| # Repair Split-Read Exon-Overlap Filtering |
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| You are working with a pinned BEDTools source snapshot used in an RNA-seq |
| quality-control workflow. |
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| 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. |
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| 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. |
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| Your repair must be general. Do not hard-code the public coordinates, record |
| names, chromosome, threshold, block count, option order, or output mode. |
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| Run the public reproduction with: |
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| ```bash |
| python reproduce.py |
| ``` |
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| The verifier will build the repaired source and exercise additional genomic |
| layouts and intersection modes in a fresh offline workspace. |
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