Spliceogen

-For variants within splice sites, a single probability value is now provided which reflects the variant's potential to disrupt the splice site, based on a logistic regression model trained on cancer-associated splice-altering variants (Shiraishi et al., 2019). The output file formats have been modified to accomodate the new scores.
-As well as VCFs, a simple tab-separated variant format is now accepted. A simplified "-input" is tag is accepted; the user no longer has to specify the variant file type. Deprecated v1.0 tags (-inputVCF and -inputBED) and BED inputs are still allowed.
-Gzipped VCF/TSV/GTF files are now accepted.
-Inconsistencies in chromosome nomenclature (eg. chrX and X) between the provided input FASTA/GTF/VCF/TSV files are now handled automatically, rather than requiring the user to edit files for consistency.
-A Reference allele check is now performed, to confirm that the specified reference allele matches the provided FASTA.