Changes in version 1.1.6
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o plotVariantsForCNV() allows multiple visual adjustements


MINOR

    o Added error control in loadVCFs(): heterozygous.range and homozygous.range cannot overlap



Changes in version 1.1.5
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Added ignore.unexpected.rows parameter to loadCNVcalls() function to ignore CNV calls which deletion/duplication value is not the expected one.


BUG FIXES

    o Some SNV callers can produce calls with a genotype indicating that the variant actually was not found. Variants with GTs like "0/0 ./. 1/0" are now discarded.
    o Certain SNV callers can produce SNV calls with more than two alt values (multiple alt alleles). These variants are now discarded.



Changes in version 1.1.4
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Improved CNVfilteR accuracy. margin.pct parameter was added to filterCNVs() and ht.deletions.threshold default value was modified to 30.
    o Loading variants process optimized (multiple times faster)
    o filterCNVs() function optimized
    o min.total.depth default value modified to 10
    o Added multiple modifications to the vignette


BUG FIXES

    o Fixed bug when plotting a CNV with no SNV variants falling in it



Changes in version 1.1.3
-------------------------

BUG FIXES

    o Fixed bug when processing variants in the limits of heterozygous.range and heterozygous.range



Changes in version 1.1.2
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Added sample.name parameter to loadCNVcalls() function to allow explicitly setting sample name
    o deletion and duplication parameters can be vectors in loadCNVcalls() function, so multiple values are allowed


BUG FIXES
    o Fixed bug happening in loadSNPsFromVCF() when ref and alt support was 0
    o Fixed bug when processing list.support.field in loadSNPsFromVCF()
    o Added error control when allele frequency is not numeric
    o Minor fixes