Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

[1.2.31] - 2024-11-6

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.

[1.2.30] - 2024-10-10

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.

[1.2.29] - 2024-09-24

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.

[1.2.28] - 2024-08-06

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.

[1.2.27] - 2024-07-18

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.