap which allows to specify the
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minimum required overlap of intersecting regions
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* Allow to transfer ALT from VCF with or without replacement
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* bcftools convert:
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* Revamp of --gensample, --hapsample and --haplegendsample
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family of options
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* New --3N6 option to output/input the new version of the .gen
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file format
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* Deprecate the --chrom option in favor of --3N6.
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* The CHROM:POS_REF_ALT IDs which are used to detect strand
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swaps are required and must appear either in the "SNP ID"
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column or the "rsID" column.
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* bcftools csq: Allow GFF files with phase column unset
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* bcftools filter: New --mask, --mask-file and --mask-overlap
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options to soft filter variants in regions
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* bcftools +fixref
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* The -m id option now works also for non-dbSNP ids
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* New -m flip-all mode for flipping all sites
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* bcftools isec: Prevent segfault on sites filtered with -i/-e
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in all files
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* bcftools mpileup: More flexible read filtering using the options
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* bcftools query: Make the --samples and --samples-file options
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work also in the --list-samples mode.
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* bcftools +setGT: Fix a bug in -t q -e EXPR logic applied on
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FORMAT fields, sites with all samples failing the expression
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EXPR were incorrectly skipped.
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* bcftools sort: make use of the TMPDIR environment variable
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when defined
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* bcftools +trio-dnm2: The --use-NAIVE mode now also adds the
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de novo allele in FORMAT/VA
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- Update to version 1.14
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* New --regions-overlap and --targets-overlap options which
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address a long-standing design problem with subsetting VCF
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files by region.
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* The --output-type option can be used to override the default
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compression level
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* bcftools annotate:
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* when --set-id and --remove are combined, --set-id cannot use
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tags deleted by --remove.
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* while non-symbolic variation are uniquely identified by
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POS,REF,ALT, symbolic alleles starting at the same position
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were indistinguishable.
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* add a new . modifier to control whether missing values should
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be carried over from a tab-delimited file or not.
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* bcftools +check-ploidy: by default missing genotypes are not
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used when determining ploidy.
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* bcftools concat: new --ligate-force and --ligate-warn options
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for finer control of -l, --ligate behavior in imperfect overlaps.
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* bcftools consensus: Apply mask even when the VCF has no notion
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about the chromosome.
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* bcftools +contrast: support for chunking within map/reduce
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framework allowing to collect NASSOC counts even for empty
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case/control sample sets
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* bcftools csq:
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* bug fix, compound indels were not recognised in some cases
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* compound variants were incorrectly marked as 'inframe' even when
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stop codon would occur before the frame was restored
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* bug fix, FORMAT/BCSQ bitmasks could have been assigned incorrectly
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to some samples at multiallelic sites, a superset of the correct
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consequences would have been set
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* bug fix, the upstream stop could be falsely assigned to all samples
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in a multi-sample VCF even if the stop was relevant for a single
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sample only
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* further improve the detection of mismatching chromosome naming
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(e.g. "chrX" vs "X") in the GFF, VCF and fasta files
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* bcftools merge: keep (sum) INFO/AN,AC values when merging VCFs
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with no samples
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* bcftools mpileup: new --indel-size option which allows to increase
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the maximum considered indel size considered, large deletions in
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long read data are otherwise lost.
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* bcftools norm:
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* atomization now supports Number=A,R string annotations
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* assign as many alternate alleles to genotypes at multiallelic
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sites in the-m + mode, disregarding the phase.
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* bcftools sort: increase accuracy of the --max-mem option limit,
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previously the limit could be exceeded by more than 20%
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* bcftools +trio-dnm: new --with-pAD option to allow processing of
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VCFs without FORMAT/QS.
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* bcftools view: the functionality of the option --compression-level
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lost in 1.12 has been restored
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- Update to version 1.13
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* bcftools annotate:
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* Fix rare a bug when INFO/END is present, all INFO fields are
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removed with bcftools annotate -x INFO and BCF output is produced.
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* Support for matching annotation line by ID, in addition to
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CHROM,POS,REF, and ALT
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* bcftools csq:
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* When GFF and VCF/fasta use a different chromosome naming convention
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no consequences would be added.
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* Parametrize brief-predictions parameter to allow explicit number
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of amino acids to be printed.
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* bcftools +fill-tags:
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* Generalization and better support for custom functions that allow
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adding new INFO tags based on arbitrary -i, --include type of expressions.
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* When FORMAT/GT is not present, the INFO/AF tag will be newly
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calculated from INFO/AC and INFO/AN.
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* bcftools gtcheck:
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* Switch between FORMAT/GT or FORMAT/PL when one is (implicitly)
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requested but only the other is available
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* Improve diagnostics, printing warnings when a line cannot be
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matched and the number of lines skipped for various reasons
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* bcftools index: The program now accepts both data file name and
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the index file name.
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* bcftools isec: Always generate sites.txt with isec -p
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* bcftools +mendelian: Consider only complete trios,
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do not crash on sample name typos
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* bcftools mpileup:
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* New --seed option for reproducibility of subsampling code in HTSlib
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* The SCR annotation which shows the number of soft-clipped reads
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now correctly pools reads together regardless of the variant type.
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* Major revamp of BAQ.
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* Modified scale of Mann-Whitney U tests.
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Newly INFO/*Z annotations will be printed
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* bcftools norm:
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* Fix Type=Flag output in norm --atomize
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* Atomization must not discard ALT=. records
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* Atomization of AD and QS tags now correctly updates occurrences
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of duplicate alleles within different haplotypes
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* Fix a bug in atomization of Number=A,R tags
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* bcftools reheader: Add -T, --temp-prefix option
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* bcftools +setGT: A wider range of genotypes can be set by the
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plugin by allowing specifying custom genotypes.
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* bcftools +split-vep:
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* New -u, --allow-undef-tags option
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* Better handling of ambiguous keys such as INFO/AF and CSQ/AD.
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* Some consequence field names may not constitute a valid tag name,
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such as "pos(1-based)".
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* bcftools +tag2tag: New --QR-QA-to-QS option to convert annotations
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generated by Freebayes to QS used by BCFtools
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* bcftools +trio-dnm:
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* Add support for sites with more than four alleles.
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* New --use-NAIVE option for a naive DNM calling based solely on
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FORMAT/GT and expected Mendelian inheritance.
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* Fix behaviour to match the documentation, the --dnm-tag DNG option
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now correctly outputs log scaled values by default, not phred scaled.
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* Fix bug in VAF calculation, homozygous de novo variants were
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incorrectly reported as having VAF=50%
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* Fix arithmetic underflow which could lead to imprecise scores
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and improve sensitivity in high coverage regions
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* Allow combining --pn and --pns to set the noise thresholds independently
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- Rebased use_python3.patch
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- Drop python3 and perl build requirements, not needed, shbang of
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executables can be patched anyway.
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-------------------------------------------------------------------
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Fri May 14 10:42:08 UTC 2021 - Ferdinand Thiessen <rpm@fthiessen.de>
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- Update to version 1.12
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* The output file type is determined from the output file name
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suffix, where available, so the -O/--output-type option is often
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no longer necessary.
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* Make F_MISSING in filtering expressions work for sites with
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multiple ALT alleles
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* Fix N_PASS and F_PASS to behave according to expectation when
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reverse logic is used (#1397). This fix has the side effect of
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query (or programs like +trio-stats) behaving differently with
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these expressions, operating now in site-oriented rather than
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sample-oriented mode.
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* bcftools annotate:
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* New --rename-annots option to help fix broken VCFs
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* New -C option allows to read a long list of options from a file
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to prevent very long command lines.
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* New append-missing logic allows annotations to be added for
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each ALT allele in the same order as they appear in the VCF.
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* bcftools concat:
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* Do not phase genotypes by mistake if they are not already
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phased with -l
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* bcftools consensus:
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* New --mask-with, --mark-del, --mark-ins, --mark-snv options
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* Symbolic <DEL> should have only one REF base. If there are
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multiple, take POS+1 as the first deleted base.
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* Make consensus work when the first base of the reference genome
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is deleted.
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* bcftools +contrast:
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* The NOVELGT annotation was previously not added when requested.
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* bcftools convert:
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* Make the --hapsample and --hapsample2vcf options consistent with
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each other and with the documentation.
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* bcftools call:
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* Revamp of call -G, previously sample grouping by population was
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not truly independent and could still be influenced by the
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presence of other sample groups.
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* Optional addition of INFO/PV4 annotation with call -a INFO/PV4
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* Remove generation of useless HOB and ICB annotation;
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use +fill-tags -- -t HWE,ExcHet instead
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* The call -f option was renamed to -a to (1) make it consistent
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with mpileup and (2) to indicate that it includes both INFO and
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FORMAT annotations
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* bcftools csq:
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* Fix a bug wich caused incorrect FORMAT/BCSQ formatting at sites
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with too many per-sample consequences
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* Fix a bug which incorrectly handled the --ncsq parameter and
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could clash with reserved BCF values, consequently producing
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truncated or even incorrect output of the %TBCSQ formatting
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expression in bcftools query.
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* bcftools +fill-tags:
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* MAF definition revised for multiallelic sites, the second most
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common allele is considered to be the minor allele
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* New FORMAT/VAF, VAF1 annotations to set the fraction of
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alternate reads provided FORMAT/AD is present
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* bcftools gtcheck:
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* support matching of a single sample against all other samples
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in the file with -s qry:sample -s gt:-.
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* bcftools merge:
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* Make merge -R behavior consistent with other commands and pull
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in overlapping records with POS outside of the regions
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* Bug fix
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* bcftools mpileup:
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* Add new optional tag mpileup -a FORMAT/QS
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* bcftools norm:
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* New -a, --atomize functionality to decompose complex variants,
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for example MNVs into consecutive SNVs
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* New option --old-rec-tag to indicate the original variant
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* bcftools query:
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* Incorrect fields were printed in the per-sample output when
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subset of samples was requested via -s/-S and the order of
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samples in the header was different from the requested -s/-S order
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* bcftools +prune:
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* New options --random-seed and --nsites-per-win-mode
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* bcftools +split-vep:
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* Transcript selection now works also on the raw CSQ/BCSQ annotation.
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* Bug fix, samples were dropped on VCF input and VCF/BCF output
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* bcftools stats:
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* Changes to QUAL and ts/tv plotting stats: avoid capping QUAL to
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predefined bins, use an open-range logarithmic binning instead
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* plot dual ts/tv stats: per quality bin and cumulative as if
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threshold applied on the whole dataset
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* bcftools +trio-dnm2:
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* Major revamp of +trio-dnm plugin, which is now deprecated
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and replaced by +trio-dnm2.
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* The original trio-dnm calling model used genotype likelihoods
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(PLs) as the input for calling.
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* This new version also implements the DeNovoGear model.
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* For more details see http://samtools.github.io/bcftools/trio-dnm.pdf
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- Update use_python3.patch
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-------------------------------------------------------------------
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Thu May 13 00:53:30 UTC 2021 - Ferdinand Thiessen <rpm@fthiessen.de>
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- Update to version 1.11
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* Breaking change in -i/-e expressions on the FILTER column.
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The new behaviour is:
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Expression Result
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FILTER="A" Exact match, for example "A;B" does not pass
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FILTER!="A" Exact match, for example "A;B" does pass
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FILTER~"A" Both "A" and "A;B" pass
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FILTER!~"A" Neither "A" nor "A;B" pass
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* Fix in commutative comparison operators, in some cases reversing
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sides would produce incorrect results
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* Better support for filtering on sample subsests
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* bcftools annotate:
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* Previously it was not possible to use --columns =TAG with INFO
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tags and the --merge-logic feature was restricted to tab files
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with BEG,END columns, now extended to work also with REF,ALT.
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* Make annotate -TAG/+TAG work also with FORMAT fields.
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* ID and FILTER can be transferred to INFO and ID can be populated
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from INFO.
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* bcftools consensus:
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* Fix in handling symbolic deletions and overlapping variants.
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* Fix --iupac-codes crash on REF-only positions with ALT=".".
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* Fix --chain crash
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* Preserve the case of the genome reference.
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* Add new -a, --absent option which allows to set positions with
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no supporting evidence to "N" (or any other character).
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* bcftools convert:
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* The option --vcf-ids now works also with -haplegendsample2vcf.
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* New option --keep-duplicates
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* bcftools csq:
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* Add misc/gff2gff.py script for conversion between various
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flavors of GFF files. The initial commit supports only one type
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* Add missing consequence types.
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* Allow overlapping CDS to support ribosomal slippage.
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* bcftools +fill-tags:
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* Added new annotations: INFO/END, TYPE, F_MISSING.
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* bcftools filter:
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* Make --SnpGap optionally filter also SNPs close to other variant
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types.
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* bcftools gtcheck:
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* Complete revamp of the command. The new version is faster and allows
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N:M sample comparisons, not just 1:N or NxN comparisons. Some
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functionality was lost (plotting and clustering) but may be added back
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on popular demand.
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* bcftools +mendelian:
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* Revamp of user options, output VCFs with mendelian errors annotation,
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read PED files
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* bcftools merge:
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* Update headers when appropriate with the '--info-rules *:join'
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INFO rule.
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* Local alleles merging that produce LAA and LPL when requested, a
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draft implementation of samtools/hts-specs#434
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* New --no-index which allows to merge unindexed files.
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* Fixes in gVCF merging.
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* bcftools norm:
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* Fixes in --check-ref s reference setting features with non-ACGT bases.
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* New --keep-sum switch to keep vector sum constant when splitting
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multiallelics.
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* bcftools +prune:
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* Extend to allow annotating with various LD metrics: r^2, Lewontin's D'
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* bcftools query:
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* New %N_PASS() formatting expression to output the number of samples
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that pass the filtering expression.
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* bcftools reheader:
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* Improved error reporting to prevent user mistakes.
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* bcftools roh:
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* The --AF-file description incorrectly suggested "REF\tALT"
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instead of the correct "REF,ALT".
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* RG lines could have negative length.
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* new --include-noalt option to allow also ALT=. records.
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* bcftools scatter:
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* New plugin intended as a convenient inverse to concat
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* bcftools +split:
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* New --groups-file option for more flexibility of defining
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desired output
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* New --hts-opts option to reduce required memory by reusing
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one output
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header and allow overriding the default hFile's block size
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* Add support for multisample output and sample renaming
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* bcftools +split-vep:
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* Add default types (Integer, Float, String) for VEP subfields
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and make --columns - extract all subfields into INFO tags
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in one go.
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-------------------------------------------------------------------
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Tue Feb 25 11:46:58 UTC 2020 - Pierre Bonamy <flyos@mailoo.org>
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- Changed python dependencies from python3 to python3-base and
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python3-matplotlib
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-------------------------------------------------------------------
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Wed Feb 12 15:10:09 UTC 2020 - Todd R <toddrme2178@gmail.com>
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- Add use_python3.patch to switch from python2 to python3
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-------------------------------------------------------------------
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Wed Feb 5 19:01:01 UTC 2020 - Todd R <toddrme2178@gmail.com>
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- Update to 1.10.2
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* This release fixes crashes reported on files including integer
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INFO tags with values outside the range officially supported
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by VCF. It also fixes a bug where invalid BCF files would be
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created if such values were present.
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- Update to 1.10.0
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+ Numerous bug fixes, usability improvements and sanity checks were added to prevent common user errors.
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+ The -r, --regions (and -R, --regions-file) option should never create unsorted VCFs or duplicates records again. This also fixes rare cases where a spanning deletion makes a subsequent record invisible to bcftools isec and other commands.
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+ Additions to filtering and formatting expressions
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* support for the spanning deletion alternate allele (ALT=*)
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* new ILEN filtering expression to be able to filter by indel length
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* new MEAN, MEDIAN, MODE, STDEV, phred filtering functions
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* new formatting expression %PBINOM (phred-scaled binomial probability), %INFO (the whole INFO column), %FORMAT (the whole FORMAT column), %END (end position of the REF allele), %END0 (0-based end position of the REF allele), %MASK (with multiple files indicates the presence of the site in other files)
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+ New plugins
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* +gvcfz: compress gVCF file by resizing gVCF blocks according to specified criteria
|
|
* +indel-stats: collect various indel-specific statistics
|
|
* +parental-origin: determine parental origin of a CNV region
|
|
* +remove-overlaps: remove overlapping variants.
|
|
* +split-vep: query structured annotations such INFO/CSQ created by bcftools/csq or VEP
|
|
* +trio-dnm: screen variants for possible de-novo mutations in trios
|
|
+ annotate
|
|
* new -l, --merge-logic option for combining multiple overlapping regions
|
|
+ call
|
|
* new bcftools call -G, --group-samples option which allows grouping samples into populations and applying the HWE assumption within but not across the groups.
|
|
+ csq
|
|
* significant reduction of memory usage in the local -l mode for VCFs with thousands of samples and 20% reduction in the non-local haplotype-aware mode.
|
|
* fixes a small memory leak and formatting issue in FORMAT/BCSQ at sites with many consequences
|
|
* do not print protein sequence of start_lost events
|
|
* support for "start_retained" consequence
|
|
* support for symbolic insertions (ALT="<INS...>"), "feature_elongation" consequence
|
|
* new -b, --brief-predictions option to output abbreviated protein predictions.
|
|
+ concat
|
|
* the --naive command now checks header compatibility when concatenating multiple files.
|
|
+ consensus
|
|
* add a new -H, --haplotype 1pIu/2pIu feature to output first/second allele for phased genotypes and the IUPAC code for unphased genotypes
|
|
* new -p, --prefix option to add a prefix to sequence names on output
|
|
+ +contrast
|
|
* added support for Fisher's test probability and other annotations
|
|
+ +fill-from-fasta
|
|
* new -N, --replace-non-ACGTN option
|
|
+ +dosage
|
|
* fix some serious bugs in dosage calculation
|
|
+ +fill-tags
|
|
* extended to perform simple on-the-fly calculations such as calculating INFO/DP from FORMAT/DP.
|
|
+ merge
|
|
* add support for merging FORMAT strings
|
|
* bug fixed in gVCF merging
|
|
+ mpileup
|
|
* a new optional SCR annotation for the number of soft-clipped reads
|
|
+ reheader
|
|
* new -f, --fai option for updating contig lines in the VCF header
|
|
+ +trio-stats
|
|
* extend output to include DNM homs and recurrent DNMs
|
|
+ VariantKey support
|
|
|
|
-------------------------------------------------------------------
|
|
Thu Sep 6 08:43:05 UTC 2018 - flyos@mailoo.org
|
|
|
|
- Update to 1.9
|
|
* `annotate`
|
|
- REF and ALT columns can be now transferred from the annotation
|
|
file.
|
|
- fixed bug when setting vector_end values.
|
|
* `consensus`
|
|
- new -M option to control output at missing genotypes
|
|
- variants immediately following insersions should not be skipped.
|
|
Note however, that the current fix requires normalized VCF and may
|
|
still falsely skip variants adjacent to multiallelic indels.
|
|
- bug fixed in -H selection handling
|
|
* `convert`
|
|
- the --tsv2vcf option now makes the missing genotypes diploid,
|
|
"./." instead of "."
|
|
- the behavior of -i/-e with --gvcf2vcf changed. Previously only
|
|
sites with FILTER set to "PASS" or "." were expanded and the -i/-e
|
|
options dropped sites completely. The new behavior is to let the -i/-e
|
|
options control which records will be expanded. In order to drop
|
|
records completely, one can stream through "bcftools view" first.
|
|
* `csq`
|
|
- since the real consequence of start/splice events are not known,
|
|
the aminoacid positions at subsequent variants should stay unchanged
|
|
- add `--force` option to skip malformatted transcripts in GFFs
|
|
with out-of-phase CDS exons.
|
|
* `+dosage`: output all alleles and all their dosages at multiallelic
|
|
sites
|
|
* `+fixref`: fix serious bug in -m top conversion
|
|
* `-i/-e` filtering expressions:
|
|
- add two-tailed binomial test
|
|
- add functions N_PASS() and F_PASS()
|
|
- add support for lists of samples in filtering expressions, with
|
|
many samples it was impractical to list them all on the command line.
|
|
Samples can be now in a file as, e.g., GT[@samples.txt]="het"
|
|
- allow multiple perl functions in the expressions and some bug
|
|
fixes
|
|
- fix a parsing problem, '@' was not removed from '@filename'
|
|
expressions
|
|
* `mpileup`: fixed bug where, if samples were renamed using the `-G`
|
|
(`--read-groups`) option, some samples could be omitted from the
|
|
output file.
|
|
* `norm`: update INFO/END when normalizing indels
|
|
* `+split`: new -S option to subset samples and to use custom file
|
|
names instead of the defaults
|
|
* `+smpl-stats`: new plugin
|
|
* `+trio-stats`: new plugin
|
|
* Fixed build problems with non-functional configure script produced
|
|
on some platforms
|
|
|
|
-------------------------------------------------------------------
|
|
Thu Jul 12 08:58:12 UTC 2018 - flyos@mailoo.org
|
|
|
|
- Cleaned spec file using spec-cleaner
|
|
- Update to 1.8
|
|
* `-i, -e` filtering: Support for custom perl scripts
|
|
* `+contrast`: New plugin to annotate genotype differences between groups of samples
|
|
* `+fixploidy`: New options for simpler ploidy usage
|
|
* `+setGT`: Target genotypes can be set to phased by giving `--new-gt p`
|
|
* `run-roh.pl`: Allow to pass options directly to `bcftools roh`
|
|
* Number of bug fixes
|
|
* `-i, -e` filtering: Major revamp, improved filtering by FORMAT fields
|
|
and missing values. New GT=ref,alt,mis etc keywords, check the documenation
|
|
for details.
|
|
* `query`: Only matching expression are printed when both the -f and -i/-e
|
|
expressions contain genotype fields. Note that this changes the original
|
|
behavior. Previously all samples were output when one matching sample was
|
|
found. This functionality can be achieved by pre-filtering with view and then
|
|
streaming to query. Compare
|
|
bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]' -i'GT="alt"' file.bcf
|
|
and
|
|
bcftools view -i'GT="alt"' file.bcf -Ou | bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]'
|
|
* `annotate`: New -k, --keep-sites option
|
|
* `consensus`: Fix --iupac-codes output
|
|
* `csq`: Homs always considered phased and other fixes
|
|
* `norm`: Make `-c none` work and remove `query -c`
|
|
* `roh`: Fix errors in the RG output
|
|
* `stats`: Allow IUPAC ambiguity codes in the reference file; report the number of missing genotypes
|
|
* `+fill-tags`: Add ExcHet annotation
|
|
* `+setGt`: Fix bug in binom.test calculation, previously it worked only for nAlt<nRef!
|
|
* `+split`: New plugin to split a multi-sample file into single-sample files in one go
|
|
* Improve python3 compatibility in plotting scripts
|
|
* New `sort` command.
|
|
* New options added to the `consensus` command. Note that the `-i, --iupac`
|
|
option has been renamed to `-I, --iupac`, in favor of the standard
|
|
`-i, --include`.
|
|
* Filtering expressions (`-i/-e`): support for `GT=<type>` expressions and
|
|
for lists and ranges (#639) - see the man page for details.
|
|
* `csq`: relax some GFF3 parsing restrictions to enable using Ensembl
|
|
GFF3 files for plants (#667)
|
|
* `stats`: add further documentation to output stats files (#316) and
|
|
include haploid counts in per-sample output (#671).
|
|
* `plot-vcfstats`: further fixes for Python3 (@nsoranzo, #645, #666).
|
|
* `query` bugfix (#632)
|
|
* `+setGT` plugin: new option to set genotypes based on a two-tailed binomial
|
|
distribution test. Also, allow combining `-i/-e` with `-t q`.
|
|
* `mpileup`: fix typo (#636)
|
|
* `convert --gvcf2vcf` bugfix (#641)
|
|
* `+mendelian`: recognize some mendelian inconsistencies that were
|
|
being missed (@oronnavon, #660), also add support for multiallelic
|
|
sites and sex chromosomes.
|
|
|
|
-------------------------------------------------------------------
|
|
Mon Jul 10 21:28:20 UTC 2017 - flyos@mailoo.org
|
|
|
|
- Update to 1.5
|
|
- Fixed some runtime dependencies (perl and python-matplotlib)
|
|
|
|
-------------------------------------------------------------------
|
|
Sun May 22 09:16:49 UTC 2016 - flyos@mailoo.org
|
|
|
|
- Initial release
|