CHANGES IN VERSION 1.2.0
-----------------------

NEW FEATURES

    o Tally, call and export indels (using same algorithm as for SNVs).
    
    o Add post-filter that discards variants that are clumped
      together on the chromosome (likely mapping errors).

    o Add filter for masking regions like simple / low complexity repeats.

    o Add a filter that performs a t-test on the alt vs. ref read positions.
      
    o 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.

    o Some functions for estimating concordance between samples have
      been added; these were developed for sample ID verification and
      should be considered experimental.
    
    o matchVariants() utility for matching variants by pos and alt.

USER-VISIBLE CHANGES

    o 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.

    o Control alt and total counts are returned from callSampleSpecificVariants.
                  
BUG FIXES

    o The power cutoff in the sample-specific algorithm was not
      considering the minimum alt read count filter.

CHANGES IN VERSION 1.0.0
-----------------------

Initial release

(start date: 12 September, 2012)