[Bug]: The processByBam now is always TRUE in single cell mode

[SuiYue-2308]

Affected Area

Transcript Discovery

Issue Description

The processByBam is always TRUE in single cell more. In future it should be removed from the parameters and we always process by each bam file.

Minimal Reproducible Example (R Code)

se <- bambu(reads = single_cell_test.bam, annotations = bambuAnnotations, genome = fa.file, demultiplexed = TRUE, processByBam = FALSE)

Input Data Details

Reproducibility

Always (every time I run this)

Session Info

Contribution

• I can provide a small public dataset/toy example for reproduction.

Checklist

• I searched existing issues to avoid duplicates.
• I included a minimal reproducible code snippet.
• I included session/environment information.