Version 1.8.0 ------------- Features: + The Python implementation of profile creation has been deprecated + SNV profiles are now stored as data frames, rather than GRanges objects + The `create_profile` function now now reads profiles into memory, instead of storing them on disk. De-duplication and removal of mitochondrial variants is now also performed at this stage + The `create_profiles` function now returns a list of data frames + A new function, `write_profile`, can write profiles to disk + The `read_profile` function now reads profiles without performing any de-duplication or removing mitochondrial chromosomes + The `compare_profiles`, `compare_many` and `list_variants` functions now converts input profiles to GRanges internally + Keep the FILTER column in created SNV profiles + Add a check for the creation of zero-variant profiles + Add a check for the existance of the specified input samples + Removal of non-standard chromosomes and variant de-duplication is now optional, and filtration documentation has been extended Version 1.6.0 ------------- Features: + Make the variant caller-specific filtering optional (on by default) and rename the relevant parameter names for increased clarity + Add a check to look for gVCF files as input, including the existance of alleles (common for gVCF files) + Add checks to see if input VCFs correctly contain DP, AD and GT data Version 1.4.0 ------------- Features: + Add convenience functions for creating and reading multiple SNV profiles + Add functionality for reading general COSMIC mutational data, not just cell line mutational data Fixes: + Fix an issue when reading COSMIC data due to new GRanges functionality Miscellaneous: + Update the citation info with the now-published seqCAT-specific article VERSION 1.2.0 ------------- Features: + Add functionality for analysing VCF files containing unannotated variants + Add functionality for listing non-overlapping variants between profiles + Mitochondrial variants can now be optionally skipped when reading SNV profiles in the `read_variants` function + Add the `list_variants` function for listing the genotypes of user-specified variants in each provided SNV profile + Add the `plot_variant_list` function for plotting a genotype grid for each variant output by the `list_variants` function Fixes: + Fix a multi-sample VCF profile creation issue (python only) + Reading zero-variant profiles now properly returns a GRanges object with a dummy-variant profile containing the sample name + Enable the `plot_impacts` function to properly analyse multi-impact SNVs + Fix reading of SNV profiles containing single-quoted strings VERSION 1.0.0 ------------- Features: + Create single nucleotide variant (SNV) profiles from RNA/DNA-seq samples + Characterise the biological equivalency and difference between samples + Evaluate putative impacts of SNVs differing between samples + Investigate and validate known variants and specific genomic regions + Authenticate cell lines with a known SNV profile or the COSMIC database