Sigprofilermatrixgenerator

Added
- Added support for processing SV input for VCF versions 4.1, 4.2, and 4.3. The tool now supports both the previous input format (requiring the first six columns and either the "svclass" column or the "strand1" & "strand2" columns) and VCF files.

Changed
- Updated the README command line examples to use CLI instead of calling the script directly.

Added
- Added environmental variable `SIGPROFILERMATRIXGENERATOR_VOLUME` to enhance configurability.
- Updated CLI to handle boolean arguments more effectively.

Changed
- Fixed `binomtest` to use the parameter `k` instead of `x` for improved accuracy and clarity.
- Updated Dockerfile to require SigProfilerMatrixGenerator version 1.2.27 (previously 1.2.25).
- Updated `numpy` dependency to require `numpy>=1.18.5,<2.0.0` to prevent compatibility issues with `numpy` 2.0.0.
- Removed incorrect print statement for the SV plot file path.

library(SigProfilerMatrixGeneratorR)
install_github("AlexandrovLab/SigProfilerMatrixGeneratorR")
library("devtools")
install_github("AlexandrovLab/SigProfilerMatrixGeneratorR")
install_github("AlexandrovLab/SigProfilerMatrixGeneratorR")
library("reticulate")