SQANTI-SIM 0.3.0

Added

• Include new R code in the evaluation module to use quant.file and compute key quantification performance metrics: Spearman Correlation Coefficient (SCC), Median Relative Difference (MRD), Normalized Root Mean Square Error (NRMSE), and Percentage of Expressed Transcripts (PET).
• Add conditional plot generation for true vs. estimated TPM, violin plot of relative differences, and an additional scatter plot.
• Added compatibility with PBSIM3 v3.0.5+, supporting BAM output from PBSIM3 simulations (#12).
• Added symbolic link for SQANTI3/cupcake.

Changed

• This commit updates the SQANTI3 version (now v5.2) used in the SQANTI-SIM pipeline to ensure compatibility and avoid the necessity of installing the Cupcake package. This change simplifies the setup process and reduces potential conflicts with other dependencies.
• Enhanced PBSIM3 simulation with robust handling of compressed/uncompressed output files.
• Standardized relative imports across cupcake modules for better package organization
• Better separation of concerns in report generation.

Fixed

• Fixed NanoSim single-threaded execution to avoid multiprocessing issues
• Updated ggplot2 syntax from deprecated ..count.. to after_stat(count) to avoid warnings.
• Fixed data filtering to include zero values (>= 0 instead of > 0).
• Added safety checks for radar charts to prevent errors when no data is available.
• Improved file existence checks and error messages.
• Added nanosim and pbsim3 to Conda environment dependencies.
• Fixed threading issues and import cleanup.