SigProfilerMatrixGenerator Versions Save

What's Changed

• Upgrade to v1.2.26 by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/180

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.25...v1.2.26

What's Changed

• v1.2.25: Add rn7 and resolve custom install tsb_BED path issue by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/175

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.24...v1.2.25

What's Changed

• Update v1.2.24: Fix ebv matrix generation by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/174

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.23...v1.2.24

What's Changed

Added to CLI:

1. SV matrix generator
2. CNV matrix generator

Additional changes:

1. Added Dockerfile
2. Modified reference_paths to accept a volume

• Upgrade to v1.2.23 by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/173

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.22...v1.2.23

What's Changed

• v1.2.22: CLI installs reference genomes using the ReferenceGenomeMana… by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/170

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.21...v1.2.22

What's Changed

• Add ReferenceGenomeManager that: by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/169
• Remove benchmark script that was run in site-packages after a reference genome was installed

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.20...v1.2.21

What's Changed

• I161 by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/163

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.19...v1.2.20

What's Changed

• Remove chdir by @mdbarnesUCSD in https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/pull/157

Full Changelog: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/compare/v1.2.18...v1.2.19

Release Notes for v1.2.18

Enhancements

• New Command-Line Interface (CLI):

  • A new and intuitive CLI, SigProfilerMatrixGenerator_CLI.py, has been launched to facilitate user interactions.
  • This interface accommodates essential tasks such as install and matrix_generator.
  • Enhanced user control for saving/loading reference genomes with the addition of the volume parameter.

• Testing Improvements:

  • Introduced additional tests to better validate the functionalities and ensure more reliable outcomes.

Additional Updates

• File Naming Update: To resolve issues with CLI imports, SigProfilerMatrixGenerator.py has been renamed to MutationMatrixGenerator.py.

• Documentation Refinement: The README has been revised to include the CLI updates.

• Added a status badge to indicate the FTP server's uptime.

Limitations

• CLI and CNV/SV Support: Please note that the current version of the CLI does not support CNV/SV functionalities. We are actively working on this and will provide updates in future releases.

Stable version after releasing a series of hotfixes for compatibility across the SigProfiler suite of tools along with the support for additional reference genomes, custom genome installations, and offline genome installations.