New
- Simulate the intron retention process
- Simulate unspliced transcripts
- Handle novel isoform count matrix if an assembled GTF file is provided
- Model transcript truncation
Update
- Replaced the GTF parser function with the HTSeq reader module for improved flexibility
- Aligned reads to the transcriptome instead of the genome to model errors
- Enabled gzip compression for output files
Add
- Unit tests for principal functions
- Pipeline trace, timeline and Dag
Fix
- Resolved the PCR total reads issue
- Ensured the length_dis option is passed to the fetch_transcript_id_by_gene function