Feature Request: Normalize by Splice Junction Count

[berntpopp]

Description:
Implement a normalization method for data based on splice junction counts. This will standardize the comparison of samples by accounting for differences in junction usage.

Tasks:

• Research and define the normalization method using splice junction counts.
• Implement the normalization in the relevant functions.
• Update any related output files to reflect normalized values.
• Test the normalization method with various datasets to ensure accuracy.

[berntpopp]

Partially resolved in v0.34.0 (Phase 15: Splice Junction Metadata). Phase 1 complete: splice junction count and exon count extracted from spliced alignment BAM CIGAR strings. Metadata stored in cDNA_positions.txt and summary.tsv. Displayed in single-sample and summary reports. Phase 2 (normalization using junction count) and Phase 3 (threshold recalibration) deferred to v0.35.0+.