e2_cov_region in intron_retention output

[perllb]

• spladder version: 3.0.5
• Python version: 3.9
• Operating System: ubuntu

Description

According to these docs: https://spladder.readthedocs.io/en/latest/file_formats.html#output-files-build-mode Intron retention output file should contain e2_cov_region: fraction of positions in the intron that have a coverage > 0 However, my IR output files do not have this column.

What I Did

spladder build \
          --bams input.bam \
          --ase-edge-limit 200 \
          --annotation input.gtf \
          --outdir output \
          --readlen 150 \
          --confidence 1 \
          --event-types exon_skip,alt_3prime,alt_5prime,mult_exon_skip,intron_retention \
          --ignore-mismatches