NEWS

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CNVfilteR 1.15.2

MINOR

• Fixed bug: CopyNumberPlots requires additional parameter

CNVfilteR 1.13.2

MINOR

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

CNVfilteR 1.13.1

MINOR

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

CNVfilteR 1.11.1

BUG FIXES

• 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.

CNVfilteR 1.7.4

MINOR

• Minor fix: removed ' from Vignette

CNVfilteR 1.7.3

SIGNIFICANT USER-VISIBLE CHANGES

• CNVfilteR specfically supports VCFs produced by Torrent Variant Caller

CNVfilteR 1.7.2

BUG FIXES

• Fixed: parsing some VCFs produced an unexpected error

MINOR

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

CNVfilteR 1.7.1

MINOR

• CITATION udpated

CNVfilteR 1.5.2

SIGNIFICANT USER-VISIBLE CHANGES

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

MINOR

• Added rmarkdown to Suggets in DESCRIPTION file

CNVfilteR 1.5.1

BUG FIXES

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

SIGNIFICANT USER-VISIBLE CHANGES

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

MINOR

• Minor vignette fixes
• Other minor fixes

CNVfilteR 1.1.6

SIGNIFICANT USER-VISIBLE CHANGES

• plotVariantsForCNV() allows multiple visual adjustements

MINOR

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

CNVfilteR 1.1.5

SIGNIFICANT USER-VISIBLE CHANGES

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

BUG FIXES

• 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.
• Certain SNV callers can produce SNV calls with more than two alt values (multiple alt alleles). These variants are now discarded.

CNVfilteR 1.1.4

SIGNIFICANT USER-VISIBLE CHANGES

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

BUG FIXES

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

CNVfilteR 1.1.3

BUG FIXES

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

CNVfilteR 1.1.2

SIGNIFICANT USER-VISIBLE CHANGES

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

BUG FIXES

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