Repair Split-Read Exon-Overlap Filtering
You are working with a pinned BEDTools source snapshot used in an RNA-seq quality-control workflow.
The workflow asks which aligned reads have enough support inside annotated exons. A junction-spanning alignment is visible when the analysis accepts any exonic contact, but it disappears when the documented fractional-overlap filter is enabled. A comparable contiguous alignment remains present. This changes the count of biologically valid spliced reads even though the input records are well-formed and sorted consistently.
Inspect the source's format handling, public fixtures, and reproduction. Repair the implementation so discontinuous genomic records are handled consistently with the documented interval semantics. Preserve ordinary non-split intersection behavior and unrelated command-line behavior.
Your repair must be general. Do not hard-code the public coordinates, record names, chromosome, threshold, block count, option order, or output mode.
Run the public reproduction with:
python reproduce.py
The verifier will build the repaired source and exercise additional genomic layouts and intersection modes in a fresh offline workspace.