Changes in version 1.15.2
-------------------------


MINOR

    o Fixed bug: CopyNumberPlots requires additional parameter



Changes in version 1.13.2
-------------------------


MINOR

    o Fixed bug: sample name column in CNV calling file is always interpreted as character, which prevents later errors.




Changes in version 1.13.1
-------------------------


MINOR

    o Vignette: genome is explicitly shown as an option in loadVCFs()
    o Vignette: mutiallelic sites are not currently supported and bcftools can be used as workaround



Changes in version 1.11.1
-------------------------

BUG FIXES

    o Minor bug fixed: now loadVCFs() properly overwrites vcf and generates tabix files if temp dir is used. It prevents an unlikely but unwanted situation: when, in a same R session, a user updates VCF content without renaming it. In this case, file already existed and the new VCF/GZ file was not being used by CNVfilteR.



Changes in version 1.7.4
-------------------------


MINOR

    o Minor fix: removed ` from Vignette



Changes in version 1.7.3
-------------------------


SIGNIFICANT USER-VISIBLE CHANGES

    o CNVfilteR specfically supports VCFs produced by Torrent Variant Caller



Changes in version 1.7.2
-------------------------

BUG FIXES

    o Fixed: parsing some VCFs produced an unexpected error

MINOR

    o Minor bug fixed: stop message was not completely shown on loadSNPsFromVCF()



Changes in version 1.7.1
-------------------------

MINOR

    o CITATION udpated



Changes in version 1.5.2
-------------------------


SIGNIFICANT USER-VISIBLE CHANGES

    o loadCNVcalls() does not check cnvs.file names by default when loading (read.csv()) the cnvs.file
    o loadCNVcalls() allows optional check.names.cnvs.file parameter
    o Vignette updated


MINOR

    o Added rmarkdown to Suggets in DESCRIPTION file



Changes in version 1.5.1
-------------------------

BUG FIXES

    o Bug fixed: SNVs were not being correctly loaded after last Bioconductor update


SIGNIFICANT USER-VISIBLE CHANGES

    o plotVariantsForCNV() allows two new parameters for customize legend visualization
    o plotAllCNVs() allows 'genome' parameter to work with different genomes


MINOR

    o Minor vignette fixes
    o Other minor fixes




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
