Sigprofilermatrixgenerator

Fixed
- SV Matrix generation compatibility: Updated remnant Pandas and NumPy < 2.0.0 syntax to ensure compatibility with newer versions.
- Indexing error in reference genome handling: Edge cases where BED file indices extended beyond the reference genome range caused crashes. Index accesses are now restricted to valid ranges, and cases where the genomic context extends beyond valid positions are skipped.
- Uninitialized variable: The dinuc_mat variable was accessed before being initialized, causing a runtime error. It is now explicitly initialized to None before use.

Changed
- Updated dependencies: Now requires **Pandas >= 2.0.0**, **NumPy >= 2.0.0**, and **Python >= 3.9**.
- Dropped support for **Python 3.8**

Fixed
- Resolved a bug where DBS and ID matrices were not being returned due to an indentation issue when the parameter 'chrom_based' was set as True.

Notice
- Python 3.8 support will be phased out in future updates as we align with Python's ongoing release cycle. Users on Python 3.8 are encouraged to consider upgrading to Python 3.9 or newer.

Fixed
- Resolved a bug that caused the code to crash when running with `exome=True` during INDEL processing. The issue was due to incorrect indentation.

Added
- Added sort function to handle non-sorted input and BED files. This posed as an issue for when the BED file was not sorted by chromosome and start position in cases when certain reference genomes were used because of roman numerals and decimal (ie ChrX vs chr10).

Changed
- Transcript files were modified to adopt the new sorting standard.

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.