File bcftools.changes of Package bcftools

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File bcftools.changes of Package bcftools (Revision 85e10cab0cbbfafaa17713299707285e)

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Wed Feb  5 19:01:01 UTC 2020 - Todd R <toddrme2178@gmail.com>

- Update to 1.10.2
  * This release fixes crashes reported on files including integer
    INFO tags with values outside the range officially supported
    by VCF. It also fixes a bug where invalid BCF files would be
    created if such values were present.
- Update to 1.10.0
  + Numerous bug fixes, usability improvements and sanity checks were added to prevent common user errors.
  + 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.
  + Additions to filtering and formatting expressions
    * support for the spanning deletion alternate allele (ALT=*)
    * new ILEN filtering expression to be able to filter by indel length
    * new MEAN, MEDIAN, MODE, STDEV, phred filtering functions
    * 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)
  + New plugins
    * +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

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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

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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.

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Mon Jul 10 21:28:20 UTC 2017 - flyos@mailoo.org

- Update to 1.5
- Fixed some runtime dependencies (perl and python-matplotlib)

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Sun May 22 09:16:49 UTC 2016 - flyos@mailoo.org

- Initial release

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