Changes in version 1.8.0
------------------------

NEW FEATURES

    o Support for off-target reads in copy number normalization and segmentation
    o Added mutation burden calculation
    o More robust mapping bias estimation
    o Added support for CNVkit coverage files (*.cnn, *.cnr)
    o IntervalFile.R can annotate targets with gene symbols and automatically
      convert chromosome naming styles
    o Better artifact filtering by using normalDB more efficiently
    o Support for mappability scores
    o Coverage calculation can now include duplicates 
    o calculateBamCoverageByInterval now provides fragment counts and 
      duplication rates
    o findBestNormal pooling now fragment count based, not coverage based  
    o Experimental support for GATK4
    o predictSomatic now reports posterior probabilites of minor segment copy
      numbers, flags segments if copy numbers are unreliable
    o Targets can be annotated with multiple gene symbols (comma separated)
    o Code cleanups (switch to GRanges where possible, switch to optparse in 
      command line tools)

API CHANGES

    o Due to novel optimizations of provided bait intervals, we highly recommend 
      to regenerate the interval files and normal databases and recalculate all 
      coverages from BAM files
    o New functions: annotateTargets, callMutationBurden
    o Defunct functions: createSNPBlacklist, getDiploid, autoCurateResults,
      readCoverageGatk
    o min.normals defaults to 2 (changed from 4) in setMappingBiasVcf
    o normalDB.min.coverage defaults to 0.25 (changed from 0.2) in filterTargets
    o log.ratio.calibration defaults to 0.1 (from 0.25) in runAbsoluteCN; now 
      relative to purity, not log-ratio noise
    o Removed gc.data from filterTargets since gc_bias is now added to tumor 
      coverage
    o dropped purecn.output from correctCoverageBias (no two-pass anymore)
    o Coverage.R argument --gatkcoverage renamed to --coverage
    o Dropped GC-normalization functionality in NormalDB, since this is 
      now conveniently done in Coverage.R
    o Renamed PureCN.R --outdir argument to --out. Can now specify a file
      prefix as in GATK. Filenames are thus not forced to sample id anymore.  
      If --out is a directory, it will behave like before and will use
      out/sampleid_suffix as filename.
 
