feature request: Add support for introns in bed format

[bfairkun]

Thanks for this tool. I find my self wanting to quantify SplicingEfficiency of unannotated introns. I was wondering if there is any chance you would implement this, perhaps by accepting user defined list of target introns to quantify. This would be useful even if the target introns were only defined by coordinates and strand (without a gene/transcript id tag, as is required in gtf), so perhaps allowing the user to define target introns in bed format or something like it would be useful. I realize you have this filter level thing, which relies on the gtf exon annotations, so perhaps this would be most straightforward if it required --FilterLevel 1.
Best,
Ben

[ddpinto]

This would indeed be a very useful addition. Instead of using a GTF file as input, this option could take e.g. the SJ.out format generated by STAR to quantify splicing efficiency for all detected intron junctions regardless of whether they are annotated.