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