Version: 1.8.0
Category: NEW FEATURES
Text: Add callGenotypes function for annotating a set of tallies with
        diploid genotype quality, likelihoods, etc in a way that is
        conformant with the gVCF spec. The methods are somewhat similar
        to those used by the GATK UnifiedGenotyper.

Version: 1.6.0
Category: NEW FEATURES
Text: Add pileupVariants function as an alternative to tallyVariants
        for computing nucleotide pileups using Rsamtools, instead of
        gmapR. In the future, this should allow VariantTools to become
        independent of gmapR, but the full variant statistics will only
        be available via tallyVariants.

Version: 1.6.0
Category: USER-VISIBLE CHANGES
Text: See the NEWS for gmapR to learn about changes to tallyVariants
        output.

Version: 1.4.0
Category: NEW FEATURES
Text: tallyVariants will now keep ref rows if variant_strand=0; this is
        useful for getting information when no alts are present (e.g.,
        for making wildtype calls). Better have a big cluster to do
        this over the whole genome.

Version: 1.4.0
Category: NEW FEATURES
Text: add a keep_extra_stats param to TallyVariantsParam; setting this
        to FALSE will speed things up when the extra stats are not
        needed.

Version: 1.4.0
Category: NEW FEATURES
Text: idVerify now supports VCF input like that output by GATK.

Version: 1.4.0
Category: NEW FEATURES
Text: callableFraction() now supports GRangesList and TranscriptDb.

Version: 1.4.0
Category: USER-VISIBLE CHANGES
Text: The API is now based on VRanges, a formal GRanges-derived class
        for representing variants; use of so-called "tally" or
        "variant" GRanges is deprecated.

Version: 1.4.0
Category: USER-VISIBLE CHANGES
Text: Disable proximity filter by default; we recommend this now only
        for whole genome calling.

Version: 1.4.0
Category: USER-VISIBLE CHANGES
Text: QA filtering is no longer a formal part of the calling pipeline;
        we recommend to apply QA filters "softly" via qaVariants() and
        use the results for diagnostics only.

Version: 1.4.0
Category: USER-VISIBLE CHANGES
Text: Use BiocParallel (BPPARAM argument) for tallyVariants

Version: 1.4.0
Category: USER-VISIBLE CHANGES
Text: VariantTallyParam deprecated; use TallyVariantsParam

Version: 1.4.0
Category: BUG FIXES
Text: idVerify now correctly computes cliques instead of connected
        components

Version: 1.4.0
Category: BUG FIXES
Text: use the total count, rather than the ref count when calculating
        the alt frequency

Version: 1.2.0
Category: NEW FEATURES
Text: Tally, call and export indels (using same algorithm as for SNVs).

Version: 1.2.0
Category: NEW FEATURES
Text: Add post-filter that discards variants that are clumped together
        on the chromosome (likely mapping errors).

Version: 1.2.0
Category: NEW FEATURES
Text: Add filter for masking regions like simple / low complexity
        repeats.

Version: 1.2.0
Category: NEW FEATURES
Text: Add a filter that performs a t-test on the alt vs. ref read
        positions.

Version: 1.2.0
Category: NEW FEATURES
Text: Add callWidtype() function for determining whether a position is
        variant, wildtype or uncallable, assuming the built-in variant
        calling filters. This is based on a power calculation that
        considers the coverage.

Version: 1.2.0
Category: NEW FEATURES
Text: Some functions for estimating concordance between samples have
        been added; these were developed for sample ID verification and
        should be considered experimental.

Version: 1.2.0
Category: NEW FEATURES
Text: matchVariants() utility for matching variants by pos and alt.

Version: 1.2.0
Category: USER-VISIBLE CHANGES
Text: The VCF output is now always in expanded form (one alt per row).
        The AD (allele depth) geno tag contains the REF and ALT counts,
        while AP (allele present) indicates presence of the REF and/or
        ALT allele. Besides the DP tag, all other tags were removed.
        These changes bring VariantTools more in line with GATK.

Version: 1.2.0
Category: USER-VISIBLE CHANGES
Text: Control alt and total counts are returned from
        callSampleSpecificVariants.

Version: 1.2.0
Category: BUG FIXES
Text: The power cutoff in the sample-specific algorithm was not
        considering the minimum alt read count filter.

Version: 1.0.0
Category: Initial release
Text: (start date: 12 September, 2012)